Last updated on 2025-07-29 21:51:28 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.1 | 390.21 | 196.49 | 586.70 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.2.1 | 342.35 | 164.76 | 507.11 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.2.1 | 939.37 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.1 | 1122.67 | ERROR | |||
| r-devel-windows-x86_64 | 1.2.1 | 376.00 | 236.00 | 612.00 | ERROR | |
| r-patched-linux-x86_64 | 1.2.1 | 402.08 | 221.41 | 623.49 | ERROR | |
| r-release-linux-x86_64 | 1.2.1 | 396.79 | 222.13 | 618.92 | ERROR | |
| r-release-macos-arm64 | 1.2.1 | 254.00 | OK | |||
| r-release-macos-x86_64 | 1.2.1 | 341.00 | OK | |||
| r-release-windows-x86_64 | 1.2.1 | 379.00 | 239.00 | 618.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.2.1 | 132.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.2.1 | 165.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.2.1 | 450.00 | 335.00 | 785.00 | ERROR |
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [34s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rbioacc)
>
> test_check("rbioacc")
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 7.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.74 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.003 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4.1e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.41 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.006 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.008 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000169 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.69 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.004 seconds (Sampling)
Chain 1: 0.008 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000121 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.21 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.004 seconds (Sampling)
Chain 2: 0.008 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.8 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.005 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.01 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 8.2e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.82 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.005 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.01 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.49 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.003 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.002 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000186 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.86 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000135 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.35 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.43 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.005 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.38 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.004 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000136 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.36 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.005 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.007 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000137 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.37 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.003 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.005 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.48 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.003 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.6e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.36 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.002 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 2.8e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.28 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 3: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 3: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 3: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 3: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 3: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 3: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 3: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 3: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 3: Iteration: 10 / 10 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 0.002 seconds (Warm-up)
Chain 3: 0.002 seconds (Sampling)
Chain 3: 0.004 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 3.1e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.31 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 4: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 4: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 4: Iteration: 4 / 10 [ 40%] (Warmup)
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Chain 4:
Chain 4: Elapsed Time: 0.002 seconds (Warm-up)
Chain 4: 0.002 seconds (Sampling)
Chain 4: 0.004 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000155 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.55 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000118 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.18 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3:
Chain 3: Gradient evaluation took 0.00012 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.2 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 3: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 3: Iteration: 10 / 10 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 0.004 seconds (Warm-up)
Chain 3: 0.005 seconds (Sampling)
Chain 3: 0.009 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4: Rejecting initial value:
Chain 4: Log probability evaluates to log(0), i.e. negative infinity.
Chain 4: Stan can't start sampling from this initial value.
Chain 4:
Chain 4: Gradient evaluation took 0.000121 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.21 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 4: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 4: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 4: Iteration: 10 / 10 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.004 seconds (Warm-up)
Chain 4: 0.004 seconds (Sampling)
Chain 4: 0.008 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 9.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.92 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 8.8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.88 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.005 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.01 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 7.6e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.76 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 3: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 3: Iteration: 10 / 10 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 0.005 seconds (Warm-up)
Chain 3: 0.005 seconds (Sampling)
Chain 3: 0.01 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 8.5e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.85 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 4: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 4: Iteration: 10 / 10 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.004 seconds (Warm-up)
Chain 4: 0.002 seconds (Sampling)
Chain 4: 0.006 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.41 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.003 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.2e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.002 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.00017 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.7 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000142 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.42 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.42 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0.004 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.34 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.004 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000133 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.33 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.003 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.004 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000136 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.36 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.005 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.003 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.7e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.37 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.004 seconds (Sampling)
Chain 2: 0.006 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000133 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.33 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.003 seconds (Warm-up)
Chain 1: 0.004 seconds (Sampling)
Chain 1: 0.007 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000127 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.27 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.004 seconds (Sampling)
Chain 2: 0.008 seconds (Total)
Chain 2:
[ FAIL 5 | WARN 88 | SKIP 9 | PASS 75 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-elim.R:3:3', 'test-fit.R:3:3', 'test-fitODE.R:3:3',
'test-predict.R:3:3', 'test-predict.R:61:3', 'test-predict_manual.R:3:3'
• empty test (3): 'test-PP.R:1:1', 'test-correlation.R:1:1', 'test-ppc.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-correlation.R:28:5'): corrPlot ───────────────────────────────
all(class(plt_MGS) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:29:5'): corrPlot ───────────────────────────────
all(class(plt_MGS_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:30:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:31:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:32:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_sto) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 5 | WARN 88 | SKIP 9 | PASS 75 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [20s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rbioacc)
>
> test_check("rbioacc")
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.46 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.003 seconds (Warm-up)
Chain 1: 0.004 seconds (Sampling)
Chain 1: 0.007 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.28 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.005 seconds (Warm-up)
Chain 2: 0.004 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000128 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.28 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.003 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.005 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 9.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.94 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.003 seconds (Warm-up)
Chain 2: 0.004 seconds (Sampling)
Chain 2: 0.007 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 6.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.62 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.005 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.01 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 5.3e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.53 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.005 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.01 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.39 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.2e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.22 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.003 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.006 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000152 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.52 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 9.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.94 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.31 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.004 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.007 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.00011 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.1 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.0001 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
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Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.003 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.004 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.18 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.004 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 2.1e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.21 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
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Chain 3:
Chain 3: Elapsed Time: 0.001 seconds (Warm-up)
Chain 3: 0.001 seconds (Sampling)
Chain 3: 0.002 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 1.5e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.15 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 4:
Chain 4: Elapsed Time: 0.001 seconds (Warm-up)
Chain 4: 0.001 seconds (Sampling)
Chain 4: 0.002 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000109 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.09 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.003 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.005 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.9 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.008 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.01 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.000104 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.04 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 3:
Chain 3: Elapsed Time: 0.013 seconds (Warm-up)
Chain 3: 0.002 seconds (Sampling)
Chain 3: 0.015 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 9.2e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.92 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 4:
Chain 4: Elapsed Time: 0.01 seconds (Warm-up)
Chain 4: 0.013 seconds (Sampling)
Chain 4: 0.023 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 7.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.79 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.006 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.011 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 5.6e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.56 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 5.4e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.54 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 3:
Chain 3: Elapsed Time: 0.004 seconds (Warm-up)
Chain 3: 0.005 seconds (Sampling)
Chain 3: 0.009 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 4.4e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.44 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 4: Iteration: 10 / 10 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.004 seconds (Warm-up)
Chain 4: 0.001 seconds (Sampling)
Chain 4: 0.005 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.31 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.006 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.007 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.006 seconds (Sampling)
Chain 2: 0.008 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.00014 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.4 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 9.3e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.93 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.006 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.31 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.005 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.1e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.21 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0 seconds (Sampling)
Chain 2: 0.001 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.00011 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.1 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 9.5e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.95 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.003 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.004 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.3 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.002 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.18 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0 seconds (Sampling)
Chain 2: 0.001 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000106 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.06 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 9.6e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.96 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.003 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.004 seconds (Total)
Chain 2:
[ FAIL 5 | WARN 86 | SKIP 9 | PASS 75 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-elim.R:3:3', 'test-fit.R:3:3', 'test-fitODE.R:3:3',
'test-predict.R:3:3', 'test-predict.R:61:3', 'test-predict_manual.R:3:3'
• empty test (3): 'test-PP.R:1:1', 'test-correlation.R:1:1', 'test-ppc.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-correlation.R:28:5'): corrPlot ───────────────────────────────
all(class(plt_MGS) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:29:5'): corrPlot ───────────────────────────────
all(class(plt_MGS_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:30:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:31:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:32:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_sto) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 5 | WARN 86 | SKIP 9 | PASS 75 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [56s/91s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rbioacc)
>
> test_check("rbioacc")
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 8.3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.83 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4.6e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.46 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.003 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.006 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000308 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.08 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.018 seconds (Warm-up)
Chain 1: 0.014 seconds (Sampling)
Chain 1: 0.032 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000146 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.46 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.025 seconds (Warm-up)
Chain 2: 0.023 seconds (Sampling)
Chain 2: 0.048 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000128 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.28 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.008 seconds (Warm-up)
Chain 1: 0.009 seconds (Sampling)
Chain 1: 0.017 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 8.6e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.86 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.008 seconds (Warm-up)
Chain 2: 0.009 seconds (Sampling)
Chain 2: 0.017 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 6.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.62 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.005 seconds (Warm-up)
Chain 1: 0.004 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4.2e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.42 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.01 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000254 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.54 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.015 seconds (Warm-up)
Chain 1: 0.007 seconds (Sampling)
Chain 1: 0.022 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000166 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.66 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.017 seconds (Warm-up)
Chain 2: 0.022 seconds (Sampling)
Chain 2: 0.039 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 6.6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.66 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.004 seconds (Sampling)
Chain 1: 0.008 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.005 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.008 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000268 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.68 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.02 seconds (Warm-up)
Chain 1: 0.017 seconds (Sampling)
Chain 1: 0.037 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000181 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.81 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.021 seconds (Warm-up)
Chain 2: 0.017 seconds (Sampling)
Chain 2: 0.038 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.48 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.008 seconds (Warm-up)
Chain 1: 0.009 seconds (Sampling)
Chain 1: 0.017 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.39 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.013 seconds (Warm-up)
Chain 2: 0.007 seconds (Sampling)
Chain 2: 0.02 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 3.7e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.37 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 3: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 3: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 3: Iteration: 10 / 10 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 0.003 seconds (Warm-up)
Chain 3: 0.006 seconds (Sampling)
Chain 3: 0.009 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 4e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 4: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 4: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 4: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 4: Iteration: 10 / 10 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.007 seconds (Warm-up)
Chain 4: 0.009 seconds (Sampling)
Chain 4: 0.016 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000179 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.79 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.006 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000167 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.67 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.005 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.008 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3:
Chain 3: Gradient evaluation took 0.00017 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.7 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 3: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 3: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 3: Iteration: 10 / 10 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 0.006 seconds (Warm-up)
Chain 3: 0.003 seconds (Sampling)
Chain 3: 0.009 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.000166 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.66 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 4: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 4: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 4: Iteration: 10 / 10 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.021 seconds (Warm-up)
Chain 4: 0.016 seconds (Sampling)
Chain 4: 0.037 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 8.3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.83 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.021 seconds (Warm-up)
Chain 1: 0.017 seconds (Sampling)
Chain 1: 0.038 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 6.8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.68 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.017 seconds (Warm-up)
Chain 2: 0.008 seconds (Sampling)
Chain 2: 0.025 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 8.2e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.82 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 3: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 3: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 3: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 3: Iteration: 10 / 10 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 0.017 seconds (Warm-up)
Chain 3: 0.021 seconds (Sampling)
Chain 3: 0.038 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 8.1e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.81 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 4: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 4: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 4: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 4: Iteration: 10 / 10 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.021 seconds (Warm-up)
Chain 4: 0.028 seconds (Sampling)
Chain 4: 0.049 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 7.3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.73 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.005 seconds (Warm-up)
Chain 1: 0.004 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4.2e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.42 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.006 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.00029 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.9 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.007 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.01 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000169 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.69 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.006 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.42 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.003 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.008 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4.1e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.41 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.006 seconds (Warm-up)
Chain 2: 0.006 seconds (Sampling)
Chain 2: 0.012 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000285 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.85 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.005 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.008 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000153 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.53 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.005 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.008 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.42 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
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Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.007 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.008 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.44 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.004 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.00018 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.8 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.013 seconds (Warm-up)
Chain 1: 0.021 seconds (Sampling)
Chain 1: 0.034 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000173 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.73 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.009 seconds (Sampling)
Chain 2: 0.016 seconds (Total)
Chain 2:
[ FAIL 5 | WARN 85 | SKIP 9 | PASS 75 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-elim.R:3:3', 'test-fit.R:3:3', 'test-fitODE.R:3:3',
'test-predict.R:3:3', 'test-predict.R:61:3', 'test-predict_manual.R:3:3'
• empty test (3): 'test-PP.R:1:1', 'test-correlation.R:1:1', 'test-ppc.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-correlation.R:28:5'): corrPlot ───────────────────────────────
all(class(plt_MGS) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:29:5'): corrPlot ───────────────────────────────
all(class(plt_MGS_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:30:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:31:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:32:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_sto) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 5 | WARN 85 | SKIP 9 | PASS 75 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [50s/69s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rbioacc)
>
> test_check("rbioacc")
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 5.3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.53 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.39 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.003 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000273 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.73 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.007 seconds (Warm-up)
Chain 1: 0.021 seconds (Sampling)
Chain 1: 0.028 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000212 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.12 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.011 seconds (Warm-up)
Chain 2: 0.017 seconds (Sampling)
Chain 2: 0.028 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000108 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.08 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.006 seconds (Warm-up)
Chain 1: 0.008 seconds (Sampling)
Chain 1: 0.014 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000114 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.14 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.016 seconds (Warm-up)
Chain 2: 0.021 seconds (Sampling)
Chain 2: 0.037 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.5e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.35 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.013 seconds (Sampling)
Chain 1: 0.017 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.006 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000291 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.91 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.008 seconds (Warm-up)
Chain 1: 0.009 seconds (Sampling)
Chain 1: 0.017 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000288 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.88 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.009 seconds (Sampling)
Chain 2: 0.016 seconds (Total)
Chain 2:
Loading required namespace: coda
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 5.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.59 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.003 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4.6e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.46 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
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Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.005 seconds (Warm-up)
Chain 2: 0.004 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.003259 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 32.59 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.01 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.013 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000276 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.76 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.009 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.012 seconds (Total)
Chain 2:
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.34 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.003 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.005 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4.9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.49 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.003 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 4.2e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.42 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 3: Iteration: 10 / 10 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 0.005 seconds (Warm-up)
Chain 3: 0.003 seconds (Sampling)
Chain 3: 0.008 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 3.7e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.37 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 4:
Chain 4: Elapsed Time: 0.001 seconds (Warm-up)
Chain 4: 0.003 seconds (Sampling)
Chain 4: 0.004 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000242 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.42 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.016 seconds (Warm-up)
Chain 1: 0.017 seconds (Sampling)
Chain 1: 0.033 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000244 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.44 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.011 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.014 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.000184 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.84 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 3:
Chain 3: Elapsed Time: 0.008 seconds (Warm-up)
Chain 3: 0.008 seconds (Sampling)
Chain 3: 0.016 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.000196 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.96 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 4:
Chain 4: Elapsed Time: 0.007 seconds (Warm-up)
Chain 4: 0.003 seconds (Sampling)
Chain 4: 0.01 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000116 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.16 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.014 seconds (Warm-up)
Chain 1: 0.007 seconds (Sampling)
Chain 1: 0.021 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 9.3e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.93 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.009 seconds (Sampling)
Chain 2: 0.016 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.000112 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.12 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 3:
Chain 3: Elapsed Time: 0.015 seconds (Warm-up)
Chain 3: 0.018 seconds (Sampling)
Chain 3: 0.033 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.00011 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.1 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 4: Iteration: 10 / 10 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.015 seconds (Warm-up)
Chain 4: 0.007 seconds (Sampling)
Chain 4: 0.022 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.41 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.003 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.004 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.2e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.002 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000213 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.13 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.011 seconds (Warm-up)
Chain 1: 0.009 seconds (Sampling)
Chain 1: 0.02 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000184 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.84 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.008 seconds (Sampling)
Chain 2: 0.015 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.44 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.005 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.3e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.33 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.004 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000182 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.82 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.008 seconds (Warm-up)
Chain 1: 0.013 seconds (Sampling)
Chain 1: 0.021 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000207 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.07 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.016 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.019 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.46 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.001 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.003 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.1e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.31 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.005 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000185 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.85 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.008 seconds (Warm-up)
Chain 1: 0.008 seconds (Sampling)
Chain 1: 0.016 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000179 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.79 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.008 seconds (Sampling)
Chain 2: 0.015 seconds (Total)
Chain 2:
[ FAIL 5 | WARN 87 | SKIP 9 | PASS 75 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-elim.R:3:3', 'test-fit.R:3:3', 'test-fitODE.R:3:3',
'test-predict.R:3:3', 'test-predict.R:61:3', 'test-predict_manual.R:3:3'
• empty test (3): 'test-PP.R:1:1', 'test-correlation.R:1:1', 'test-ppc.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-correlation.R:28:5'): corrPlot ───────────────────────────────
all(class(plt_MGS) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:29:5'): corrPlot ───────────────────────────────
all(class(plt_MGS_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:30:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:31:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:32:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_sto) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 5 | WARN 87 | SKIP 9 | PASS 75 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.2.1
Check: tests
Result: ERROR
Running 'testthat.R' [28s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(rbioacc)
>
> test_check("rbioacc")
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000124 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.24 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.014 seconds (Warm-up)
Chain 1: 0.076 seconds (Sampling)
Chain 1: 0.09 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.002 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000176 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.76 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.012 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.015 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000177 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.77 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.01 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.013 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 6.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.69 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.008 seconds (Warm-up)
Chain 1: 0.013 seconds (Sampling)
Chain 1: 0.021 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 6.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.64 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.23 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.007 seconds (Warm-up)
Chain 1: 0.007 seconds (Sampling)
Chain 1: 0.014 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0 seconds (Warm-up)
Chain 2: 0 seconds (Sampling)
Chain 2: 0 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000123 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.23 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.01 seconds (Warm-up)
Chain 1: 0.012 seconds (Sampling)
Chain 1: 0.022 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.00014 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.4 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.014 seconds (Sampling)
Chain 2: 0.021 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.001 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.002 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.18 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.008 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000161 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.61 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.013 seconds (Warm-up)
Chain 1: 0.013 seconds (Sampling)
Chain 1: 0.026 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000157 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.57 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.015 seconds (Warm-up)
Chain 2: 0.018 seconds (Sampling)
Chain 2: 0.033 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.5e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.25 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.013 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.014 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.18 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.007 seconds (Sampling)
Chain 2: 0.014 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 1.9e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 3: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 3: Iteration: 10 / 10 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 0.001 seconds (Warm-up)
Chain 3: 0.001 seconds (Sampling)
Chain 3: 0.002 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 3.2e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 4: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 4: Iteration: 10 / 10 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.009 seconds (Warm-up)
Chain 4: 0.001 seconds (Sampling)
Chain 4: 0.01 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000144 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.44 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.009 seconds (Warm-up)
Chain 1: 0.012 seconds (Sampling)
Chain 1: 0.021 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000139 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.39 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.000126 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.26 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 3: Iteration: 10 / 10 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 0.007 seconds (Warm-up)
Chain 3: 0.01 seconds (Sampling)
Chain 3: 0.017 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.00018 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.8 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 4: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 4: Iteration: 10 / 10 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.01 seconds (Warm-up)
Chain 4: 0.012 seconds (Sampling)
Chain 4: 0.022 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 7.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.78 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.013 seconds (Warm-up)
Chain 1: 0.013 seconds (Sampling)
Chain 1: 0.026 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 6.7e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.67 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.008 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 4.9e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.49 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 3: Iteration: 10 / 10 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 0.005 seconds (Warm-up)
Chain 3: 0.007 seconds (Sampling)
Chain 3: 0.012 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 6.4e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.64 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 4: Iteration: 10 / 10 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.01 seconds (Warm-up)
Chain 4: 0.012 seconds (Sampling)
Chain 4: 0.022 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.008 seconds (Warm-up)
Chain 1: 0 seconds (Sampling)
Chain 1: 0.008 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.18 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.011 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.014 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000131 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.31 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.008 seconds (Warm-up)
Chain 1: 0.01 seconds (Sampling)
Chain 1: 0.018 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000121 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.21 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.009 seconds (Warm-up)
Chain 2: 0.01 seconds (Sampling)
Chain 2: 0.019 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.3 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.003 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.3e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.23 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.018 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.023 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000126 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.26 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.005 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000122 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.22 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.009 seconds (Warm-up)
Chain 2: 0.012 seconds (Sampling)
Chain 2: 0.021 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 1.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0 seconds (Warm-up)
Chain 1: 0.008 seconds (Sampling)
Chain 1: 0.008 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.14 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0 seconds (Warm-up)
Chain 2: 0 seconds (Sampling)
Chain 2: 0 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000155 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.55 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.012 seconds (Warm-up)
Chain 1: 0.014 seconds (Sampling)
Chain 1: 0.026 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000153 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.53 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.012 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.014 seconds (Total)
Chain 2:
[ FAIL 5 | WARN 87 | SKIP 9 | PASS 75 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-elim.R:3:3', 'test-fit.R:3:3', 'test-fitODE.R:3:3',
'test-predict.R:3:3', 'test-predict.R:61:3', 'test-predict_manual.R:3:3'
• empty test (3): 'test-PP.R:1:1', 'test-correlation.R:1:1', 'test-ppc.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-correlation.R:28:5'): corrPlot ───────────────────────────────
all(class(plt_MGS) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:29:5'): corrPlot ───────────────────────────────
all(class(plt_MGS_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:30:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:31:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:32:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_sto) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 5 | WARN 87 | SKIP 9 | PASS 75 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [32s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rbioacc)
>
> test_check("rbioacc")
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.41 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.007 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.003 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000173 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.73 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000128 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.28 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.005 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.01 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 5.5e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.55 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.004 seconds (Sampling)
Chain 1: 0.008 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 6.8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.68 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.7e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.37 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.007 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.008 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.007 seconds (Sampling)
Chain 2: 0.008 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.00016 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.6 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.007 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000137 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.37 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.005 seconds (Warm-up)
Chain 2: 0.007 seconds (Sampling)
Chain 2: 0.012 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.003 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.004 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000151 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.51 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.005 seconds (Warm-up)
Chain 1: 0.004 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000134 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.34 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
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Chain 2:
Chain 2: Elapsed Time: 0.003 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.005 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.38 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.001 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.002 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.002 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 3e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.3 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 3:
Chain 3: Elapsed Time: 0.002 seconds (Warm-up)
Chain 3: 0.001 seconds (Sampling)
Chain 3: 0.003 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 2.4e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 4:
Chain 4: Elapsed Time: 0.002 seconds (Warm-up)
Chain 4: 0.001 seconds (Sampling)
Chain 4: 0.003 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000147 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.47 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.004 seconds (Sampling)
Chain 1: 0.008 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.00011 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.1 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.003 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.005 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3:
Chain 3: Gradient evaluation took 9.4e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.94 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 3:
Chain 3: Elapsed Time: 0.004 seconds (Warm-up)
Chain 3: 0.002 seconds (Sampling)
Chain 3: 0.006 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 9.9e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.99 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 4:
Chain 4: Elapsed Time: 0.004 seconds (Warm-up)
Chain 4: 0.005 seconds (Sampling)
Chain 4: 0.009 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 7.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.78 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.006 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.011 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 5.9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.59 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.003 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.005 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 5.6e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.56 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 3:
Chain 3: Elapsed Time: 0.004 seconds (Warm-up)
Chain 3: 0.002 seconds (Sampling)
Chain 3: 0.006 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 6.1e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.61 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 4:
Chain 4: Elapsed Time: 0.003 seconds (Warm-up)
Chain 4: 0.002 seconds (Sampling)
Chain 4: 0.005 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.003 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.6e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.003 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000142 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.42 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.004 seconds (Sampling)
Chain 1: 0.008 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000114 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.14 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.006 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.004 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.7e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.27 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.002 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000133 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.33 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.003 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.004 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000119 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.19 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.005 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.28 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0 seconds (Sampling)
Chain 1: 0.002 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.004 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000115 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.15 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.00012 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.2 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.004 seconds (Sampling)
Chain 2: 0.008 seconds (Total)
Chain 2:
[ FAIL 5 | WARN 86 | SKIP 9 | PASS 75 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-elim.R:3:3', 'test-fit.R:3:3', 'test-fitODE.R:3:3',
'test-predict.R:3:3', 'test-predict.R:61:3', 'test-predict_manual.R:3:3'
• empty test (3): 'test-PP.R:1:1', 'test-correlation.R:1:1', 'test-ppc.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-correlation.R:28:5'): corrPlot ───────────────────────────────
all(class(plt_MGS) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:29:5'): corrPlot ───────────────────────────────
all(class(plt_MGS_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:30:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:31:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:32:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_sto) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 5 | WARN 86 | SKIP 9 | PASS 75 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [33s/37s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rbioacc)
>
> test_check("rbioacc")
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.43 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.003 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.003 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.004 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.00015 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.5 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000197 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.97 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.004 seconds (Sampling)
Chain 2: 0.008 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.6 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 7.1e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.71 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.012 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.33 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.003 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.004 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.3e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.23 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.002 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000233 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.33 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.00012 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.2 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.003 seconds (Warm-up)
Chain 2: 0.004 seconds (Sampling)
Chain 2: 0.007 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.28 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.003 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.3e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.23 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.004 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000127 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.27 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000124 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.24 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.005 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.01 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.005 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.3e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.23 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.003 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 2.2e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.22 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 3:
Chain 3: Elapsed Time: 0.001 seconds (Warm-up)
Chain 3: 0.001 seconds (Sampling)
Chain 3: 0.002 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 2.3e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.23 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 4: Iteration: 10 / 10 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.001 seconds (Warm-up)
Chain 4: 0.001 seconds (Sampling)
Chain 4: 0.002 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000198 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.98 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.003 seconds (Warm-up)
Chain 1: 0.004 seconds (Sampling)
Chain 1: 0.007 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000125 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.25 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3:
Chain 3: Gradient evaluation took 0.000128 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.28 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 3: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 3: Iteration: 10 / 10 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 0.004 seconds (Warm-up)
Chain 3: 0.004 seconds (Sampling)
Chain 3: 0.008 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4: Rejecting initial value:
Chain 4: Log probability evaluates to log(0), i.e. negative infinity.
Chain 4: Stan can't start sampling from this initial value.
Chain 4:
Chain 4: Gradient evaluation took 0.000121 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.21 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 4: Iteration: 10 / 10 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.004 seconds (Warm-up)
Chain 4: 0.005 seconds (Sampling)
Chain 4: 0.009 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 7e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.7 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.009 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 7.5e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.75 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.006 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 7.2e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.72 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 3: Iteration: 10 / 10 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 0.004 seconds (Warm-up)
Chain 3: 0.004 seconds (Sampling)
Chain 3: 0.008 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 6.1e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.61 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 4: Iteration: 10 / 10 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.005 seconds (Warm-up)
Chain 4: 0.005 seconds (Sampling)
Chain 4: 0.01 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3.3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.33 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.005 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.28 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.003 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000127 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.27 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.004 seconds (Sampling)
Chain 1: 0.008 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000121 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.21 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.3 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.001 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.002 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.28 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.002 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.004 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000128 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.28 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.003 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.004 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000128 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.28 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.004 seconds (Sampling)
Chain 2: 0.008 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.001 seconds (Warm-up)
Chain 1: 0.007 seconds (Sampling)
Chain 1: 0.008 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.005 seconds (Warm-up)
Chain 2: 0 seconds (Sampling)
Chain 2: 0.005 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000131 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.31 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.008 seconds (Warm-up)
Chain 1: 0.006 seconds (Sampling)
Chain 1: 0.014 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000153 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.53 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.009 seconds (Warm-up)
Chain 2: 0.013 seconds (Sampling)
Chain 2: 0.022 seconds (Total)
Chain 2:
[ FAIL 5 | WARN 88 | SKIP 9 | PASS 75 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-elim.R:3:3', 'test-fit.R:3:3', 'test-fitODE.R:3:3',
'test-predict.R:3:3', 'test-predict.R:61:3', 'test-predict_manual.R:3:3'
• empty test (3): 'test-PP.R:1:1', 'test-correlation.R:1:1', 'test-ppc.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-correlation.R:28:5'): corrPlot ───────────────────────────────
all(class(plt_MGS) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:29:5'): corrPlot ───────────────────────────────
all(class(plt_MGS_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:30:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:31:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:32:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_sto) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 5 | WARN 88 | SKIP 9 | PASS 75 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 1.2.1
Check: tests
Result: ERROR
Running 'testthat.R' [28s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(rbioacc)
>
> test_check("rbioacc")
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.00018 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.8 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.001 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.002 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.6e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.01 seconds (Warm-up)
Chain 2: 0.004 seconds (Sampling)
Chain 2: 0.014 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000126 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.26 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.005 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.0001 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 7.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.72 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.009 seconds (Warm-up)
Chain 1: 0.006 seconds (Sampling)
Chain 1: 0.015 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.44 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.012 seconds (Warm-up)
Chain 2: 0.017 seconds (Sampling)
Chain 2: 0.029 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.014 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.015 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.2 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.002 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000147 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.47 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.009 seconds (Warm-up)
Chain 1: 0.012 seconds (Sampling)
Chain 1: 0.021 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.00014 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.4 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.006 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.008 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.5e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.25 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.009 seconds (Warm-up)
Chain 1: 0.005 seconds (Sampling)
Chain 1: 0.014 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.2 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.008 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000131 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.31 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.008 seconds (Warm-up)
Chain 1: 0.012 seconds (Sampling)
Chain 1: 0.02 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000132 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.32 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.006 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.008 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 1: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 1: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.001 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.003 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
Chain 2: Iteration: 5 / 10 [ 50%] (Warmup)
Chain 2: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.002 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 1.9e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 3: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 3: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 3: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 3: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 3: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 3: Iteration: 10 / 10 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 0.008 seconds (Warm-up)
Chain 3: 0.001 seconds (Sampling)
Chain 3: 0.009 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 1.9e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 4: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 4: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 4: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 4: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 4: Iteration: 10 / 10 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.006 seconds (Warm-up)
Chain 4: 0.001 seconds (Sampling)
Chain 4: 0.007 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000191 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.91 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.008 seconds (Warm-up)
Chain 1: 0.013 seconds (Sampling)
Chain 1: 0.021 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.00016 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.6 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
Chain 2: Iteration: 4 / 10 [ 40%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.011 seconds (Warm-up)
Chain 2: 0.013 seconds (Sampling)
Chain 2: 0.024 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.000139 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.39 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 3: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 3: Iteration: 10 / 10 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 0.005 seconds (Warm-up)
Chain 3: 0.007 seconds (Sampling)
Chain 3: 0.012 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4: Rejecting initial value:
Chain 4: Log probability evaluates to log(0), i.e. negative infinity.
Chain 4: Stan can't start sampling from this initial value.
Chain 4: Rejecting initial value:
Chain 4: Log probability evaluates to log(0), i.e. negative infinity.
Chain 4: Stan can't start sampling from this initial value.
Chain 4: Rejecting initial value:
Chain 4: Log probability evaluates to log(0), i.e. negative infinity.
Chain 4: Stan can't start sampling from this initial value.
Chain 4: Rejecting initial value:
Chain 4: Log probability evaluates to log(0), i.e. negative infinity.
Chain 4: Stan can't start sampling from this initial value.
Chain 4: Rejecting initial value:
Chain 4: Log probability evaluates to log(0), i.e. negative infinity.
Chain 4: Stan can't start sampling from this initial value.
Chain 4: Rejecting initial value:
Chain 4: Log probability evaluates to log(0), i.e. negative infinity.
Chain 4: Stan can't start sampling from this initial value.
Chain 4: Rejecting initial value:
Chain 4: Log probability evaluates to log(0), i.e. negative infinity.
Chain 4: Stan can't start sampling from this initial value.
Chain 4: Rejecting initial value:
Chain 4: Log probability evaluates to log(0), i.e. negative infinity.
Chain 4: Stan can't start sampling from this initial value.
Chain 4: Rejecting initial value:
Chain 4: Log probability evaluates to log(0), i.e. negative infinity.
Chain 4: Stan can't start sampling from this initial value.
Chain 4: Rejecting initial value:
Chain 4: Log probability evaluates to log(0), i.e. negative infinity.
Chain 4: Stan can't start sampling from this initial value.
Chain 4:
Chain 4: Gradient evaluation took 0.000103 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.03 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 4: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 4: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 4: Iteration: 10 / 10 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.009 seconds (Warm-up)
Chain 4: 0.002 seconds (Sampling)
Chain 4: 0.011 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 8.4e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.84 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 1: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.008 seconds (Warm-up)
Chain 1: 0.012 seconds (Sampling)
Chain 1: 0.02 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 6.3e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.63 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 2: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 2: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 2: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.006 seconds (Warm-up)
Chain 2: 0.007 seconds (Sampling)
Chain 2: 0.013 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 4.5e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.45 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 3: Iteration: 2 / 10 [ 20%] (Warmup)
Chain 3: Iteration: 3 / 10 [ 30%] (Warmup)
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Chain 3: Iteration: 6 / 10 [ 60%] (Sampling)
Chain 3: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 3: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 3: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 3: Iteration: 10 / 10 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 0.01 seconds (Warm-up)
Chain 3: 0.002 seconds (Sampling)
Chain 3: 0.012 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 6.9e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.69 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 4: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 4: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 4: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 4: Iteration: 10 / 10 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 0.01 seconds (Warm-up)
Chain 4: 0.012 seconds (Sampling)
Chain 4: 0.022 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 7 / 10 [ 70%] (Sampling)
Chain 1: Iteration: 8 / 10 [ 80%] (Sampling)
Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.015 seconds (Warm-up)
Chain 1: 0.006 seconds (Sampling)
Chain 1: 0.021 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.2e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.22 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.002 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000175 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.75 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
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Chain 1:
Chain 1: Elapsed Time: 0.009 seconds (Warm-up)
Chain 1: 0.011 seconds (Sampling)
Chain 1: 0.02 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000138 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.38 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.012 seconds (Warm-up)
Chain 2: 0.014 seconds (Sampling)
Chain 2: 0.026 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.23 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.001 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.002 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 1.6e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.16 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.005 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.008 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000126 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.26 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.005 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 8.3e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.83 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.004 seconds (Warm-up)
Chain 2: 0.005 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.9e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.001 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.003 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.34 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.002 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000155 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.55 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.009 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.011 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000149 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.49 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.01 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.012 seconds (Total)
Chain 2:
[ FAIL 5 | WARN 85 | SKIP 9 | PASS 75 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-elim.R:3:3', 'test-fit.R:3:3', 'test-fitODE.R:3:3',
'test-predict.R:3:3', 'test-predict.R:61:3', 'test-predict_manual.R:3:3'
• empty test (3): 'test-PP.R:1:1', 'test-correlation.R:1:1', 'test-ppc.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-correlation.R:28:5'): corrPlot ───────────────────────────────
all(class(plt_MGS) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:29:5'): corrPlot ───────────────────────────────
all(class(plt_MGS_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:30:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:31:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:32:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_sto) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 5 | WARN 85 | SKIP 9 | PASS 75 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 1.2.1
Check: installed package size
Result: NOTE
installed size is 66.1Mb
sub-directories of 1Mb or more:
libs 65.5Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.2.1
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.2.1
Check: tests
Result: ERROR
Running 'testthat.R' [36s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(rbioacc)
>
> test_check("rbioacc")
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000264 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.64 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.002 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.004 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.7e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.37 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.01 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.011 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000178 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.78 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.007 seconds (Warm-up)
Chain 1: 0.01 seconds (Sampling)
Chain 1: 0.017 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000162 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.62 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.007 seconds (Warm-up)
Chain 2: 0.002 seconds (Sampling)
Chain 2: 0.009 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000119 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.19 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.016 seconds (Warm-up)
Chain 1: 0.018 seconds (Sampling)
Chain 1: 0.034 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000118 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.18 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.008 seconds (Warm-up)
Chain 2: 0.003 seconds (Sampling)
Chain 2: 0.011 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 2.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.28 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.001 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.002 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 2.3e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.23 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.001 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000312 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.12 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.012 seconds (Warm-up)
Chain 1: 0.017 seconds (Sampling)
Chain 1: 0.029 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000257 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.57 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.009 seconds (Warm-up)
Chain 2: 0.011 seconds (Sampling)
Chain 2: 0.02 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 3e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.3 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.001 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.002 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.8e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.38 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.02 seconds (Warm-up)
Chain 2: 0.013 seconds (Sampling)
Chain 2: 0.033 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000219 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.19 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.01 seconds (Warm-up)
Chain 1: 0.01 seconds (Sampling)
Chain 1: 0.02 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.00016 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.6 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.012 seconds (Warm-up)
Chain 2: 0.01 seconds (Sampling)
Chain 2: 0.022 seconds (Total)
Chain 2:
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
Loading required namespace: coda
Failed with error: 'there is no package called 'coda''
Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.7e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.47 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 1: Iteration: 10 / 10 [100%] (Sampling)
Chain 1:
Chain 1: Elapsed Time: 0.01 seconds (Warm-up)
Chain 1: 0.015 seconds (Sampling)
Chain 1: 0.025 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.39 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 2: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.009 seconds (Warm-up)
Chain 2: 0.008 seconds (Sampling)
Chain 2: 0.017 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 3.5e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.35 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 3: Iteration: 9 / 10 [ 90%] (Sampling)
Chain 3: Iteration: 10 / 10 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 0.019 seconds (Warm-up)
Chain 3: 0.002 seconds (Sampling)
Chain 3: 0.021 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 4.3e-05 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.43 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 4:
Chain 4: Elapsed Time: 0.018 seconds (Warm-up)
Chain 4: 0.008 seconds (Sampling)
Chain 4: 0.026 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000167 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.67 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
Chain 1: Iteration: 2 / 10 [ 20%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.011 seconds (Warm-up)
Chain 1: 0.017 seconds (Sampling)
Chain 1: 0.028 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000266 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.66 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2: Iteration: 10 / 10 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 0.014 seconds (Warm-up)
Chain 2: 0.016 seconds (Sampling)
Chain 2: 0.03 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3: Rejecting initial value:
Chain 3: Log probability evaluates to log(0), i.e. negative infinity.
Chain 3: Stan can't start sampling from this initial value.
Chain 3:
Chain 3: Gradient evaluation took 0.000168 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.68 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 3:
Chain 3: Elapsed Time: 0.011 seconds (Warm-up)
Chain 3: 0.016 seconds (Sampling)
Chain 3: 0.027 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.000232 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 2.32 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 4:
Chain 4: Elapsed Time: 0.009 seconds (Warm-up)
Chain 4: 0.01 seconds (Sampling)
Chain 4: 0.019 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000129 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.29 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
Chain 1: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 1:
Chain 1: Elapsed Time: 0.011 seconds (Warm-up)
Chain 1: 0.017 seconds (Sampling)
Chain 1: 0.028 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000133 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.33 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
Chain 2: performed for num_warmup < 20
Chain 2:
Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.008 seconds (Warm-up)
Chain 2: 0.013 seconds (Sampling)
Chain 2: 0.021 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.00012 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 1.2 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: No variance estimation is
Chain 3: performed for num_warmup < 20
Chain 3:
Chain 3: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 3:
Chain 3: Elapsed Time: 0.017 seconds (Warm-up)
Chain 3: 0.017 seconds (Sampling)
Chain 3: 0.034 seconds (Total)
Chain 3:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.000127 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.27 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: No variance estimation is
Chain 4: performed for num_warmup < 20
Chain 4:
Chain 4: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 4:
Chain 4: Elapsed Time: 0.012 seconds (Warm-up)
Chain 4: 0.017 seconds (Sampling)
Chain 4: 0.029 seconds (Total)
Chain 4:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.8e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.48 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
Chain 1: performed for num_warmup < 20
Chain 1:
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Chain 1:
Chain 1: Elapsed Time: 0.004 seconds (Warm-up)
Chain 1: 0.002 seconds (Sampling)
Chain 1: 0.006 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.4e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.34 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
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Chain 2: performed for num_warmup < 20
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Chain 2: Iteration: 1 / 10 [ 10%] (Warmup)
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Chain 2:
Chain 2: Elapsed Time: 0.001 seconds (Warm-up)
Chain 2: 0.01 seconds (Sampling)
Chain 2: 0.011 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000284 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.84 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
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Chain 1:
Chain 1: Elapsed Time: 0.012 seconds (Warm-up)
Chain 1: 0.017 seconds (Sampling)
Chain 1: 0.029 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.00016 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.6 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: No variance estimation is
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Chain 2:
Chain 2: Elapsed Time: 0.012 seconds (Warm-up)
Chain 2: 0.017 seconds (Sampling)
Chain 2: 0.029 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 5.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.52 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: No variance estimation is
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Chain 1:
Chain 1: Elapsed Time: 0.011 seconds (Warm-up)
Chain 1: 0.014 seconds (Sampling)
Chain 1: 0.025 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 3.9e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.39 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
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Chain 2:
Chain 2: Elapsed Time: 0.011 seconds (Warm-up)
Chain 2: 0.017 seconds (Sampling)
Chain 2: 0.028 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.000231 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.31 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
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Chain 1:
Chain 1: Elapsed Time: 0.015 seconds (Warm-up)
Chain 1: 0.003 seconds (Sampling)
Chain 1: 0.018 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000268 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.68 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
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Chain 2:
Chain 2: Elapsed Time: 0.012 seconds (Warm-up)
Chain 2: 0.017 seconds (Sampling)
Chain 2: 0.029 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 4.6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.46 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
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Chain 1:
Chain 1: Elapsed Time: 0.01 seconds (Warm-up)
Chain 1: 0.001 seconds (Sampling)
Chain 1: 0.011 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 4.5e-05 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.45 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
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Chain 2:
Chain 2: Elapsed Time: 0.015 seconds (Warm-up)
Chain 2: 0.001 seconds (Sampling)
Chain 2: 0.016 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 1).
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1: Log probability evaluates to log(0), i.e. negative infinity.
Chain 1: Stan can't start sampling from this initial value.
Chain 1:
Chain 1: Gradient evaluation took 0.000159 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.59 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
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Chain 1:
Chain 1: Elapsed Time: 0.01 seconds (Warm-up)
Chain 1: 0.01 seconds (Sampling)
Chain 1: 0.02 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'TK' NOW (CHAIN 2).
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2: Rejecting initial value:
Chain 2: Log probability evaluates to log(0), i.e. negative infinity.
Chain 2: Stan can't start sampling from this initial value.
Chain 2:
Chain 2: Gradient evaluation took 0.000157 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.57 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
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Chain 2: performed for num_warmup < 20
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Chain 2:
Chain 2: Elapsed Time: 0.008 seconds (Warm-up)
Chain 2: 0.01 seconds (Sampling)
Chain 2: 0.018 seconds (Total)
Chain 2:
[ FAIL 5 | WARN 89 | SKIP 9 | PASS 75 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-elim.R:3:3', 'test-fit.R:3:3', 'test-fitODE.R:3:3',
'test-predict.R:3:3', 'test-predict.R:61:3', 'test-predict_manual.R:3:3'
• empty test (3): 'test-PP.R:1:1', 'test-correlation.R:1:1', 'test-ppc.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-correlation.R:28:5'): corrPlot ───────────────────────────────
all(class(plt_MGS) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:29:5'): corrPlot ───────────────────────────────
all(class(plt_MGS_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:30:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:31:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_det) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-correlation.R:32:5'): corrPlot ───────────────────────────────
all(class(plt_MGSG_sto) == c("gg", "ggmatrix")) is not TRUE
`actual`: FALSE
`expected`: TRUE
[ FAIL 5 | WARN 89 | SKIP 9 | PASS 75 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64