[Rd] update.lme trouble (PR#2985)
Peter Dalgaard BSA
p.dalgaard at biostat.ku.dk
Thu May 15 20:45:50 MEST 2003
Douglas Bates <bates at stat.wisc.edu> writes:
> p.dalgaard at biostat.ku.dk writes:
>
> > Try this
> >
> > data(Assay)
> > as1 <- lme(logDens~sample*dilut, data=Assay,
> > random=pdBlocked(list(
> > pdIdent(~1),
> > pdIdent(~sample-1),
> > pdIdent(~dilut-1))))
> >
> > update(as1,random=pdCompSymm(~sample-1))
> > update(as1,random=pdCompSymm(~sample-1))
> > update(as1,random=pdCompSymm(~sample-1))
> > update(as1,random=pdCompSymm(~sample-1))
> >
> > I'm getting different results on different invocations!
>
> I'm not sure exactly what the problem was but it could be triggered by
> calling lme directly rather than through update. That is, successive
> calls to
> lme(logDens~sample*dilut, data=Assay, random=pdCompSymm(~sample-1))
> would alternate between a successful fit and an error.
>
> The problem does *not* occur with the current r-patched, which will be
> released as R-1.7.1 in early June.
It does for me! (RedHat 8.0):
R : Copyright 2003, The R Development Core Team
Version 1.7.0 Patched (2003-05-15)
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You are welcome to redistribute it under certain conditions.
Type `license()' or `licence()' for distribution details.
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Type `contributors()' for more information.
Type `demo()' for some demos, `help()' for on-line help, or
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Type `q()' to quit R.
> library(nlme)
Loading required package: lattice
Loading required package: grid
> data(Assay)
> lme(logDens~sample*dilut, data=Assay, random=pdCompSymm(~sample-1))
Error in if ((aux <- mean(aux[row(aux) != col(aux)])) <= -1/(nc - 1))
{ :
missing value where TRUE/FALSE needed
In addition: There were 25 warnings (use warnings() to see them)
> lme(logDens~sample*dilut, data=Assay, random=pdCompSymm(~sample-1))
Linear mixed-effects model fit by REML
Data: Assay
Log-restricted-likelihood: 38.47943
Fixed: logDens ~ sample * dilut
(Intercept) sampleb samplec sampled
samplee
-0.182791540 0.080753295 0.133976305 0.207698745
-0.023672400
samplef dilut2 dilut3 dilut4
dilut5
0.073569240 0.204429030 0.405863085 0.573191050
0.720635465
sampleb:dilut2 samplec:dilut2 sampled:dilut2 samplee:dilut2 samplef:dilut2
0.008938930 -0.008495275 0.001079295 -0.041917525
0.019352105
sampleb:dilut3 samplec:dilut3 sampled:dilut3 samplee:dilut3 samplef:dilut3
-0.025066045 0.018645100 0.003988575 -0.027712815
0.054316035
sampleb:dilut4 samplec:dilut4 sampled:dilut4 samplee:dilut4 samplef:dilut4
0.060788600 0.005259755 -0.016485510 0.049798755
0.063371900
sampleb:dilut5 samplec:dilut5 sampled:dilut5 samplee:dilut5 samplef:dilut5
-0.045762455 -0.072598205 -0.177756610 0.013610930
0.004023400
Random effects:
Formula: ~sample - 1 | Block
Structure: Compound Symmetry
StdDev Corr
samplea 0.02712464
sampleb 0.02712464 0.154
samplec 0.02712464 0.154 0.154
sampled 0.02712464 0.154 0.154 0.154
samplee 0.02712464 0.154 0.154 0.154 0.154
samplef 0.02712464 0.154 0.154 0.154 0.154 0.154
Residual 0.04255631
Number of Observations: 60
Number of Groups: 2
> lme(logDens~sample*dilut, data=Assay, random=pdCompSymm(~sample-1))
Linear mixed-effects model fit by REML
Data: Assay
Log-restricted-likelihood: 36.62856
Fixed: logDens ~ sample * dilut
(Intercept) sampleb samplec sampled
samplee
-0.182791540 0.080753295 0.133976305 0.207698745
-0.023672400
samplef dilut2 dilut3 dilut4
dilut5
0.073569240 0.204429030 0.405863085 0.573191050
0.720635465
sampleb:dilut2 samplec:dilut2 sampled:dilut2 samplee:dilut2 samplef:dilut2
0.008938930 -0.008495275 0.001079295 -0.041917525
0.019352105
sampleb:dilut3 samplec:dilut3 sampled:dilut3 samplee:dilut3 samplef:dilut3
-0.025066045 0.018645100 0.003988575 -0.027712815
0.054316035
sampleb:dilut4 samplec:dilut4 sampled:dilut4 samplee:dilut4 samplef:dilut4
0.060788600 0.005259755 -0.016485510 0.049798755
0.063371900
sampleb:dilut5 samplec:dilut5 sampled:dilut5 samplee:dilut5 samplef:dilut5
-0.045762455 -0.072598205 -0.177756610 0.013610930
0.004023400
Random effects:
Formula: ~sample - 1 | Block
Structure: Compound Symmetry
StdDev Corr
samplea 1.464982e-141
sampleb 1.464982e-141 0
samplec 1.464982e-141 0 0
sampled 1.464982e-141 0 0 0
samplee 1.464982e-141 0 0 0 0
samplef 1.464982e-141 0 0 0 0 0
Residual 5.046555e-02
Number of Observations: 60
Number of Groups: 2
There were 50 or more warnings (use warnings() to see the first 50)
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
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