[R-pkg-devel] cran submission check produces note on news file
Richard Shefferson
cdorm @end|ng |rom g@ecc@u-tokyo@@c@jp
Sat Aug 6 23:16:30 CEST 2022
Hi,
I am the creator and maintainer of package lefko3, which creates matrix
projections for use in population ecology. I just submitted a version of
this package to CRAN, and got a Note on the debian check that showed that
it could not process the NEWS file. All other system pretests (including
Windows and MAC) were fine, and my own checks on Mac, Ubuntu, and Windows
had no such issues. I have looked through the CRAN documentation seeing if
there is any formatting issue, but I cannot find any problems. Can anyone
provide any help?
Here is a link to my R Forge site holding the NEWS file itself:
https://r-forge.r-project.org/scm/viewvc.php/pkg/?root=lefko3
The check log from the pretest is here:
https://win-builder.r-project.org/incoming_pretest/lefko3_5.4.1_20220805_235501/Debian/00check.log
The particular Note that appears to have failed CRANs prechecks is the
following:
Flavor: r-devel-linux-x86_64-debian-gcc
Check: package subdirectories, Result: NOTE
Problems with news in 'NEWS':
Cannot process chunk/lines:
CHANGES IN VERSION 5.4.1 (2022-07-29)
USER-VISIBLE CHANGES
1. Output to summary_hfv() now fits within screen width.
2. Exponent tolerance limits and warnings added to functions
projection3()
and f_projection3(). Warnings and help file notes have also
been added.
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CHANGES IN VERSION 5.4.0 (2022-07-21)
NEW FEATURES
1. Function actualstage3() has been rewritten in C++ to handle
all stage,
age-by-stage, and age inputs. Can now remove stages as
necessary, and
allows different stages to be removed in times t1 and t2 in
historical
stage pair assessments.
2. Function hist_null() can now produce historically-formatted
ahistorical
matrices that do not include impossible transitions.
3. Anthyllis matrices are now also provided as a new dataset, in
lefkoMat
format.
USER-VISIBLE CHANGES
1. Updates and corrections to help files.
BUG FIXES
1. Lathyrus vignettes corrected to account for duplicated
individual
identity across subpopulations.
2. Corrected issue in repvalue3() causing warnings in MPMs with
certain rare
conditions.
3. Corrected issue in lambda3() causing rare eigen analysis
failure in
sparse matrices.
4. Reference matrix warnings in ltre3() have been corrected.
Cannot process chunk/lines:
CHANGES IN VERSION 5.3.0 (2022-06-24)
NEW FEATURES
1. Function actualstage3() now also outputs proportions of ages
and age-
stages within hfv datasets.
2. Function vrm_import() created to allow IPM and other
function-based model
slope coefficients can now be imported directly without
conducting linear
model searches through modelsearch().
3. Functions flefko3(), flefko2(), aflefko2(), fleslie(), and
f_projection3() have been updated to allow the use of
vrm_input objects,
allowing slope coefficients to be imported directly.
4. Function hfv_qc() developed to test hfv datasets for quality
control
using the same parameterizations and subsetting strategies
used in
function modelsearch().
USER-VISIBLE CHANGES
1. Function create_pm() can now yield paramnames objects with
default
model variable names used instead of "none" strings.
2. Vignettes updated with new functions. Particularly, material
for
sf_distrib() replaced with material for hfv_qc().
3. Tweaks and corrections to help files.
BUG FIXES
1. Fixed bug causing substochasticity setting 2 in functions
projection3()
and f_projection3() to yield negative survival probabilities
under some
circumstances in which survival column sums totaled more than
1.0.
2. Fix bug omitting substochasticity correction in fecundity
under some
conditions when function f_projection3() is run with substoch
= 2.
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CHANGES IN VERSION 5.2.0 (2022-05-18)
NEW FEATURES
1. Function f_projection3() can now run density dependent
projections in
which the vital rates used are modified by projected density.
2. Function density_vr() created to provide vital rate density
dependence
information for function f_projection3().
3. Option added to functions projection3() and f_projection3() to
suppress
warnings.
4. Function summary.lefkoProj() now has an option to interpret
NaN values as
positive infinity, changing the count of replicates still
alive in the
milepost section. This option, inf_alive, may also be set to
FALSE to
count NaNs as evidence of extinction.
5. A new summary_hfv() function has been created to simplify
quality
control checks on historical vertical format datasets.
6. Function verticalize3() now warns the user to check the
resulting dataset
if the dataset is censored and the blocksize option is used
without
the censorRepeat option being set to TRUE, as these cases may
result in
excessive data pruning.
7. Function summary.lefkoProj() now calculates mean extinction
time when
prompted.
USER-VISIBLE CHANGES
1. Function modelsearch() now allows an "age" setting for the
suite option,
which yields the same results as "cons" but checks to make
sure that an
age variable is properly added.
2. Function modelsearch() now allows a "leslie" setting for the
vitalrates
option, which provides a shorthand for c("surv", "fec") as
would be used
by fleslie().
3. The documentation for functions modelsearch() and fleslie()
have been
updated to provide more information for handling Leslie MPMs.
4. Added series of new error messages if expected data frame size
input in
verticalize3() is too large.
5. Vignettes have been updated with new functions.
6. Some error messages made more informative.
BUG FIXES
1. The stageframe developed with functions rleslie() and
fleslie() has been
fixed to include stage_id, alive, and almost_born variables,
allowing
Leslie-formatted lefkoMat objects to be passed to all lefko3
functions
analyzing them, including lmean().
2. Fixed bug yielding vector leaks from other variables when
using the
blocksize feature in verticalize3().
3. Fixed incorrect fecundity summation in rlefko3(), resulting
from
miscounting offspring from individuals dying the transition in
which they
reproduced.
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CHANGES IN VERSION 5.1.0 (2022-04-01)
NEW FEATURES
1. Added ability to run ordered annual matrix progressions in
function
projection3().
2. Function projection3() can now run arithmetic mean matrix
projections
without any modifications required to the input lefkoMat
object.
3. Function plot.lefkoProj() now has an auto-title feature.
USER-VISIBLE CHANGES
1. Added cancel handling to verticalize3(), historicalize3(),
slambda3(),
sensitivity3(), elasticity3(), and ltre3().
2. Added transitions to some supplemental() in function examples
and
vignettes, reflecting more exact transition specification.
BUG FIXES
1. Fixed incorrect substochastic correction in projection3() and
f_projection3() when substoch = 2 and negative survival
entries occur.
2. Cleaned up minor memory issues in some functions.
3. Corrected class lefkoProj structure output by function
f_projection3()
to correspond exactly to that produced by function
projection3().
4. Fixed bug preventing proxy multipliers from being properly
integrated in
function-based and raw MPMs.
5. Corrected issue in which truncated distributions occasionally
led to NA
size probabilities when the probability of a 0 under the
un-truncated
distribution was sufficiently high.
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CHANGES IN VERSION 5.0.1 (2022-03-08)
USER-VISIBLE CHANGES
1. Updated help files for projection functions.
BUG FIXES
1. Updated primitive class checks in some functions.
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CHANGES IN VERSION 5.0.0 (2022-03-01)
NEW FEATURES
1. New function arlefko2() created to handle raw age-by-stage MPM
estimation.
2. Function aflefko2() now fixes the starting age by whether the
life
history model is pre-breeding or post-breeding.
3. Functions verticalize3() and historicalize3() now handle age
offsets and
automatically offset age by 1 if set to prebreeding = TRUE.
4. Further output has been added when err_check = TRUE is set in
all
function-based matrix estimators.
5. New function f_projection3() runs MPM and IPM projections in
which
matrices are developed from vital rate models at each step.
USER-VISIBLE CHANGES
1. Default final_age in function aflefko2() is now the final age
at time t
in the original dataset.
2. All function-based matrix estimators have been sped up.
3. Population dynamics functions have been sped up.
4. All population dynamics functions involving actual projection
can now be
cancelled during runs.
5. Function create_lM() now produces a properly edited stageframe
usable
with all other functions taking lefkoMat objects as input.
BUG FIXES
1. Function plot.lefkoProj() now uses the correct default axis
labels when
conducting a state-space plot.
2. Function hist_null() now correctly estimates the numbers of
survival and
fecundity elements.
3. Eliminated bug in functions flefko3(), flefko2(), and
aflefko2()
preventing incorporation of random year effects into matrix
estimation.
4. Eliminated bug causing inflation of lambda under some
instances of the
Poisson distribution in function-based matrix estimation.
5. Fixed erroneous mixing of QC information in lmean() output.
6. Fixed issue preventing multiple replicates from being
displayed in
plot.lefkoProj under the timeseries option.
7. Fixed issue causing certain impossible transitions linked to
the
prior stage to be estimated as non-zero in deVries-format
function-based
hMPMs.
8. Fixed incorrect formatting of deVries hMPMs resulting from
function
hist_null().
9. Function create_pm() updated to handle maturity status models.
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CHANGES IN VERSION 4.2.0 (2022-01-17)
NEW FEATURES
1. Functions rleslie() and fleslie() created to estimate raw and
function-based Leslie MPMs, respectively.
2. Added a beta term setting K as hard maximum in the logistic
function
using functions density_input() and projection3().
3. Accuracy check added to size and fecundity models in
modelsearch().
4. Function modelsearch() new runs exhaustive model selection
under the
`suite = "cons"` setting if age, density, or any individual
covariate is
added to the analysis.
5. Function modelsearch() now performs accuracy checks by
default, and
allows an opt-out.
6. Function actualstage3() now removes stages if wished,
including stage
NotAlive be default.
7. New plot.lefkoProj() function added.
8. All function-based matrix estimators now incorporate a default
method
for continuous distributions using cumulative density
functions to
estimate size transition probabilities. The midpoint rule is
now only an
option (and not advised).
9. New standalone density dependence functions ricker3(),
beverton3(),
usher3(), and logistic3() added.
10. Substochasticity options for projection3() now include the
option to
force fecundity to stay non-negative.
11. Function projection3() now issues warnings if density
dependence yields
matrix impossible matrix values.
12. Function modelsearch() now also estimates maturity status
probability in
juveniles.
13. Functions supplemental(), density_input(), and start_input()
now also
include automated handling of keywords "obs" and "nobs",
which specify
the use of all observable or unobservable stages,
respectively.
USER-VISIBLE CHANGES
1. Functions rlefko2() and rlefko3() now provide warnings if
individual
identity variable name or column number is not provided.
2. Function summary.lefkoMat() now provides appropriate
descriptions of
data quality control sections with missing values.
3. Added spatial coordinates to cypdata and cypvert.
4. Function modelsearch() is now more flexible with input errors
in some
key settings.
5. Ended dependence on package stringr.
6. Expanded data frame output with actualstage3() to give
individual stage
designations in times t and t-1.
7. Function summary.lefkoMat() now yields warnings if any
fecundity matrix
contains a negative value, and if any matrix contains an NA
value.
8. Added equations in key help files.
9. Corrections and updates to all vignettes.
10. Function modelsearch() now tries several more
parameterizations if the
global model fails.
11. Function lmean() now also incorporates modelqc and dataqc
elements for
quality control purposes.
12. Function aflefko2() now treats missing minimum ages as
zeroes, allowing
estimation even when age info is missing from stageframes.
BUG FIXES
1. Matrix quality control summaries corrected when functions
add_lM(),
delete_lM(), and subset_lM() are used.
2. Corrected errors in documentation regatding censoring
variables used in
rlefko3() and rlefko2().
3. Corrected issue yielding fatal error in historicalize3() when
spatial
coordinates are set and reduce = TRUE.
4. Corrected improper matrix formatting in some integer variables
used in
historicalize3().
5. Fixed bug ignoring coordsRepeat setting in verticalize3().
6. Fixed bug causing inconsistent coordinate assignment under
unobserved
stages in historicalize3().
7. Corrected bug capable of causing the logistic function to
yield negative
matrix elements.
8. Fixed improper handling of numeric entries for year and patch
options in
function modelsearch().
9. Corrected issue in flefko3(), flefko2(), and aflefko2()
affecting the
incorporation of zero-inflated Poisson and negative binomial
models.
10. Fixed fecundity estimation issue arising in some
circumstances with
deVries-formatted historical models.
11. Fixed bug leading size of 0 to be treated as zero-inflated in
Poisson
and negative binomial models.
12. Added tolerance limit to binomial probability estimation in
all
function-based matrix estimators, to prevent some conditions
yielding
NA probabilities.
13. Eliminated bug causing rare error in formulae creation in
modelsearch().
14. Eliminated bug causing unrealistic pseudo-R^2 in rare runs of
modelsearch().
15. Eliminated fatal error in modelsearch() occurring under rare
instances
when all attempts to build a working global model fail.
16. Fixed bug incorrectly importing non-standard variable names
into
modelsearch().
17. Fixed error causing density dependent projections under large,
historical MPMs in projection3() to issue substochasticity
warnings
continuously regardless of actual substochasticity violation.
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CHANGES IN VERSION 4.1.1 (2021-12-07)
BUG FIXES
1. Fixed C++ runtime error in function hist_null().
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CHANGES IN VERSION 4.1.0 (2021-12-06)
NEW FEATURES
1. Included option to ignore observation status during stage
assignment in
verticalize3() and historicalize3().
2. Included option to quiet all warnings in verticalize3() and
historicalize3().
3. New options to prevent display of overdispersion and
zero-inflation tests
in sf_distrib().
4. Added hist_null() function to create historically-structured
MPM to serve
as a null model MPM assuming no individual history.
5. Created function diff_lM() that creates lefkoDiff objects,
which are
MPM style objects that are actually matrix differences between
two lefkoMat objects with equivalent dimensions.
6. Added cond_diff() function to create conditional difference
matrices
from supplied lefkoDiff objects.
7. Created actualstage3() function to calculate actual stage
frequencies and
proportions from input hfv dataset.
8. Created create_pm() function to create a skeleton paramnames
object for
users building vital rate models manually.
USER-VISIBLE CHANGES
1. Introduced an integer check in function sf_distrib() that
stops tests on
non-integer variables.
2. All vignettes have been updated to the latest functions and
results.
BUG FIXES
1. Fixed incorrect time step calculation in summary.lefkoMat().
2. Fixed incorrect P values for zero-inflation when fewer than
expected 0s
found in sf_distrib().
3. Fixed fatal issue affecting certain kinds of proxy transitions
in
function-based matrix estimation.
4. Fixed incorrect stage distribution calculation in stochastic
stablestage3() and projection3().
5. Fixed fatal error in summary.lefkoProj() that occurred when
summarizing
projections with single replicates.
6. Fixed fatal errors in flefko2(), flefko3(), aflefko2(), and
summary.lefkoMat() relating to the use of user-defined vital
rate
functions.
7. Corrected incorrect assignment of stages in flefko3(),
flefko2(), and
aflefko2() based on use of groups in supplement tables.
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CHANGES IN VERSION 4.0.1 (2021-11-15)
BUG FIXES
1. Function aflefko2() now properly removes agestages rows when
reduce = TRUE.
2. Problems with mathjaxr integration fixed.
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CHANGES IN VERSION 4.0.0 (2021-11-14)
NEW FEATURES
1. Function projection3() can now run density dependent
projections using
the Ricker, Beverton-Holt, Usher, and logistic functions.
2. Functions start_input() and density_input() have been created
to describe
starting vectors and density dependence in the simplest format
possible.
3. Function modelsearch() now also calculates the accuracy of
binomial
models and adds the output to the QC section of the output.
Function
summary.lefkoMod() reports this output.
4. Function sf_create() now handles dual- and triple-size
classification
5. Functions sf_create() and supplemental() now handle the
designation of
core stage groups.
6. Functions verticalize3() and historicalize3() now handle dual-
and
triple-size metric classification.
7. Function modelsearch() can now test the impacts of three
different size
variables, and can also develop vital rate models for up to
three
separate response size variables.
8. Function modelsearch() can now test the impacts of spatial
density and
stage group.
9. Function modelsearch() now allows individual covariates to be
incorporated as random categorical variables, as well as fixed
continuous quantitative variables.
10. Function modelsearch() now also allows the Gamma distribution
for size
and fecundity.
11. Function flefko2() now handles up to three size metrics,
stage groups,
random categorical variables, and density.
12. Function sf_distrib() now handles up to three size metrics,
and also
handles fecundity estimation in both times t and t+1.
13. Function projection3() now allows two forms of enforced
substochasticity. The first keeps all survival-transition
probabilities
within bounds, while the second keeps all stage survival
probabilities
within bounds.
USER-VISIBLE CHANGES
1. Function projection3() now creates easier-to-understand output
structures
clearly dividing numbers of individuals from stage
distributions from
reproductive values and population sizes.
2. Function supplemental() now takes proxy multipliers, and gives
errors for
negative given rates and multipliers.
3. Corrected some figure dimensions in vignettes.
4. Corrected help text for some functions.
5. Functions sf_distrib(), summary.lefkoMat(),
summary.lefkoCondMat(),
summary.lefkoMod(), and image3() no longer return a NULL to
the console.
6. The default for option censorRepeat in function verticalize3()
has been
changed to FALSE, in order to prevent overzealous censoring by
default.
7. Text output from summary functions and sf_distrib() has been
altered to
fit within standard output consoles, including typical page
widths.
8. Added sparse matrix override to slambda3() in case of errors
incurred in
eigen analysis.
BUG FIXES
1. Corrected bug causing code "npr" to yield propagule stages in
time t+1
in supplement and overwrite tables.
2. Fixed issue preventing estimation of size transition into
observable
classes with size 0 under the Poisson distribution in
flefko3() and
flefko2().
3. Corrected porous stage assignment handling in historicalize3().
4. Eliminated incorrect projection set assignment when running
multiple
patches or populations through function projection3().
5. Eliminated bug giving warnings when running rlefko2() and
rlefko3() with
specific choices of patches or populations given as input
options.
6. Fixed issue causing rlefko2() and rlefko3() to estimate only
some
transition-survival probabilities and fecundities when
patchcol or popcol
is given without any respective specific patch or pop options
given.
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CHANGES IN VERSION 3.8.0 (2021-09-08)
NEW FEATURES
1. Function projection3() now includes the ability to produce
replicate
simulations.
2. Function summary.lefkoProj() created to summarize the results
of
population projection using function projection3().
3. Functions verticalize3() and historicalize3() now handle true
radial
density estimation, if X and Y coordinates and a valid spacing
threshold
are supplied.
4. Functions add_lM() and delete_lM() added to add and delete
matrices from
lefkoMat objects.
5. Function subset_lM() added to create new lefkoMat objects as
subsets of
other lefkoMat objects.
USER-VISIBLE CHANGES
1. Sensitivity and elasticity descriptions corrected in vignettes.
2. Increased consistency in terminology used in output for
stablestage3()
and repvalue3().
3. Function create_lM() now handles age-by-stage matrices.
BUG FIXES
1. Fixed issue that could lead rlefko2() and rlefko3() to stop
processing
matrices if specific years or patches are called.
2. Fixed issue affecting stochastic reproductive value estimation
in
historical lefkoMat objects.
3. Fixed issue affecting some deterministic reproductive value
estimates,
particularly in large historical MPMs, where a base reference
value for
standardization cannot be determined.
4. Fixed issue preventing proper handling of historical matrix
inputs in
create_lM().
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CHANGES IN VERSION 3.7.0 (2021-08-18)
NEW FEATURES
1. Function ltre3() developed to conduct deterministic and
stochastic life
table response experiments.
2. Function create_lM() developed to allow the incorporation of
lists of
matrices developed outside of package lefko3.
3. Function summary.lefkoLTRE() developed to quickly summarize
LTRE
contributions according to transition type.
4. Added new vignette to showcase LTRE and sLTRE analysis, and
the import of
matrices as lefkoMat objects.
USER-VISIBLE CHANGES
1. Altered some terminology in help files and vignettes to
reflect most
recent best practice in population ecology. Updated vignettes
with new
information, particularly related to LTRE and sLTRE analysis.
2. Option append_mats has been added to sensitivity3.lefkoMat(),
sensitivity3.list(), elasticity3.lefkoMat(), and
elasticity3.list(). This
option allows users to prevent the incorporation of the
original matrices
into output lefkoSens and lefkoElas objects, resulting in
lower memory
usage.
3. Function summary.lefkoElas() can now handle age-by-stage MPMs.
4. Corrected problematic Cypripedium examples involving the
construction of
matrices with stage survival probabilities rising above 1.0.
BUG FIXES
1. Fixed indexing bug in function summary.lefkoElas() that had
led to
incorrect elasticity summation.
2. Fixed memory leak affecting sparse matrices in projection3()
and related
functions.
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CHANGES IN VERSION 3.6.0 (2021-07-21)
NEW FEATURES
1. Automatic sparse matrix detection and override options have
been added to
all population dynamics functions.
USER-VISIBLE CHANGES
1. All population dynamics analysis functions have been
substantially sped
up through better memory management techniques.
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CHANGES IN VERSION 3.5.3 (2021-07-14)
NEW FEATURES
1. Function summary.lefkoMat() now also displays column sums from
all
U (survival-transition) matrices as a quality control check.
USER-VISIBLE CHANGES
1. Package glmmTMB has been reintegrated, allowing mixed modeling
of
negative binomial, zero-inflated, and zero-truncated response
distributions again.
2. Error and warning messages from compiled functions provide
cleaner
messages.
BUG FIXES
1. Corrected incorrect handling of missing patch terms in lm,
glm, vglm, and
zeroinfl objects.
2. Corrected static_cast issue that might prevent package
installation in
Solaris systems.
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CHANGES IN VERSION 3.5.2 (2021-07-12)
USER-VISIBLE CHANGES
1. Negative binomial response, zero-truncated, and zero-inflated
have been temporarily disabled in function modelsearch() while
package
glmmTMB() is being reprogrammed for compatibility with R
4.1.0. These
distributions are still available through the glm approach.
2. Examples have been updated for clarity and consistency.
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CHANGES IN VERSION 3.5.1 (2021-07-07)
NEW FEATURES
1. Function supplemental() now allows entry stage proxies to be
marked for
raw historical MPMs.
2. Shortcuts included covering non-propagule stages and
non-reproductive
mature stages for functions overwrite() and supplemental().
USER-VISIBLE CHANGES
1. Updated Lathyrus vignettes to correct improper handling of
entry stages.
2. Negative binomial response in mixed modeling has been moved to
package
lme4, and zero-truncated and zero-inflated distributions are
available
only through the glm approach in modelsearch() for the time
being.
BUG FIXES
1. Corrected improper handling of prior forms of entry stages in
raw
historical MPMs.
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CHANGES IN VERSION 3.5.0 (2021-06-29)
NEW FEATURES
1. Historical MPM estimating functions can now estimate hMPMs in
deVries
format, in which newborns have an unique prior stage. All
population
dynamics functions have also been reworked to handle this
format.
2. New output has been added showing the exact order of age-stage
combinations across all rows in estimated age-by-stage MPMs,
as output
from function aflefko2().
3. Stochastic sensitivities of historical MPMs now yield
ahistorical
equivalents in all output.
4. Added manual designation of ahistorical vs. historical output
in
functions sensitivity3.list() and elasticity3.list().
USER-VISIBLE CHANGES
1. Function modelsearch() can now handle invariant response terms.
2. Functions flefko3() and flefko2() can now handle invariant
fecundity.
3. Function verticalize3() can now handle horizontal datasets
without clear
patterns in order.
4. Amended overwrite() and supplemental() functions to account
for possible
prior newborn stage in deVries formatted hMPMs.
5. Function supplemental() now details stage names not accounted
for in the
input stageframe in error messages.
6. Some error and warning messages have been clarified for better
understanding.
7. Many examples have been expanded to include extra conditions.
BUG FIXES
1. Function rlefko3() now handles dimension reduction properly.
2. Function cond_hmpm() now produces conditional matrices from all
combinations of population, subpopulation, and year, and also
properly
labels them.
3. Typos and other issues corrected in vignettes.
Cannot process chunk/lines:
CHANGES IN VERSION 3.4.0 (2021-03-31)
NEW FEATURES
1. Zero-truncated Poisson and negative binomial distributions
have been
added to function modelsearch(), and as underlying size and
fecundity
distributions in flefko3(), flefko2(), and aflefko2().
2. New function image3() created to easily create matrix images
for lefkoMat
and other objects. Function acts as a wrapper for the image()
function in
package SparseM.
3. New vignette showcasing the estimation and analysis of age x
stage MPMs.
USER-VISIBLE CHANGES
1. Added err_check option to function-based matrix estimators,
allowing the
output of vital rates used in the estimation of U matrices.
2. The test used to assess overdispersion in size and fecundity
has been
changed to deal more accurately with count-based variance
(including
tests performed and how data are subsetted), and to offer more
choices in
which tests to run.
3. Function modelsearch() has been rewritten to result in a
smaller
installed package size.
4. Function parasearch() has been removed pending revision of
modeling
methodology.
5. Reproductive value vectors are now all standardized to the
first non-zero
value in the vector.
6. Function sf_create() can now handle stage comments as input.
7. Functions sensitivity3() and elasticity3() have been
redesigned for
increased speed with unusually large matrices.
8. Stochastic analysis functions have been streamlined for speed
and
efficiency.
9. Expanded all examples to include both Lathyrus and Cypripedium
versions.
10. Corrections and expansions to package vignettes.
BUG FIXES
1. Fixed issue in which loss of one of the year or patch terms in
modeling
of zero-inflated mixed models could lead to errors in
function-based
matrix estimation.
2. Corrected error in estimation algorithm for size transition
probability
under negative binomial distribution, and difficulty in
handling low
levels of overdispersion in some negative binomial models.
3. Fixed issue making lmean() unable to take element-wise mean
matrices of
age x stage MPMs produced using aflefko2().
4. Fixed bug yielding erroneous reproductive values in historical
matrices.
5. Fixed bug yielding erroneous sensitivity elements in
historically-
corrected ahistorical sensitivity matrices.
6. Fixed bug occasionally yielding 3d arrays in response to
stochastic
calls of sensitivity3() and elasticity3().
7. Corrected stablestage3() and repvalue3() to properly handle
age x stage
MPMs.
8. Corrected memory leak issue in aflefko2().
Cannot process chunk/lines:
CHANGES IN VERSION 3.3.2 (2021-02-25)
BUG FIXES
1. Fixed Imports field related to function parasearch().
2. Fixed loss of fecundity placement in age-by-stage matrices
when using
function supplemental() with function aflefko2().
3. Fixed default year and patch settings in aflefko2().
4. Corrected memory allocation issue in historicalize3().
Cannot process chunk/lines:
CHANGES IN VERSION 3.3.1 (2021-02-23)
USER-VISIBLE CHANGES
1. Corrections to vignettes.
2. Help file typos fixed.
Cannot process chunk/lines:
CHANGES IN VERSION 3.3.0 (2021-02-21)
NEW FEATURES
1. Function supplemental() created to allow greater flexibility
in the input
of reproductive multipliers. All matrix creation functions can
now handle
its output.
2. Stochastic sensitivity and elasticity analyses now enabled
through
functions sensitivity3() and elasticity3(), respectively.
3. Functions sensitivity3() and elasticity3() now handle simple
lists of A
matrices, in addition to lefkoMat objects and simple matrices.
4. Function parasearch() created to allow parallelized model
building and
selection.
USER-VISIBLE CHANGES
1. Censoring options in verticalize3() and historicalize3() can
now handle
both static and temporally-variable censor variables.
2. Overwrite and supplemental tables can now include "prop",
"immat", and
"mat" as shorthand for suites of all propagule, immature, and
mature
stages.
3. Function modelsearch() now gives warning if a dataset is used
with NAs in
individual ID when a mixed modeling approach is requested. It
now also
provides standard diagnostic messages at each step.
4. Corrections and additions to help files.
BUG FIXES
1. Fixed censoring protocols in verticalize3(), historicalize3()
rlefko3(),
and rlefko2().
2. Corrected distribtution algorithm for zero inflation and text
output in
sf_distrib().
3. Eliminated bug causing high overdispersion parameters from
negative
binomial-based size models to yield function-based matrices
with NA
values for all transitions to stages with positive size.
4. Fixed issue in which mixed models with a non-zero-inflated
negative
binomial distribution fails to estimate function-based
martrices.
5. Fixed compatibility issues in matrix creation functions with R
3.6.3.
6. Fixed minor issue in summary.lefkoMat output text.
Cannot process chunk/lines:
CHANGES IN VERSION 3.2.0 (2021-01-03)
NEW FEATURES
1. Function cond_hmpm() added to create conditional hMPMs.
2. Function slambda3() added to estimate the log stochastic
growth rate.
3. Function summary.lefkoElas() added to summarize elasticities
by kind of
transition.
4. Added citation() data for package.
5. Added NEWS section, using package lme4 NEWS as a template.
USER-VISIBLE CHANGES
1. Corrected inconsistent stage name variable in stage frame
creation and
manipulation functions.
2. Updated and reorganized vignettes.
3. Modified stageframes exported by matrix creation functions now
include
entry status variable.
4. Objects of class lefkoElas now include the original A, U, and
F matrices.
5. Elasticity and sensitivity outputs for lefkoMat objects now
include the
original A, U, and F matrices used as input.
BUG FIXES
1. Matrix estimation function now create loy tables treating pop
and patch
as strings by default, eliminating possible conversion errors.
2. Corrected incorrect overwrite() call in lathyrus example used
in function
flefko3() and all population dynamics analysis functions.
Cannot process chunk/lines:
CHANGES IN VERSION 3.1.2 (2020-11-16)
BUG FIXES
1. Corrected auto-conversion of characters to factors occurring
on R 3.6.3,
which affected the creation and interpretation of the $labels
element in
matrix estimation.
Cannot process chunk/lines:
CHANGES IN VERSION 3.1.1 (2020-11-13)
BUG FIXES
1. Fixed bug in lmean() function resulting from an implicit cast
and
affecting users operating lefko3 on Solaris systems.
Cannot process chunk/lines:
CHANGES IN VERSION 3.1.0 (2020-11-08)
NEW FEATURES
1. Added function sfdistrib() to test whether mean = var and the
level of
zero-inflation in count variable data to be used for size and
fecundity.
2. Added zero-inflated Poisson and negative binomial
distributions as
choices for the underlying distribution of size and fecundity.
3. Added individual and environmental covariates to function-based
MPM estimation functions.
USER-VISIBLE CHANGES
1. Corrected, updated, and reorganized vignettes.
BUG FIXES
1. Corrected parameterization of negative binomial distribution in
function modelsarch().
Cannot process chunk/lines:
CHANGES IN VERSION 3.0.0 (2020-10-22)
NEW FEATURES
1. Added function aflefko2() function to estimate age x stage
MPMs.
2. Added function sensitivity3() to estimate sensitivity matrices
of
historical and ahistorical MPMs.
3. Added Function elasticity3() to estimate elasticity matrices of
historical and ahistorical MPMs.
USER-VISIBLE CHANGES
1. Increased consistency of output variable names across
functions.
2. Corrected, updated, and reorganized vignettes.
3. Eliminated faulty parameterization of matrix geometric mean in
lmean()
function.
BUG FIXES
1. Corrected core kernel underlying lmean(), and redeveloped in
C++ to yield
faster results.
2. Corrected parameterization of negative binomial distribution.
3. Function summary.lefkoMat() now shows which vital rate models
were not
estimated.
Cannot process chunk/lines:
CHANGES IN VERSION 2.4.2 (2020-09-12)
USER-VISIBLE CHANGES
1. All matrix estimators sped up through lapply()-based calls to
C++
kernels.
2. Function lmean() now keeps the original names of populations
and patches.
3. Corrected incorrect reference links in vignettes.
BUG FIXES
1. Fixed memory leak in kernel behind function historicalize3().
2. Fixed faulty indexing affecting all matrix estimators under
certain
conditions.
3. Bugs in Cypripedium candidum vignettes and examples caused by
incomplete
overwrite tables fixed.
Cannot process chunk/lines:
CHANGES IN VERSION 2.3.0 (2020-08-18)
USER-VISIBLE CHANGES
1. Major speed up to flefko2() and flefko3() through the
incorporation of
C++ core kernels.
BUG FIXES
1. Bug fixed that could lead to the erroneous incorporation of
mature
stages as immature in flefko3() under certain rare
circumstances.
2. Bug fixed that could fit proxy rates into the wrong elements
in all
matrix construction under certain rare circumstances.
3. Bug fixed that could, under some circumstances, lead to
individuals
being treated as dead when not observed for a period of more
than a year.
Cannot process chunk/lines:
CHANGES IN VERSION 2.2.2 (2020-07-28)
USER-VISIBLE CHANGES
1. Revised vignettes.
2. Improved default handling of reproductive ratio and fecundity
ratio.
BUG FIXES
1. Fixed calculation of observed lifespan in functions
verticalize3()
and historicalize3().
Cannot process chunk/lines:
CHANGES IN VERSION 2.2.1 (2020-07-18)
USER-VISIBLE CHANGES
1. Removed some vignettes to reduce size.
2. Added greater detail to Metadata in DESCRIPTION file
BUG FIXES
1. Added on.exit() to modelsearch() to keep user options through
that
routine.
2. Fixed bugs in repvalue3.lefkoMat() and repvalue3.matrix().
Cannot process chunk/lines:
CHANGES IN VERSION 2.2.0 (2020-07-08)
USER-VISIBLE CHANGES
1. All internal function documentation now complete.
2. Reduced vignette sizes.
BUG FIXES
1. Fixed bugs in summary.lefkoMod().
Cannot process chunk/lines:
CHANGES IN VERSION 2.1.0 (2020-07-06)
NEW FEATURES
1. Advanced routines developed for deterministic analysis
functions,
including repvalue3() and stablestage3().
USER-VISIBLE CHANGES
1. Cleaned up all help pages.
BUG FIXES
1. Scattered bugs eliminated.
Cannot process chunk/lines:
CHANGES IN VERSION 2.0.0 (2020-06-27)
NEW FEATURES
1. Stageframe objects now have their own class, and stageframes
now handle
log-size based bin widths.
2. Sf_create() also now stops if vector lengths are not equal,
and can
create stageframes for IPMs.
3. Mean matrix function lmean() created.
4. Added size in time t to juvenile models.
5. Fecundity models can now use fecundity in t+1 as a response.
6. Integrated estimation function into verticalize3() and
historicalize3().
USER-VISIBLE CHANGES
1. All matrix creation functions have been fully rewritten for
speed
(eliminated extraneous find() calls and long loops).
2. Vignettes split up across chapter files.
BUG FIXES
1. Eliminated problems with class interpretation in modelsearch().
Cannot process chunk/lines:
CHANGES IN VERSION 1.0.0 (2020-03-24)
NEW FEATURES
1. Lathyrus dataset added.
2. Examples added to all core functions.
USER-VISIBLE CHANGES
1. All matrix estimation functions have been rewritten to include
core C++
functions, for speed up and memory efficiency.
2. Added patch functionality to modelsearch(), flefko3(), and
flefko2().
BUG FIXES
1. Bugs corrected in probability and rate estimation functions.
Cannot process chunk/lines:
CHANGES IN VERSION 0.13.1 (2020-02-16)
USER-VISIBLE CHANGES
1. Reorganized flefko2() around Rcpp functions.
BUG FIXES
1. Cleaned up bugs discovered in rlefko3().
Cannot process chunk/lines:
CHANGES IN VERSION 0.13.0 (2020-02-14)
USER-VISIBLE CHANGES
1. Re-developed core functions of rlefko3() with Rcpp and
RcppArmadillo.
Functions now run lightning quick.
Cannot process chunk/lines:
CHANGES IN VERSION 0.12.1 (2020-02-11)
USER-VISIBLE CHANGES
1. Re-developed rlefko3() function per new approach to rlefko2().
Cannot process chunk/lines:
CHANGES IN VERSION 0.12.0 (2020-02-05)
NEW FEATURES
1. Developed rlefko2() function.
USER-VISIBLE CHANGES
1. Developed rlefko2() function.
2. Redesigned all matrix functions to handle different
populations and
patches.
3. Made core matrix creators invisible.
4. Increased standardization of inputs.
5. Eliminated class lefkoMatMulti.
Cannot process chunk/lines:
CHANGES IN VERSION 0.11.0 (2020-01-31)
NEW FEATURES
1. Created the hfvdata class for standardized, vertical
demographic data
frames.
2. Added quality control sections to lefkoMod and lefkoMatMulti
objects,
including functions that create these objects.
3. Created new summary.lefkoMatMulti function.
Cannot process chunk/lines:
CHANGES IN VERSION 0.10.2 (2020-01-29)
NEW FEATURES
1. Added negative binomial functionality to vital rate estimators.
USER-VISIBLE CHANGES
1. Massive changes and improvements to tutorials.
Cannot process chunk/lines:
CHANGES IN VERSION 0.10.1 (2020-01-22)
NEW FEATURES
1. Added negative binomial functionality to modelsearch().
2. Added a summary function for class lefkoMod.
Cannot process chunk/lines:
CHANGES IN VERSION 0.10.0 (2020-01-19)
NEW FEATURES
1. Added Cypripedium candidum vignette.
2. Data mgmt functions can now prune unused variables from output.
USER-VISIBLE CHANGES
1. Replaced all flw and frt entries with repst and fec.
Cannot process chunk/lines:
CHANGES IN VERSION 0.9.0 (2020-01-15)
NEW FEATURES
1. Added cypdata.
USER-VISIBLE CHANGES
1. Formatted code and help files.
Cannot process chunk/lines:
CHANGES IN VERSION 0.8.3 (2020-01-11)
USER-VISIBLE CHANGES
1. Eliminated year effect warnings by option.
Cannot process chunk/lines:
CHANGES IN VERSION 0.8.2 (2020-01-10)
NEW FEATURES
1. Added the lefkoMatMulti class.
2. Gave matrix creation functions the ability to create output
with lists of
A, T, and F matrices for all years requested.
Cannot process chunk/lines:
CHANGES IN VERSION 0.8.1 (2020-01-10)
NEW FEATURES
1. Added greater flexibility to modelsearch() function to allow
it to
estimate binomial models under constant response.
USER-VISIBLE CHANGES
1. Synchronized data management function to modelsearch()
function.
Cannot process chunk/lines:
CHANGES IN VERSION 0.8.0 (2020-01-01)
NEW FEATURES
1. Added modelsearch function to handle model building and
selection workflow.
Cannot process chunk/lines:
CHANGES IN VERSION 0.7.0 (2019-11-22)
NEW FEATURES
1. All workhorse functions are now generally debugged C++
functions.
BUG FIXES
1. Fixed overwriting and estimating portions of matrix creation
functions.
Cannot process chunk/lines:
CHANGES IN VERSION 0.6.1 (2019-11-22)
BUG FIXES
1. Fixed overwriting portion of matrix design, so that given
transitions are
properly added to historical matrices.
Cannot process chunk/lines:
CHANGES IN VERSION 0.6.0 (2019-11-20)
NEW FEATURES
1. Fully rebuilt flefko3 and flefko2 so that fecundity is now
estimated
using binaries written in C++.
USER-VISIBLE CHANGES
1. Matrix design is reworked to make everything faster.
Cannot process chunk/lines:
CHANGES IN VERSION 0.5.1 (2019-11-19)
NEW FEATURES
1. Rebuilt flefko2 to use C++ precompiled probability density
functions.
Cannot process chunk/lines:
CHANGES IN VERSION 0.5.0 (2019-11-18)
NEW FEATURES
1. Rewrote workhorse portions of survival transition estimators as
precompiled binaries in C++.
2. Rewrote historical matrix function (flefko3()) to handle
reworked pxy
functions.
BUG FIXES
1. Corrected issues in help files.
Cannot process chunk/lines:
CHANGES IN VERSION 0.4.4 (2019-11-11)
NEW FEATURES
1. Added a patch term to ahv2hv() function.
USER-VISIBLE CHANGES
1. Changed plantid variable to individ.
Cannot process chunk/lines:
CHANGES IN VERSION 0.4.3 (2019-11-08)
NEW FEATURES
1. Added density3() function.
USER-VISIBLE CHANGES
1. Sped up verticalize3() and ahv2hv() functions.
BUG FIXES
1. Corrected links throughout.
Cannot process chunk/lines:
CHANGES IN VERSION 0.4.2 (2019-11-07)
NEW FEATURES
1. Added ability to handle character column names to
verticalize_h().
Cannot process chunk/lines:
CHANGES IN VERSION 0.4.1 (2019-11-06)
BUG FIXES
1. Corrected issues in verticalize_h function.
Cannot process chunk/lines:
CHANGES IN VERSION 0.4.0 (2019-11-03)
NEW FEATURES
1. Added RSpectra-based population matrix projection analysis
functions.
USER-VISIBLE CHANGES
1. Added GPL license.
Cannot process chunk/lines:
CHANGES IN VERSION 0.3.1 (2019-11-02)
BUG FIXES
1. Corrected bug leading to infinite mu values in probbin for
some models.
2. Corrected the method of using proxy transitions from certain
juvenile
stages to mature stages in all lefko functions.
Cannot process chunk/lines:
CHANGES IN VERSION 0.3.0 (2019-11-01)
USER-VISIBLE CHANGES
1. Increased ability to choose which unobserved stages lead to
which
vobserved stages.
2. Standardized terms in more functions for cross-compatibility
and easier
workflow.
Cannot process chunk/lines:
CHANGES IN VERSION 0.2.1 (2019-10-29)
NEW FEATURES
1. Added Gaussian probability calculation.
2. Developed sf_create function.
3. First version of rlefko3() created.
Cannot process chunk/lines:
CHANGES IN VERSION 0.1.1 (2019-10-26)
NEW FEATURES
1. Matrix creation functions now discriminate size and fecundity
on the
basis of probability distribution.
USER-VISIBLE CHANGES
1. Adds numeric class recognition.
2. Documentation improvements.
Cannot process chunk/lines:
CHANGES IN VERSION 0.1.0 (2019-10-25)
NEW FEATURES
1. First development version. Main 2d and 3d matrix functions
created.
--
-------------------------------------------------------
Dr. Richard P. Shefferson
Associate Professor
Organization for Programs on Environmental Sciences
Graduate School of Arts and Sciences
University of Tokyo
3-8-1 Komaba
Meguro-ku, Tokyo 153-8902, Japan
リチャードシェファーソン 准教授
東京大学総合文化研究科国際環境学教育機構
153-8902 東京都目黒区駒場 3-8-1 (新6号館209A号室）
E-mail:cdorm using g.ecc.u-tokyo.ac.jp <cdorm using g.ecc.u-tokyo.ac.jp>
Tel: +81-3-5465-7235
Fax: +81-3-5465-7236
Web: www.sheffersonlab.com
Book on the Evolution of Senescence in the Tree of Life
http://tinyurl.com/SenescenceBook
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