fix for #143 (remove LBFGS_NOCEDAL variant from the possible
algorithms)
PLNmodels 1.2.1 (2025-03-10)
fix NOTES in CRAN due to missing packages in (PR #142)
Now requires R >= 4.1.0 because package code uses the pipe |>
(PR #142)
fix sandwich variance estimation (PR #140)
fix use of native pipe to ensure compatibility with R 3.6 (merge PR
#125, fix #124)
PLNmodels 1.2.0 (2024-03-05)
new feature: ZIPLN (PLN with zero inflation) for standard PLN and
PLN Network
ZIPLN() and ZIPLNfit-class to allow for zero-inflation in the
standard PLN model (merge PR #116)
ZIPLNnetwork() and ZIPLNfit_sparse-class to allow for zero-inflation
in the PLNnetwork model (merge PR #118)
Code factorization between PLNnetwork and ZIPLNnetwork (and
associated classes)
fix inconsistency between fitted and predict (merge PR #115)
PLNmodels 1.1.0 (2024-01-08)
Update documentation of PLN*_param() functions to include torch
optimization parameters
Add (somehow) explicit error message when torch convergence
fails
Change initialization in variance_jackknife() and
variance_bootstrap() to prevent estimation recycling,
results from those functions are now comparable to doing jackknife /
bootstrap “by hand”.
Merge PR #110 from Cole Trapnell to add:
bootstrap estimation of the variance of model parameter
improved interface for model initialization / optimisation
parameters, which are now passed on to jackknife / bootstrap
post-treatments
better support of GPU when using torch backend
Change behavior of predict() function for PLNfit model
to (i) return fitted values if newdata is missing or (ii) perform one VE
step to improve fit if responses are provided (fix issue #114)
PLNmodels 1.0.4 (2023-08-24)
changed initial value in optim for variational variance (1 ->
0.1) in VE-step of PLN and PLNPCA
fix sign in objective of VE_step for PLN with full covariance Issue
#100
add a scale argument compute_offset() to force the
offsets (RLE, CSS, GMPR, Wrench) to be on the same scale as the counts,
like TSS.
add a new “TMM” for compute_offset()
fix nb_param for PLNLDA, which caused wrong BIC/ICL and erratic
model selection
higher tolerance on a single test (among 700) that fails on the
‘noLD’ additional architecture on CRAN (tests without long double)
PLNmodels 1.0.2 (2023-06-21)
changed initial value in optim for variational variance (1 ->
0.1), which caused failure in some cases
fix bug when using inception in PLNnetwork()
starting handling of missing data
slightly faster (factorized) initialization for PCA
PLNmodels 1.0.1 (2023-02-12)
fix in the use of future_lapply which used to make post-Treatments
in PLNPCA last for ever with multicore in v1.0.0…
prevent use of bootstrap/jackknife when not appropriate
fix bug in PLNmixture() when the sequence of cluster numbers
(clusters) is not of the form 1:K_max
use bibentry to replace citEntry in CITATION
PLNmodels 1.0.0
Breaking changes
interface for controlling the fits now use list generated by
dedicated functions
PLN_param() for PLN
PLNLDA_param() for PLNLDA
PLNnetwork_param() for PLNnetwork
PLNPCA_param() for PLNPCA
PLNmixture_param() for PLNmixture The use of ‘control = list()’ is
deprecated: the code stop and send an error.
The regression coefficients are now denoted by B, not Theta, such as
B = t(Theta). We keep on sending back Theta as a field of myPLN\(model_par\)Theta, but this will soon be
deprecated
New features
added Barents fish data set
support for PLN when (inverse) covariance is known/fixed
estimator of the variance of the model parameters
integration of sandwich estimator of the variance-covariance of
Theta when Sigma is fixed
variational estimation of the variance-covariance based on
variational approximation of the Fisher information
jackknife estimation of the variance of Theta and Sigma
bootstrap estimation of the variance of Theta and Sigma
handle list of penalty weights in PLNnetwork
first support for torch optimizers (for PLN and PLNLDA)
Bug fixes
fix in objective functions of ve_step of standard PLN models
fix in objective functions of main of standard PLN models
PLNmodels 0.11.7
fix expression of ELBO in VEstep, related to #91
typos and regeneration of documentation( HTML5)
added an S3 method predict_cond to perform conditional
predictions
fix #89 bug by forcing an intercept in PLNLDA() and
changing extract_model() to conform with
model.frame()
PLNmodels 0.11.6
fix wrong use of all.equal
fix linking problem in new version of nloptr (>=2.0.0)
PLNmodels 0.11.5
fixing #79 by using the same variational distribution to approximate
the spherical case as in the fully parametrized and diagonal cases
faster examples and build for vignettes
additional R6 method $VEStep() for PLN-PCA, dealing
with low rank matrices
additional R6 method $project() for PLN-PCA, used to
project newdata into PCA space
use future_lapply in PLNmixture_family
remove a NOTE due to a DESeq2 link and a failure on solaris on CRAN
machines
some bug fixes
PLNmodels 0.11.4
use future_lapply in PLNPCA, PLNmixture and stability_selection
(plan must be set by the user)
bug fix in prediction for PLN-LDA
bug fix in gradients of PLN-network and PLN-spherical
suppressing method $latent_pos() which is equivalent to
active binding $latent
finalizing integration of PLNmixture (in particular faster
smoothing)
added an argument ‘reverse’ to the plot methods for criteria, so
that users can get their “usual” BIC definition (-2 loglik)
PLNmodels 0.11.3
support for covariates in PLNmixture (spherical, diagonal,
full)
more support for PLNmixture (S3/R6 methods, vignette)
PLNmodels 0.11.2
Rewriting C++ by merging modern_cpp to dev, thanks to François
Gindraud
various bug fixes in offset
less verbose about R squared when questionable
correction in BIC/ICL for PLNPCA
Enhanced vignettes for PLNPCA and PLNmixture
PLNmodels 0.11.1
Add compatibility with factoextra for PLNPCA
PLNmodels 0.11.0
Add development version of PLNmixture
PLNmodels 0.10.7
add type = “poscounts” option to RLE normalization
added wrench normalization to the list of available offsets
added the oaks data set from Jakuschkin et al (2016)
PLNmodels 0.10.6
Correction in likelihood of diagonal PLN
amending test-pln to fulfill CRAN request (error on ATLAS variant of
BLAS…)
PLNmodels 0.10.5
Refactor code of R6 classes to benefit from Roxygen 7.0.0 R6-related
new features for documentation
PLNmodels 0.10.4
Change name of variational variance parameters to S2 (used to be
S)
use spell_check to check spelling, found many typos
PLNmodels 0.10.3
Change in optimization for all PLN models (PLNs, PCA, LDA,
networks): solving in S such that S = S² for the variational parameters,
thus avoiding lower bound and constrained optimization. Slightly finer
results/estimations for similar computational cost, but easier to
maintain.
PLNmodels 0.10.2
Fix bug in predict() methods when factor levels differ between train
and test datasets.
Fix bug in PLNPCAfit S3 plot() method
Some simplification in C++ code
correction/changes in PLN likelihoods? + added constant terms in all
likelihoods of all PLN models
VEstep now available for all model of covariance in PLN (full,
diagonal, spherical)
PLNmodels 0.9.5 - minor
release
removed any use of rmarkdown::paged_table() in the vignettes
added screenshot.force = FALSE, in knitr options in the
vignettes
PLNmodels 0.9.4 - minor
release
removing dependencies to bioconductor packages, too cumbersome to
maintain on CRAN
PLNmodels 0.9.3 - minor
release
correction in test to comply new class of matrix object
PLNmodels 0.9.2.9002
- development version
added the possibility for matrix of weights for the penalty in
PLNnetworks
PLNmodels 0.9.2
various bug fixes
PLNmodels 0.9.1
Use nloptr to prepare CRAN release
PLNmodels 0.8.2
Enhancement in PLNLDA
PLNmodels 0.8.1
Preparing first CRAN release
PLNmodels 0.7.0.1
Added a NEWS.md file to track changes to the
package.