plnmodels - v1.2.1 - new CRAN release

PLNmodels 1.2.1 (2025-03-10)

• fix NOTES in CRAN due to missing packages in \link{} (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)

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Published by jchiquet 12 months ago

plnmodels - v1.2.0 - new CRAN release

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)

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Published by jchiquet almost 2 years ago

plnmodels - v1.1.0 - new CRAN release

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)

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Published by jchiquet about 2 years ago

plnmodels - v1.0.4 - new CRAN release

• 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.
• fix nb_param for PLNLDA, which caused wrong BIC/ICL and erratic model selection
• fix minor issues #102, #103 plus some others
• fix package file documentation as suggested in https://github.com/r-lib/roxygen2/issues/1491

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Published by jchiquet over 2 years ago

plnmodels - v1.0.3 - new CRAN release

PLNmodels 1.0.3

• higher tolerance on a single test (among 700) that fails on the 'noLD' additional architecture on CRAN (tests without long double)

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Published by jchiquet over 2 years ago

plnmodels - v1.0.2 - new CRAN release

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

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Published by jchiquet over 2 years ago

plnmodels - v1.0.1 - new CRAN release

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

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Published by jchiquet about 3 years ago

plnmodels - v1.0.0 - new CRAN release

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

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Published by jchiquet about 3 years ago

plnmodels - v0.11.7 - new CRAN release

• 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()

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Published by jchiquet over 3 years ago

plnmodels - v0.11.6 - new CRAN release

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 futurelapply in PLNmixturefamily
• remove a NOTE due to a DESeq2 link and a failure on solaris on CRAN machines
• some bug fixes

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Published by jchiquet about 4 years ago

plnmodels - v0.11.4 - CRAN release

New CRAN release, first since the beginning of the development of PLNmixture

Major changes are

• new function PLNmixture and series of objects, methods and vignette
• use future for parallel computing with future_lapply in PLNPCA, smoothing of PLNmixture and StARS in PLNnetwork
• bug fixes: offset, prediction for PLN-LDA, gradients of PLN-network and PLN-spherical
• added an argument ‘reverse’ to the plot methods for criteria, so that users can get their “usual” BIC definition (-2 loglik)
• Rewriting C++ by merging modern_cpp to dev, thanks to François Gindraud
• less verbose about R squared when questionable
• correction in BIC/ICL for PLNPCA
• Add compatibility with factoextra for PLNPCA and PLNLDA

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Published by jchiquet almost 5 years ago

plnmodels - v0.10.6 - new CRAN release( minor/technical)

• correction in likelihood of diagonal PLN
• amending test-pln to fullfil CRAN request (error on ATLAS variant of BLAS…)

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Published by jchiquet over 5 years ago

plnmodels - v0.10.5 - new CRAN release

version published on CRAN on 2019-06-16

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Published by jchiquet over 5 years ago

plnmodels - v0.10.4 - 'intermediary' release with various updates

Reporting changes since last Release (0.9.5)

PLNmodels 0.10.4

• Change name of variational variance parameters to S2 (use 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)

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Published by jchiquet over 5 years ago

plnmodels - v0.9.5 - new CRAN release

minor release avoiding warning in vignette build on Solaris and OS X

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Published by jchiquet about 6 years ago

plnmodels - v0.9.3 - new CRAN release

• minor changes to comply tests in R 3.6.2

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Published by jchiquet about 6 years ago

plnmodels - v0.9.2 - first CRAN release

version published on CRAN on 2019-05-17

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Published by jchiquet almost 7 years ago

plnmodels - v0.9.1

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Published by jchiquet almost 7 years ago

plnmodels - v0.8.2

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Published by jchiquet almost 7 years ago

plnmodels - Release for NGB tutorials

Some bug fixes compared to v0.7.0.1

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Published by jchiquet about 7 years ago

plnmodels - Release for NGB tutorials

• PLNmodels_0.7.0.1.zip is a binary version of the package for Windows user.
• PLNmodels_0.7.0.1.tar.gz is a source version of the package that requires compilation tools.

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Published by jchiquet about 7 years ago