NEWS.md

In PLNmodels: Poisson Lognormal Models

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.
• 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

PLNmodels 1.0.3 (2023-07-06)

• 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.

PLNmodels documentation built on Aug. 24, 2023, 5:11 p.m.