• 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()
  • fix wrong use of all.equal
  • fix linking problem in new version of nloptr (>=2.0.0)
  • 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
  • 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)
  • support for covariates in PLNmixture (spherical, diagonal, full)
  • more support for PLNmixture (S3/R6 methods, vignette)
  • 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
  • Add compatibility with factoextra for PLNPCA
  • Add development version of PLNmixture
  • 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)
  • Correction in likelihood of diagonal PLN
  • amending test-pln to fulfill CRAN request (error on ATLAS variant of BLAS…)
  • Refactor code of R6 classes to benefit from Roxygen 7.0.0 R6-related new features for documentation
  • Change name of variational variance parameters to S2 (used to be S)
  • use spell_check to check spelling, found many typos
  • 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.
  • 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)
  • removed any use of rmarkdown::paged_table() in the vignettes
  • added screenshot.force = FALSE, in knitr options in the vignettes
  • removing dependencies to bioconductor packages, too cumbersome to maintain on CRAN
  • correction in test to comply new class of matrix object
  • added the possibility for matrix of weights for the penalty in PLNnetworks
  • various bug fixes
  • Use nloptr to prepare CRAN release
  • Enhancement in PLNLDA
  • Preparing first CRAN release
  • Added a NEWS.md file to track changes to the package.