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)

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)

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 r-lib/roxygen2#1491

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)

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

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

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

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()

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

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