Changelog

Source: NEWS.md

PLNmodels 1.0.4 (2023-08-24)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)2023-07-01

  • 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)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)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 1.0.02023-01-06

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 myPLNmodelparTheta, 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 0.11.72022-08-25

  • 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 0.11.62022-02-01

  • fix wrong use of all.equal
  • fix linking problem in new version of nloptr (>=2.0.0)

PLNmodels 0.11.52022-01-20

  • 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 0.11.42021-03-16

  • 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 0.10.62020-06-22

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

PLNmodels 0.10.52020-06-16

  • 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 release2020-01-27

  • 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 release2020-01-14

  • removing dependencies to bioconductor packages, too cumbersome to maintain on CRAN

PLNmodels 0.9.3 - minor release2019-12-05

  • 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 0.9.22019-05-17

  • 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.