- 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)

- 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. - add a new “TMM” for compute_offset()
- 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

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

- 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

- 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

- 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

- 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)

- fix in objective functions of ve_step of standard PLN models
- fix in objective functions of main of standard PLN models

- 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.