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
PLNmodels 0.9.1
- Use nloptr to prepare CRAN release
PLNmodels 0.8.2
PLNmodels 0.8.1
- Preparing first CRAN release
PLNmodels 0.7.0.1
- Added a
NEWS.md file to track changes to the
package.