Files in PLN-team/PLNmodels
Poisson Lognormal Models
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
AUTHORS
CRAN-SUBMISSION
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
PLNmodels.Rproj
R/PLN.R
R/PLNLDA.R
R/PLNLDAfit-S3methods.R
R/PLNLDAfit-class.R
R/PLNPCA.R
R/PLNPCAfamily-S3methods.R
R/PLNPCAfamily-class.R
R/PLNPCAfit-S3methods.R
R/PLNPCAfit-class.R
R/PLNfamily-S3methods.R
R/PLNfamily-class.R
R/PLNfit-S3methods.R
R/PLNfit-class.R
R/PLNmixture.R
R/PLNmixturefamily-S3methods.R
R/PLNmixturefamily-class.R
R/PLNmixturefit-S3methods.R
R/PLNmixturefit-class.R
R/PLNmodels-package.R
R/PLNnetwork.R
R/PLNnetworkfamily-S3methods.R
R/PLNnetworkfamily-class.R
R/PLNnetworkfit-S3methods.R
R/PLNnetworkfit-class.R
R/RcppExports.R
R/ZIPLN.R
R/ZIPLNfit-S3methods.R
R/ZIPLNfit-class.R
R/ZIPLNnetwork.R
R/barents.R
R/import_utils.R
R/mollusk.R
R/oaks.R
R/plot_utils.R
R/scRNA.R
R/trichoptera.R
R/utils-pipe.R
R/utils-zipln.R
R/utils.R
R/zzz.R
README.Rmd
README.md
_pkgdown.yml
codecov.yml
cran-comments.md
data-raw/oaks.R
data-raw/oaks/counts.tsv
data-raw/oaks/metadata.tsv
data-raw/oaks/offsets.tsv
data-raw/scRNA.R
data/barents.rda
data/mollusk.rda
data/oaks.rda
data/scRNA.rda
data/trichoptera.rda
inst/CITATION
inst/WORDLIST
inst/case_studies/.gitignore
inst/case_studies/metaweb.R
inst/case_studies/mixture_iris.R
inst/case_studies/mollusk.R
inst/case_studies/oaks_tree.R
inst/case_studies/oaks_widgets.Rmd
inst/case_studies/scRNA.R
inst/check/check_grad_genet.cpp
inst/check/inconsistency_VEM.R
inst/check/jackknife_variance.R
inst/check/mwe_vestep_pln.R
inst/check/variance_estimates.R
inst/missing_data/call_optim_PCA.R
inst/simus_PLNnetwork/AUC.png
inst/simus_PLNnetwork/AUPR.png
inst/simus_PLNnetwork/assesNetworkInference.R
inst/simus_PLNnetwork/func_data_generation.R
inst/simus_PLNnetwork/func_networks.R
inst/simus_PLNnetwork/func_utils.R
inst/simus_ZIPLN/essai_ZIPLN.R
inst/sticker/PLNmodels.png
inst/sticker/PLNmodels_large.png
inst/sticker/create_sticker.R
inst/sticker/poissonnet.png
inst/sticker/poissonnet_vague.png
inst/torch_for_r/torch_PLN.R
inst/torch_for_r/torchpca.R
man/Networkfamily.Rd
man/PLN.Rd
man/PLNLDA.Rd
man/PLNLDA_param.Rd
man/PLNLDAfit.Rd
man/PLNLDAfit_diagonal.Rd
man/PLNPCA.Rd
man/PLNPCA_param.Rd
man/PLNPCAfamily.Rd
man/PLNPCAfit.Rd
man/PLN_param.Rd
man/PLNfamily.Rd
man/PLNfit.Rd
man/PLNfit_diagonal.Rd
man/PLNfit_fixedcov.Rd
man/PLNfit_spherical.Rd
man/PLNmixture.Rd
man/PLNmixture_param.Rd
man/PLNmixturefamily.Rd
man/PLNmixturefit.Rd
man/PLNmodels-package.Rd
man/PLNnetwork.Rd
man/PLNnetwork_param.Rd
man/PLNnetworkfamily.Rd
man/PLNnetworkfit.Rd
man/ZIPLN.Rd
man/ZIPLN_param.Rd
man/ZIPLNfit.Rd
man/ZIPLNfit_diagonal.Rd
man/ZIPLNfit_fixed.Rd
man/ZIPLNfit_sparse.Rd
man/ZIPLNfit_spherical.Rd
man/ZIPLNnetwork.Rd
man/ZIPLNnetwork_param.Rd
man/ZIPLNnetworkfamily.Rd
man/barents.Rd
man/coef.PLNLDAfit.Rd
man/coef.PLNfit.Rd
man/coef.PLNmixturefit.Rd
man/coef.ZIPLNfit.Rd
man/coefficient_path.Rd
man/compute_PLN_starting_point.Rd
man/compute_offset.Rd
man/extract_probs.Rd
man/figures/PLN-1.png
man/figures/PLNLDA-1.png
man/figures/PLNPCA-1.png
man/figures/PLNPCA-2.png
man/figures/PLNnetwork-1.png
man/figures/PLNnetwork-2.png
man/figures/logo.png
man/fitted.PLNfit.Rd
man/fitted.PLNmixturefit.Rd
man/fitted.ZIPLNfit.Rd
man/getBestModel.Rd
man/getModel.Rd
man/mollusk.Rd
man/oaks.Rd
man/pipe.Rd
man/plot.Networkfamily.Rd
man/plot.PLNLDAfit.Rd
man/plot.PLNPCAfamily.Rd
man/plot.PLNPCAfit.Rd
man/plot.PLNfamily.Rd
man/plot.PLNmixturefamily.Rd
man/plot.PLNmixturefit.Rd
man/plot.PLNnetworkfit.Rd
man/plot.ZIPLNfit_sparse.Rd
man/predict.PLNLDAfit.Rd
man/predict.PLNfit.Rd
man/predict.PLNmixturefit.Rd
man/predict.ZIPLNfit.Rd
man/predict_cond.Rd
man/prepare_data.Rd
man/rPLN.Rd
man/scRNA.Rd
man/sigma.PLNfit.Rd
man/sigma.PLNmixturefit.Rd
man/sigma.ZIPLNfit.Rd
man/stability_selection.Rd
man/standard_error.Rd
man/trichoptera.Rd
man/vcov.PLNfit.Rd
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/lambertW.cpp
src/lambertW.h
src/nlopt_wrapper.cpp
src/nlopt_wrapper.h
src/optim_diag_cov.cpp
src/optim_fixed_cov.cpp
src/optim_full_cov.cpp
src/optim_genet_cov.cpp
src/optim_rank_cov.cpp
src/optim_spherical.cpp
src/optim_zi-pln.cpp
src/packing.cpp
src/packing.h
src/utils.h
tests/testthat.R
tests/testthat/test-cpp.R
tests/testthat/test-import-utils.R
tests/testthat/test-pln.R
tests/testthat/test-plnfamily.R
tests/testthat/test-plnfit.R
tests/testthat/test-plnlda-fit.R
tests/testthat/test-plnlda.R
tests/testthat/test-plnmixture.R
tests/testthat/test-plnnetworkfamily.R
tests/testthat/test-plnnetworkfit.R
tests/testthat/test-plnpcafamily.R
tests/testthat/test-plnpcafit.R
tests/testthat/test-standard-error.R
tests/testthat/test-zipln.R
tests/testthat/test-ziplnfit.R
tests/testthat/test-ziplnnetworkfamily.R
vignettes/.gitignore
vignettes/Import_data.Rmd
vignettes/PLN.Rmd
vignettes/PLNLDA.Rmd
vignettes/PLNPCA.Rmd
vignettes/PLNmixture.Rmd
vignettes/PLNnetwork.Rmd
vignettes/Trichoptera.Rmd
vignettes/article/PLNreferences.bib
vignettes/figures/PLN_geometry.jpg
vignettes/figures/macronema_zebratum.jpg
