Merge pull request #121 from PLN-team/zipln

Zipln

NEWS.md

@@ -1,6 +1,6 @@
-# PLNmodels 1.2.0 (2024-02-24)
+# PLNmodels 1.2.0 (2024-03-05)
 
-* new feature: ZIPLN (PLN with zero inflation) 
+* 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)

R/ZIPLN.R

@@ -23,20 +23,14 @@
 #' @examples
 #' data(trichoptera)
 #' trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
-#' myPLN <- PLN(Abundance ~ 1, data = trichoptera)
 #' ## Use different models for zero-inflation...
 #' myZIPLN_single <- ZIPLN(Abundance ~ 1, data = trichoptera, zi = "single")
+#' \dontrun{
 #' myZIPLN_row    <- ZIPLN(Abundance ~ 1, data = trichoptera, zi = "row")
 #' myZIPLN_col    <- ZIPLN(Abundance ~ 1, data = trichoptera, zi = "col")
 #' ## ...including logistic regression on covariates
 #' myZIPLN_covar  <- ZIPLN(Abundance ~ 1 | 1 + Wind, data = trichoptera)
-#' dplyr::bind_rows(
-#'   myPLN$criteria,
-#'   myZIPLN_single$criteria,
-#'   myZIPLN_row$criteria,
-#'   myZIPLN_col$criteria,
-#'   myZIPLN_covar$criteria
-#' )
+#' }
 #' @seealso The class [`ZIPLNfit`]
 #' @importFrom stats model.frame model.matrix model.response model.offset terms as.formula
 #' @export

cran-comments.md

@@ -1,37 +1,43 @@
 
-Submitting PLNmodels version 1.1.0 to CRAN
+Submitting PLNmodels version 1.2.0 to CRAN
 
-Fix various bugs, update package documentation for controlling optimization, better integration of the torch backend, better jackknife estimation for PLN.
+new feature: ZIPLN (PLN with zero inflation) for standard PLN and PLN Network
 
 ## Tested environments
 
 * tested locally on Ubuntu Linux 22.04.3 LTS, R-release, GCC
 
 * tested remotely with win-builder 
   - Windows Server 2022, R-devel, 64 bit
-  - Windows Server 2022, R-release (4.3.2), 64 bit
-  - Windows Server 2022, R-old (4.2.3), 64 bit
+  - Windows Server 2022, R-release, 64 bit
+  - Windows Server 2022, R-old, 64 bit
 
 * tested remotely with github-action
   - Linux Ubuntu 22.04, R-release
-  - Linux Ubuntu 22.04, R-oldrel 
   - Linux Ubuntu 22.04, R-devel 
   - Windows Server 2022, R-release, 64 bit
+  - Windows Server 2022, R-oldrel , 64 bit
   - macOS Big Sur 11, R-release 
+  - macOS Big Sur 11, R-oldrel 
 
 all status OK except for
 
 * the usual NOTE about libs size (RcppArmadillo)
 
-── R CMD check results ─────────────────────────── PLNmodels 1.1.0 ────
-Duration: 4m 32.7s
+ R CMD check results  PLNmod
+Duration: 6m 27.6s
 
 ❯ checking installed package size ... NOTE
-    installed size is 11.2Mb
+    installed size is 23.4Mb
     sub-directories of 1Mb or more:
-      doc    2.0Mb
-      libs   7.8Mb
+      data   1.4Mb
+      doc    2.1Mb
+      libs  18.3Mb
 
 0 errors ✔ | 0 warnings ✔ | 1 note ✖
 
 R CMD check succeeded
+
+── R CMD check results ─────────────────────────── PLNmodels 1.2.0 ────
+
+

inst/WORDLIST

@@ -11,8 +11,10 @@ Bournaud
 CAH
 CCSA
 CCSAQ
+CMD
 Chessel
 Coulet
+Cpp
 DESeq
 EBIC
 ELBO
@@ -66,7 +68,6 @@ PLNmixturefit
 PLNmodel
 PLNnetwork
 PLNnetworkfamily
-PLNnetworkfit
 PLNnetworks
 PLNs
 Pathobiome
@@ -92,6 +93,10 @@ Usseglio
 VE
 VEstep
 Variational
+ZI
+ZIPLN
+ZIPLNfit
+ZIPLNnetwork
 Zhang
 abundancies
 ade
@@ -117,6 +122,7 @@ compositional
 compositionality
 cond
 corrplot
+covar
 covariations
 cpp
 cumNormStat
@@ -162,6 +168,7 @@ leq
 les
 lm
 loadings
+logarithmically
 loglik
 lr
 lumineux
@@ -216,13 +223,17 @@ rescaled
 rmarkdown
 rsquared
 résultats
+scRNA
+scRNAseq
 solaris
 sparsification
+sparsify
 sparsifying
 sur
 texttt
 th
 tibble
+trancript
 triangleq
 trichoptera
 uncond