Updated CITATION.

.github/workflows/R-CMD-check.yaml

@@ -16,7 +16,6 @@ jobs:
       _R_CHECK_FORCE_SUGGESTS_: false
     steps:
       - uses: actions/checkout@v3
-
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true

DESCRIPTION

@@ -1,8 +1,8 @@
 Encoding: UTF-8
 Type: Package
 Package: fastTopics
-Version: 0.6-158
-Date: 2023-09-15
+Version: 0.6-159
+Date: 2023-10-22
 Title: Fast Algorithms for Fitting Topic Models and Non-Negative
     Matrix Factorizations to Count Data
 Authors@R: c(person("Peter","Carbonetto",role=c("aut","cre"),

R/fit_poisson_nmf.R

@@ -428,7 +428,7 @@ fit_poisson_nmf <- function (X, k, fit0, numiter = 100,
       method.text <- "CCD"
     cat(sprintf("Running %d %s updates, %s extrapolation ",numiter,
         method.text,ifelse(control$extrapolate,"with","without")))
-    cat("(fastTopics 0.6-158).\n")
+    cat("(fastTopics 0.6-159).\n")
   }
 
   # INITIALIZE ESTIMATES

inst/CITATION

@@ -48,13 +48,14 @@ bibentry(header = "If de_analysis is used, please also cite:",
               person("Karl Tayeb"),
               person("Sebastian Pott"),
               person("Matthew Stephens")),
-  journal = "bioRxiv",
-  doi = "10.1101/2023.03.03.531029",       
-  volume = "10.1101/2023.03.03.531029",
+  journal = "Genome Biology",
+  doi = "10.1186/s13059-023-03067-9",
+  volume = 24,
+  pages = 236,
   year = 2023,
   textVersion = paste("Peter Carbonetto, Kaixuan Luo, Abhishek Sarkar,",
-    "Anthony Hung, Karl Tayeb, Sebastian Pott and Matthew Stephens (2023).",
-    "Interpreting structure in sequence count data with differential",
-    "expression analysis allowing for grades of membership. bioRxiv",
-    "doi:10.1101/2023.03.03.531029."))
+    "Anthony Hung, Karl Tayeb, Sebastian Pott and Matthew Stephens.",
+    "GoM DE: interpreting structure in sequence count data with differential",
+    "expression analysis allowing for grades of membership. Genome Biology",
+    "24: 236 (2023). https://doi.org/10.1186/s13059-023-03067-9"))