diff --git a/DESCRIPTION b/DESCRIPTION index 4bbfdd5..c8c265f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Encoding: UTF-8 Type: Package Package: fastTopics -Version: 0.6-189 -Date: 2024-07-07 +Version: 0.6-190 +Date: 2024-07-08 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"), diff --git a/R/fit_poisson_nmf.R b/R/fit_poisson_nmf.R index c0f9c89..20c7728 100644 --- a/R/fit_poisson_nmf.R +++ b/R/fit_poisson_nmf.R @@ -449,7 +449,7 @@ fit_poisson_nmf <- function (X, k, fit0, numiter = 100, cat(sprintf("Running at most %d %s updates, %s extrapolation ", numiter,method.text, ifelse(control$extrapolate,"with","without"))) - cat("(fastTopics 0.6-189).\n") + cat("(fastTopics 0.6-190).\n") } # INITIALIZE ESTIMATES diff --git a/README.md b/README.md index d4b08a0..d7b53dc 100644 --- a/README.md +++ b/README.md @@ -81,9 +81,9 @@ See the [package documentation][pkgdown] for more information. ## Developer notes -To prepare the package for CRAN, remove the "Remotes" field in the -DESCRIPTION file, and set `on_cran <- TRUE` in `helper_functions.R`, -then run `R CMD build fastTopics` to build the source package. +To prepare the package for CRAN, remove the +"single_cell_rnaseq_practical" vignette, then run `R CMD build +fastTopics` to build the source package. This is the command used to check the package before submitting to CRAN: diff --git a/vignettes/single_cell_rnaseq_basic.Rmd b/vignettes/single_cell_rnaseq_basic.Rmd index 53c3c5e..2224387 100644 --- a/vignettes/single_cell_rnaseq_basic.Rmd +++ b/vignettes/single_cell_rnaseq_basic.Rmd @@ -18,7 +18,10 @@ The aim of this vignette is to introduce the basic concepts behind an analysis of single-cell RNA-seq data using a topic model, and to show how to use 'fastTopics' to implement this analysis. This first vignette explains the analysis steps at only a high level---see -[Part 2][vignette-part-2] for additional explanations and guidance. +[Part 2][vignette-part-2] for additional explanations and +guidance. (Note that Part 2 was not included with the fastTopics +package on CRAN. It is only included with the fastTopics package on +GitHub.) Since a topic model analysis is quite different from most conventional analyses of single-cell RNA-seq data, we point out key