From 12171ed8d8cce6eadec093a2b561b9f557f41cd0 Mon Sep 17 00:00:00 2001
From: Peter Carbonetto <peter.carbonetto@gmail.com>
Date: Wed, 24 Aug 2022 13:00:11 -0500
Subject: [PATCH] Replaced more instances of dgCMatrix with CsparseMatrix.

---
 DESCRIPTION         | 2 +-
 R/datasim.R         | 6 +++---
 R/fit_poisson_nmf.R | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 09039406..65c97e5d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Encoding: UTF-8
 Type: Package
 Package: fastTopics
-Version: 0.6-139
+Version: 0.6-140
 Date: 2022-08-24
 Title: Fast Algorithms for Fitting Topic Models and Non-Negative
     Matrix Factorizations to Count Data
diff --git a/R/datasim.R b/R/datasim.R
index fa1fdf67..1fe9acb5 100644
--- a/R/datasim.R
+++ b/R/datasim.R
@@ -60,7 +60,7 @@ simulate_count_data <- function (n, m, k, fmax = 1, lmax = 1, sparse = FALSE) {
   L <- rand(n,k,0,lmax)
   X <- generate_poisson_nmf_counts(F,L)
   if (sparse)
-    X <- as(X,"dgCMatrix")
+    X <- as(X,"CsparseMatrix")
 
   # Add row and column names to outputs.
   rownames(X) <- paste0("i",1:n)
@@ -254,7 +254,7 @@ simulate_poisson_gene_data <- function (n, m, k, s, p = 1, sparse = FALSE) {
   L <- generate_mixture_proportions(n,k)
   X <- generate_poisson_nmf_counts(F,s*L)
   if (sparse)
-    X <- as(X,"dgCMatrix")
+    X <- as(X,"CsparseMatrix")
 
   # Add row and column names to outputs.
   rownames(X) <- paste0("i",1:n)
@@ -293,7 +293,7 @@ simulate_multinom_gene_data <- function (n, m, k, sparse = FALSE) {
   F <- normalize.cols(generate_poisson_rates(m,k))
   X <- generate_multinom_topic_model_counts(F,L,s)
   if (sparse)
-    X <- as(X,"dgCMatrix")
+    X <- as(X,"CsparseMatrix")
   
   # Add row and column names to outputs.
   rownames(X) <- paste0("i",1:n)
diff --git a/R/fit_poisson_nmf.R b/R/fit_poisson_nmf.R
index e81daaf6..f856292c 100644
--- a/R/fit_poisson_nmf.R
+++ b/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 0.6-139).\n")
+    cat("(fastTopics 0.6-140).\n")
   }
   
   # INITIALIZE ESTIMATES