From adf04d25c2bbf9e93b3e170cdfa1f3c971fdab6c Mon Sep 17 00:00:00 2001
From: Sarah Teichman <teichs@uw.edu>
Date: Tue, 18 Mar 2025 12:11:43 -0700
Subject: [PATCH] fix example in constrasts_Test to only run if limma is
 installed

---
 R/contrastsTest.R    | 24 ++++++++++++++----------
 man/contrastsTest.Rd | 24 ++++++++++++++----------
 2 files changed, 28 insertions(+), 20 deletions(-)

diff --git a/R/contrastsTest.R b/R/contrastsTest.R
index 3c80469..396cd86 100644
--- a/R/contrastsTest.R
+++ b/R/contrastsTest.R
@@ -23,16 +23,20 @@
 #' @examples
 #'
 #' # data frame example
-#' data(soil_phylum_contrasts_sample)
-#' data(soil_phylum_contrasts_otu)
-#' da_analysis <- contrastsTest(formula = ~ DayAmdmt,
-#'                              phi.formula = ~ DayAmdmt,
-#'                              contrasts_DA = list("DayAmdmt21 - DayAmdmt11",
-#'                                                  "DayAmdmt22 - DayAmdmt21"),
-#'                              data = soil_phylum_contrasts_otu,
-#'                              sample_data = soil_phylum_contrasts_sample,
-#'                              fdr_cutoff = 0.05,
-#'                              try_only = 1:5)
+#' # note that this function will only run if the `limma` package is installed
+#' limma_install <- try(find.package("limma"), silent = TRUE)
+#' if (!(inherits(limma_install, "try-error"))) {
+#'   data(soil_phylum_contrasts_sample)
+#'   data(soil_phylum_contrasts_otu)
+#'   da_analysis <- contrastsTest(formula = ~ DayAmdmt,
+#'                               phi.formula = ~ DayAmdmt,
+#'                               contrasts_DA = list("DayAmdmt21 - DayAmdmt11",
+#'                                                    "DayAmdmt22 - DayAmdmt21"),
+#'                               data = soil_phylum_contrasts_otu,
+#'                                sample_data = soil_phylum_contrasts_sample,
+#'                                fdr_cutoff = 0.05,
+#'                               try_only = 1:5)
+#' }
 #'
 #' # phyloseq example (only run if you have phyloseq installed)
 #' \dontrun{
diff --git a/man/contrastsTest.Rd b/man/contrastsTest.Rd
index adb9fc7..878734a 100644
--- a/man/contrastsTest.Rd
+++ b/man/contrastsTest.Rd
@@ -65,16 +65,20 @@ This function uses contrast matrices to test for differential abundance and diff
 \examples{
 
 # data frame example
-data(soil_phylum_contrasts_sample)
-data(soil_phylum_contrasts_otu)
-da_analysis <- contrastsTest(formula = ~ DayAmdmt,
-                             phi.formula = ~ DayAmdmt,
-                             contrasts_DA = list("DayAmdmt21 - DayAmdmt11",
-                                                 "DayAmdmt22 - DayAmdmt21"),
-                             data = soil_phylum_contrasts_otu,
-                             sample_data = soil_phylum_contrasts_sample,
-                             fdr_cutoff = 0.05,
-                             try_only = 1:5)
+# note that this function will only run if the `limma` package is installed
+limma_install <- try(find.package("limma"), silent = TRUE)
+if (!(inherits(limma_install, "try-error"))) {
+  data(soil_phylum_contrasts_sample)
+  data(soil_phylum_contrasts_otu)
+  da_analysis <- contrastsTest(formula = ~ DayAmdmt,
+                              phi.formula = ~ DayAmdmt,
+                              contrasts_DA = list("DayAmdmt21 - DayAmdmt11",
+                                                   "DayAmdmt22 - DayAmdmt21"),
+                              data = soil_phylum_contrasts_otu,
+                               sample_data = soil_phylum_contrasts_sample,
+                               fdr_cutoff = 0.05,
+                              try_only = 1:5)
+}
 
 # phyloseq example (only run if you have phyloseq installed)
 \dontrun{