Run mediation example only if miaTime installed

microbiome · Apr 19, 2024 · 6336cac · 6336cac
1 parent 1caeb00
commit 6336cac
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Showing 5 changed files with 36 additions and 24 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -82,9 +82,7 @@ Suggests:
     reldist,
     ade4,
     microbiomeDataSets,
-    miaTime,
     rmarkdown
-Remotes: microbiome/miaTime
 URL: https://github.com/microbiome/mia
 BugReports: https://github.com/microbiome/mia/issues
 Roxygen: list(markdown = TRUE)

diff --git a/NEWS b/NEWS
@@ -108,3 +108,4 @@ Changes in version 1.11.x
 + Rename cluster to addCluster
 + rename importers loadFromBiom, loadFromQIIME2, readQZA, loadFromMothur, 
 loadFromMetaphlan, loadFromHumann
++ add new functions getMediation and addMediation
diff --git a/R/mediate.R b/R/mediate.R
@@ -74,6 +74,7 @@
 #' @name getMediation
 #'
 #' @examples
+#' if( require("miaTime") ){
 #' # Import libraries
 #' library(mia)
 #' library(miaTime)
@@ -143,6 +144,7 @@
 #' 
 #' # Show results for first 5 mediators
 #' head(metadata(tse)$reddim_mediation, 5)
+#' }
 #' 
 NULL
 

diff --git a/man/getMediation.Rd b/man/getMediation.Rd
diff --git a/tests/testthat/test-mediate.R b/tests/testthat/test-mediate.R
@@ -1,5 +1,6 @@
 test_that("getMediation", {
 
+  if( require("miaTime") ){
   data("hitchip1006", package = "miaTime")
   tse <- hitchip1006
 
@@ -81,5 +82,6 @@ test_that("getMediation", {
   expect_named(tse, med_df[["Mediator"]])
 
   expect_named(med_df, c("Mediator", "ACME_estimate", "ADE_estimate", "ACME_pval", "ADE_pval"))
+  }
 
 })