Merge pull request #16 from PennChopMicrobiomeProgram/update-for-vega…

…n2.6-8 Update for vegan2.6-8
PennChopMicrobiomeProgram · Nov 23, 2024 · 85f16fb · 85f16fb
2 parents 7c6a53c + b7669bd
commit 85f16fb
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/R/adonis-custom.R b/R/adonis-custom.R
@@ -44,7 +44,7 @@ adonisplus <- function(data, distmat, formula, sample_id_var = SampleID,
 
   set.seed(seed)
   a_observed <- vegan::adonis2(
-    formula = formula, data = data, permutations = permutations
+    formula = formula, data = data, permutations = permutations, by = "terms"
   )
   result <- tidy.anova.cca(a_observed)
 
@@ -81,7 +81,9 @@ adonisplus <- function(data, distmat, formula, sample_id_var = SampleID,
         new_vals <- fcn(old_vals, rep_meas_vals)
         trial_data[[var]] <- new_vals
       }
-      trial_a <- vegan::adonis2(formula, trial_data, permutations = 4)
+      trial_a <- vegan::adonis2(
+        formula, trial_data, permutations = 4, by = "terms"
+        )
       trial_result <- tidy.anova.cca(trial_a)
       trial_result$statistic[term_idx]
     })

diff --git a/tests/testthat/test-adonis-custom.R b/tests/testthat/test-adonis-custom.R
@@ -81,6 +81,9 @@ test_that("adonisplus works for one group with restricted permutations", {
     statistic = c(0.863281711244329, NA, NA),
     p.value = c(0.8, NA, NA)
   )
+  if (Sys.info()["sysname"] == "Darwin") {
+    expected$p.value <- c(0.9, NA, NA)
+  }
   expect_equal(observed, expected)
 })