Set "by" argument in adonis2 to replicate old behavior

PennChopMicrobiomeProgram · Nov 22, 2024 · 6a60f80 · 6a60f80
1 parent 7c6a53c
commit 6a60f80
Showing 1 changed file with 4 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]
     })