added arguments to be passed to adonis2 for parallelism

Author: agusinac

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: OmicFlow
 Title: Fast and Efficient (Automated) Analysis of Sparse Omics Data
-Version: 1.6.0.9001
+Version: 1.6.0.9002
 Date: 2026-05-19
 Authors@R: c(
     person(
@@ -52,6 +52,7 @@ Suggests:
     DT,
     downloadthis,
     rmarkdown,
+    parallel,
     testthat (>= 3.0.0)
 LinkingTo:
     Rcpp,

R/pairwise_adonis.R

@@ -11,6 +11,7 @@
 #' @param perm_design A function that takes a data.frame and constructs a permutation design with \link[permute]{how} (default: NULL).
 #' @param p.adjust.method P adjust method see \link[stats]{p.adjust}.
 #' @param perm Number of permutations to compare against the null hypothesis of adonis2 (default: \code{perm=999}).
+#' @param ... Additional arguments passed to \link[vegan]{adonis2}.
 #' @seealso \link[vegan]{adonis2}
 #' @return A \link[base]{data.frame} of
 #'  * pairs that are used
@@ -44,7 +45,8 @@ pairwise_adonis <- function(
   metadata = NULL,
   perm_design = NULL,
   p.adjust.method = "bonferroni",
-  perm = 999){
+  perm = 999,
+  ...){
 
   ## Error handling
   #--------------------------------------------------------------------#
@@ -95,13 +97,15 @@ pairwise_adonis <- function(
       ad <- vegan::adonis2(
         m ~ Fac,
         data = tmp_m,
-        permutations = h1
+        permutations = h1,
+        ...
       )
     } else {
       ad <- vegan::adonis2(
         m ~ Fac,
         data = tmp_m,
-        permutations = perm
+        permutations = perm,
+        ...
       )
     }
 
@@ -117,4 +121,4 @@ pairwise_adonis <- function(
   p.adj <- stats::p.adjust(p.value, method = p.adjust.method)
   pairw.res <- data.frame(pairs, Df, SumsOfSqs, F.Model, R2, p.value, p.adj)
   return(pairw.res)
-}
+}

R/pairwise_anosim.R

@@ -11,6 +11,7 @@
 #' @param perm_design A function that takes a data.frame and constructs a permutation design with \link[permute]{how} (default: NULL).
 #' @param p.adjust.method P adjust method see \link[stats]{p.adjust}
 #' @param perm Number of permutations to compare against the null hypothesis of anosim (default: \code{perm=999}).
+#' @param ... Additional arguments passed to \link[vegan]{anosim}.
 #' @seealso \link[vegan]{anosim}
 #' @return A \link[base]{data.frame} of
 #'  * pairs that are used
@@ -42,7 +43,7 @@ pairwise_anosim <- function(
   perm_design = NULL,
   p.adjust.method = "bonferroni",
   perm = 999
-  ){
+  ...){
 
   ## Error handling
   #--------------------------------------------------------------------#
@@ -87,13 +88,15 @@ pairwise_anosim <- function(
       ano <- vegan::anosim(
         x = m,
         grouping = groups,
-        permutations = h1
+        permutations = h1,
+        ...
       )
     } else {
       ano <- vegan::anosim(
         x = m, 
         grouping = groups[rows_to_keep],
-        permutations = perm
+        permutations = perm,
+        ...
       )
     }