From eb5f3d8427ed528bd00190e9b85f2c8446a0c255 Mon Sep 17 00:00:00 2001
From: Stijn <wittouck_stijn@hotmail.com>
Date: Tue, 16 Nov 2021 10:29:28 +0000
Subject: [PATCH] Improve the documentation of perform_adonis

---
 R/getters.R           | 14 ++++++++++----
 man/perform_adonis.Rd | 18 ++++++++++++++----
 2 files changed, 24 insertions(+), 8 deletions(-)

diff --git a/R/getters.R b/R/getters.R
index 3b9a994..c845409 100644
--- a/R/getters.R
+++ b/R/getters.R
@@ -317,11 +317,17 @@ abundances <- function(ta) ta$abundances
 
 #' Perform an adonis test
 #'
-#' This function executes the adonis function of the vegan package and returns
-#' the result.
+#' This function executes the \link[vegan]{adonis} function of the vegan package
+#' and returns the result.
 #'
-#' Predictors should be a character vector. Samples where one of the predictors
-#' is NA are removed.
+#' Samples where one or more predictors are NA are removed.
+#'
+#' @param ta A tidyamplicons object.
+#' @param predictors A character vector with predictors to include in the model.
+#' @param permutations The number of permutations (more permutations takes
+#'   longer but gives a more accurate p-value).
+#'
+#' @return An object of class "adonis" (see \link[vegan]{adonis}).
 #'
 #' @export
 perform_adonis <- function(ta, predictors, permutations = 999) {
diff --git a/man/perform_adonis.Rd b/man/perform_adonis.Rd
index 4483bf0..242697e 100644
--- a/man/perform_adonis.Rd
+++ b/man/perform_adonis.Rd
@@ -6,11 +6,21 @@
 \usage{
 perform_adonis(ta, predictors, permutations = 999)
 }
+\arguments{
+\item{ta}{A tidyamplicons object.}
+
+\item{predictors}{A character vector with predictors to include in the model.}
+
+\item{permutations}{The number of permutations (more permutations takes
+longer but gives a more accurate p-value).}
+}
+\value{
+An object of class "adonis" (see \link[vegan]{adonis}).
+}
 \description{
-This function executes the adonis function of the vegan package and returns
-the result.
+This function executes the \link[vegan]{adonis} function of the vegan package
+and returns the result.
 }
 \details{
-Predictors should be a character vector. Samples where one of the predictors
-is NA are removed.
+Samples where one or more predictors are NA are removed.
 }