From da2ecb60d2648f2c9b161a21e18f0f859da83949 Mon Sep 17 00:00:00 2001
From: "Adam H. Sparks" <adam.sparks@curtin.edu.au>
Date: Thu, 16 May 2024 11:55:44 +0800
Subject: [PATCH] Tidy up @return text in fn documentation

---
 R/calculate_complexities.R    | 3 +--
 R/calculate_diversities.R     | 4 +++-
 R/create_binary_matrix.R      | 3 +--
 R/summarize_gene.R            | 3 ++-
 codemeta.json                 | 2 +-
 man/calculate_complexities.Rd | 3 +--
 man/calculate_diversities.Rd  | 4 +++-
 man/create_binary_matrix.Rd   | 3 +--
 man/summarize_gene.Rd         | 3 ++-
 9 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/R/calculate_complexities.R b/R/calculate_complexities.R
index 071a55a1..f65a3c60 100644
--- a/R/calculate_complexities.R
+++ b/R/calculate_complexities.R
@@ -22,8 +22,7 @@
 #'
 #' summary(complexities)
 #'
-#' @return `calculate_complexities` returns an object of class
-#' `hagis.complexities`.
+#' @return An object of class `hagis.complexities`.
 #'
 #' An object of class `hagis.complexities` is a `list` containing the following
 #'  components
diff --git a/R/calculate_diversities.R b/R/calculate_diversities.R
index f3e03552..4fc7449a 100644
--- a/R/calculate_diversities.R
+++ b/R/calculate_diversities.R
@@ -54,7 +54,9 @@
 #' diversities
 #'
 #' @export calculate_diversities
-#' @return hagis.diversities object containing
+#' @return a `hagis.diversities` object.
+#' 
+#' A `hagis.diversities` object is a `list` containing:
 #'   * Number of Samples
 #'   * Number of Pathotypes
 #'   * Simple Diversity Index
diff --git a/R/create_binary_matrix.R b/R/create_binary_matrix.R
index fd4c6d82..8bc238ba 100644
--- a/R/create_binary_matrix.R
+++ b/R/create_binary_matrix.R
@@ -24,8 +24,7 @@
 #'                                     perc_susc = "perc.susc")
 #' final_matrix
 #'
-#' @return `create_binary_matrix` returns a binary matrix of pathotype data as
-#' a [matrix] object
+#' @return a binary matrix of pathotype data
 #' 
 #' @export create_binary_matrix
 #' 
diff --git a/R/summarize_gene.R b/R/summarize_gene.R
index 35672b6a..4a5957aa 100644
--- a/R/summarize_gene.R
+++ b/R/summarize_gene.R
@@ -29,7 +29,8 @@
 #'                        perc_susc = "perc.susc")
 #' susc
 #'
-#' @return  returns an object of [class] `hagis.gene.summary`
+#' @return a `hagis.gene.summary` object.
+#' 
 #' An object of class `hagis.gene.summary` is a\cr [data.table::data.table()]
 #'  containing the following components columns
 #'   \describe{
diff --git a/codemeta.json b/codemeta.json
index 09763566..2c4c9b1f 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -249,7 +249,7 @@
   "applicationCategory": "Tools",
   "isPartOf": "https://openplantpathology.org",
   "keywords": ["plant-pathology", "pathotype", "pathogen-survey", "virulenceanalysis", "differentialset", "assessmentscale", "plant-disease", "pathotype-complexities", "population-diversities"],
-  "fileSize": "295.82KB",
+  "fileSize": "295.707KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",
diff --git a/man/calculate_complexities.Rd b/man/calculate_complexities.Rd
index 5551eeee..75814c46 100644
--- a/man/calculate_complexities.Rd
+++ b/man/calculate_complexities.Rd
@@ -23,8 +23,7 @@ being tested. \code{Character}.}
 \code{Character}.}
 }
 \value{
-\code{calculate_complexities} returns an object of class
-\code{hagis.complexities}.
+An object of class \code{hagis.complexities}.
 
 An object of class \code{hagis.complexities} is a \code{list} containing the following
 components
diff --git a/man/calculate_diversities.Rd b/man/calculate_diversities.Rd
index 958db3fe..ea7401f6 100644
--- a/man/calculate_diversities.Rd
+++ b/man/calculate_diversities.Rd
@@ -23,7 +23,9 @@ being tested. \code{Character}.}
 \code{Character}.}
 }
 \value{
-hagis.diversities object containing
+a \code{hagis.diversities} object.
+
+A \code{hagis.diversities} object is a \code{list} containing:
 \itemize{
 \item Number of Samples
 \item Number of Pathotypes
diff --git a/man/create_binary_matrix.Rd b/man/create_binary_matrix.Rd
index 60e1a49f..fe2824ac 100644
--- a/man/create_binary_matrix.Rd
+++ b/man/create_binary_matrix.Rd
@@ -23,8 +23,7 @@ being tested. \code{Character}.}
 \code{Character}.}
 }
 \value{
-\code{create_binary_matrix} returns a binary matrix of pathotype data as
-a \link{matrix} object
+a binary matrix of pathotype data
 }
 \description{
 Creates a binary data matrix from pathotype data representing
diff --git a/man/summarize_gene.Rd b/man/summarize_gene.Rd
index 202d7e6e..8838c4dd 100644
--- a/man/summarize_gene.Rd
+++ b/man/summarize_gene.Rd
@@ -23,7 +23,8 @@ being tested. \code{Character}.}
 \code{Character}.}
 }
 \value{
-returns an object of \link{class} \code{hagis.gene.summary}
+a \code{hagis.gene.summary} object.
+
 An object of class \code{hagis.gene.summary} is a\cr \code{\link[data.table:data.table]{data.table::data.table()}}
 containing the following components columns
 \describe{