From 44e170f5a65b32457beb7e0a6b15b41f7b89bf3b Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Wed, 27 Sep 2023 13:24:23 +0200
Subject: [PATCH] Small documentation improvements

---
 R/method_clustering.R | 2 ++
 R/preset.R            | 2 +-
 man/clustering.Rd     | 4 ++++
 man/preset.Rd         | 2 +-
 4 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/R/method_clustering.R b/R/method_clustering.R
index f8bb869..7ba54cc 100644
--- a/R/method_clustering.R
+++ b/R/method_clustering.R
@@ -56,6 +56,8 @@ clusteriness <- function(data, span = 500000, weight = 0.5) {
 #' @param id Unique ID for the method and its results.
 #' @param name Human readable name for the method.
 #' @param description Method description.
+#' @param span See [clusteriness()].
+#' @param weight See [clusteriness()].
 #'
 #' @return An object of class `geposan_method`.
 #'
diff --git a/R/preset.R b/R/preset.R
index 88828db..d44d8d2 100644
--- a/R/preset.R
+++ b/R/preset.R
@@ -6,7 +6,7 @@
 #' filtered based on how many species have data for them. Afterwards, species
 #' that still have many missing genes will also be excluded. See the different
 #' method functions for the available methods: [clustering()], [correlation()],
-#' [neural()], [adjacency()] and [species_adjacency()].
+#' [distance()], [neural()] and [random_forest()].
 #'
 #' @param reference_gene_ids IDs of reference genes to compare to.
 #' @param methods List of methods to apply.
diff --git a/man/clustering.Rd b/man/clustering.Rd
index e5fdf43..3cd9a0a 100644
--- a/man/clustering.Rd
+++ b/man/clustering.Rd
@@ -18,6 +18,10 @@ clustering(
 \item{name}{Human readable name for the method.}
 
 \item{description}{Method description.}
+
+\item{span}{See \code{\link[=clusteriness]{clusteriness()}}.}
+
+\item{weight}{See \code{\link[=clusteriness]{clusteriness()}}.}
 }
 \value{
 An object of class \code{geposan_method}.
diff --git a/man/preset.Rd b/man/preset.Rd
index 41b1085..c53fc9e 100644
--- a/man/preset.Rd
+++ b/man/preset.Rd
@@ -38,5 +38,5 @@ reference genes to be able to assess the results later. The genes will be
 filtered based on how many species have data for them. Afterwards, species
 that still have many missing genes will also be excluded. See the different
 method functions for the available methods: \code{\link[=clustering]{clustering()}}, \code{\link[=correlation]{correlation()}},
-\code{\link[=neural]{neural()}}, \code{\link[=adjacency]{adjacency()}} and \code{\link[=species_adjacency]{species_adjacency()}}.
+\code{\link[=distance]{distance()}}, \code{\link[=neural]{neural()}} and \code{\link[=random_forest]{random_forest()}}.
 }