From 53b4941a3c96213406825e2171db39cf32f7f678 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Thu, 22 Aug 2024 15:30:23 +0100
Subject: [PATCH] Document use of returned matching

---
 R/VisualizeMatching.R    | 4 +++-
 man/GeneralizedRF.Rd     | 3 ++-
 man/VisualizeMatching.Rd | 4 +++-
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/R/VisualizeMatching.R b/R/VisualizeMatching.R
index 59eebfdd..f2edc23c 100644
--- a/R/VisualizeMatching.R
+++ b/R/VisualizeMatching.R
@@ -41,7 +41,9 @@
 #' tree2 <- TreeTools::PectinateTree(6)
 #' 
 #' VisualizeMatching(RobinsonFouldsMatching, tree1, tree2)
-#' VisualizeMatching(SharedPhylogeneticInfo, tree1, tree2, matchZeros = FALSE)
+#' matching <- VisualizeMatching(SharedPhylogeneticInfo, tree1, tree2,
+#'                               matchZeros = FALSE)
+#' attributes(matching)
 #' @template MRS
 #' @encoding UTF-8
 #' @importFrom ape nodelabels edgelabels plot.phylo
diff --git a/man/GeneralizedRF.Rd b/man/GeneralizedRF.Rd
index 547f97e4..22ebb376 100644
--- a/man/GeneralizedRF.Rd
+++ b/man/GeneralizedRF.Rd
@@ -40,8 +40,9 @@ specified pair scorer. If \code{reportMatching = TRUE}, attribute also list:
 \itemize{
 \item \code{matching}: which split in \code{splits2} is optimally matched to each split in
 \code{split1} (\code{NA} if not matched);
-\item \code{pairScores}: Calculated scores for each possible matching of each split.
 \item \code{matchedSplits}: Textual representation of each match
+\item \code{matchedScores}: Scores for matched split.
+\item \code{pairScores}: Calculated scores for each possible matching of each split.
 }
 }
 \description{
diff --git a/man/VisualizeMatching.Rd b/man/VisualizeMatching.Rd
index d3725f10..bb3ea1c1 100644
--- a/man/VisualizeMatching.Rd
+++ b/man/VisualizeMatching.Rd
@@ -76,7 +76,9 @@ tree1 <- TreeTools::BalancedTree(6)
 tree2 <- TreeTools::PectinateTree(6)
 
 VisualizeMatching(RobinsonFouldsMatching, tree1, tree2)
-VisualizeMatching(SharedPhylogeneticInfo, tree1, tree2, matchZeros = FALSE)
+matching <- VisualizeMatching(SharedPhylogeneticInfo, tree1, tree2,
+                              matchZeros = FALSE)
+attributes(matching)
 }
 \author{
 \href{https://orcid.org/0000-0001-5660-1727}{Martin R. Smith}