From 86d42647e026cdaf6474d350744add18290eaa26 Mon Sep 17 00:00:00 2001
From: emmanuelparadis <Emmanuel.Paradis@ird.fr>
Date: Sun, 28 Jan 2024 09:43:15 +0700
Subject: [PATCH] ace() now uses node labels if available

---
 DESCRIPTION |  2 +-
 NEWS        |  2 ++
 R/ace.R     | 10 ++++++++--
 3 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 2c22db5..fece96e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
 Version: 5.7-1.8
-Date: 2024-01-15
+Date: 2024-01-28
 Title: Analyses of Phylogenetics and Evolution
 Authors@R: c(person("Emmanuel", "Paradis", role = c("aut", "cre", "cph"), email = "Emmanuel.Paradis@ird.fr", comment = c(ORCID = "0000-0003-3092-2199")),
   person("Simon", "Blomberg", role = c("aut", "cph"), comment = c(ORCID = "0000-0003-1062-0839")),
diff --git a/NEWS b/NEWS
index eca7543..2788505 100644
--- a/NEWS
+++ b/NEWS
@@ -68,6 +68,8 @@ OTHER CHANGES
       size. The code is three times faster with small trees; twice
       faster with ~1000 tips (the gain is less with bigger trees).
 
+    o ace() now uses node labels, if available, in the output.
+
 
 
 		CHANGES IN APE VERSION 5.7-1
diff --git a/R/ace.R b/R/ace.R
index fe5aec2..1deadff 100644
--- a/R/ace.R
+++ b/R/ace.R
@@ -1,8 +1,8 @@
-## ace.R (2022-03-02)
+## ace.R (2024-01-28)
 
 ##   Ancestral Character Estimation
 
-## Copyright 2005-2022 Emmanuel Paradis and 2005 Ben Bolker
+## Copyright 2005-2024 Emmanuel Paradis and 2005 Ben Bolker
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -298,6 +298,12 @@ ace <-
             obj$lik.anc <- lik.anc
         }
     }
+    ## edited from Thomas G (PR #106):
+    if (!is.null(phy$node.label)) {
+        names(obj$ace) <- phy$node.label
+        if (!is.null(obj$CI95))
+            rownames(obj$CI95) <- phy$node.label
+    }
     obj$call <- match.call()
     class(obj) <- "ace"
     obj