From a7971d9b403938c2033f2e50735610b889d00239 Mon Sep 17 00:00:00 2001
From: Klaus Schliep <klaus.schliep@gmail.com>
Date: Tue, 27 Aug 2024 11:56:59 +0200
Subject: [PATCH] bug fixes

---
 NEWS                   | 13 ++++++-------
 R/draw_CI.R            |  2 +-
 R/gap_as_state.R       |  5 +++--
 man/add_edge_length.Rd |  2 +-
 man/gap_as_state.Rd    |  5 +++--
 5 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/NEWS b/NEWS
index 9416a4ee..d555445b 100644
--- a/NEWS
+++ b/NEWS
@@ -1,4 +1,4 @@
-    CHANGES in PHANGORN VERSION 3.0.0
+    CHANGES in PHANGORN VERSION 2.12.0
 
 NEW FEATURES
 
@@ -18,15 +18,15 @@ NEW FEATURES
 
       character vector for the node argument and not only integers.
 
-    o Ancestral state reconstructionwas in parts rewritten. Output is now an
+    o Ancestral state reconstruction was rewritten. Output is now an object of
 
-      object of class ancestral. E.g. ancestral states of constant sites are now
+      class ancestral. E.g. ancestral states of constant sites are now always
 
-      always this state.
+      this state.
 
     o Improvements to several plot functions to get nicer plots out of the box.
 
-    o Nicer defaults for plot.pml, mainly for rooted trees.
+      Nicer defaults for plot.pml, mainly for rooted trees.
 
     o plotAnc got an argument scheme allowing to use different color schemes,
 
@@ -38,8 +38,7 @@ NEW FEATURES
 
     o new function composition_test comparing indicating possible problems
 
-      with base / state composition.
-
+      with base / state composition as in iqtree.
 
 OTHER CHANGES
 
diff --git a/R/draw_CI.R b/R/draw_CI.R
index 3d6d34ce..b33f9437 100644
--- a/R/draw_CI.R
+++ b/R/draw_CI.R
@@ -58,7 +58,7 @@ edge_length_matrix <- function(tree, trees, rooted=TRUE){
 ##'               add_edge_length(bs)
 ##' plot(tree_compat)
 ##' add_boxplot(tree_compat, bs, boxwex=.7)
-##' @seealso \code{\link[ape::node.depth]{node.depth.edgelength}},
+##' @seealso \code{\link[ape]{node.depth}},
 ##' \code{\link[ape]{consensus}}, \code{\link{maxCladeCred}},
 ##' \code{\link{add_boxplot}}
 ##' @keywords aplot
diff --git a/R/gap_as_state.R b/R/gap_as_state.R
index 5d0897f1..b7d1555e 100644
--- a/R/gap_as_state.R
+++ b/R/gap_as_state.R
@@ -10,8 +10,9 @@
 #' @param ambiguous a character which codes for the ambiguous state
 #' @return The functions return an object of class \code{phyDat}.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
-#' @seealso \code{\link{phyDat}}, \code{\link[ape]{ltg2amb}}, \code{\link{latag2n}},
-#' \code{\link{ancestral.pml}}, \code{\link{gap_as_state}}
+#' @seealso \code{\link{phyDat}}, \code{\link{ltg2amb}},
+#' \code{\link[ape]{latag2n}}, \code{\link{ancestral.pml}},
+#' \code{\link{gap_as_state}}
 #' @keywords cluster
 #' @examples
 #' data(Laurasiatherian)
diff --git a/man/add_edge_length.Rd b/man/add_edge_length.Rd
index 4b25d978..cfc75e67 100644
--- a/man/add_edge_length.Rd
+++ b/man/add_edge_length.Rd
@@ -38,7 +38,7 @@ plot(tree_compat)
 add_boxplot(tree_compat, bs, boxwex=.7)
 }
 \seealso{
-\code{\link[ape::node.depth]{node.depth.edgelength}},
+\code{\link[ape]{node.depth}},
 \code{\link[ape]{consensus}}, \code{\link{maxCladeCred}},
 \code{\link{add_boxplot}}
 }
diff --git a/man/gap_as_state.Rd b/man/gap_as_state.Rd
index 6f0fc687..76148104 100644
--- a/man/gap_as_state.Rd
+++ b/man/gap_as_state.Rd
@@ -36,8 +36,9 @@ rownames(contr) <- attr(tmp, "allLevels")
 contr
 }
 \seealso{
-\code{\link{phyDat}}, \code{\link[ape]{ltg2amb}}, \code{\link{latag2n}},
-\code{\link{ancestral.pml}}, \code{\link{gap_as_state}}
+\code{\link{phyDat}}, \code{\link{ltg2amb}},
+\code{\link[ape]{latag2n}}, \code{\link{ancestral.pml}},
+\code{\link{gap_as_state}}
 }
 \author{
 Klaus Schliep \email{klaus.schliep@gmail.com}