From d7da7afedcc19259cf32a728c387ea0761091dd9 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Fri, 14 Feb 2025 09:42:07 +0000
Subject: [PATCH 1/6] Update SiteConcordance.Rd

---
 man/SiteConcordance.Rd | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/man/SiteConcordance.Rd b/man/SiteConcordance.Rd
index 85e38d090..fc78c6792 100644
--- a/man/SiteConcordance.Rd
+++ b/man/SiteConcordance.Rd
@@ -23,7 +23,8 @@ SharedPhylogeneticConcordance(tree, dataset)
 \item{tree}{A tree of class \code{\link{phylo}}.}
 
 \item{dataset}{A phylogenetic data matrix of \pkg{phangorn} class
-\code{phyDat}, whose names correspond to the labels of any accompanying tree.}
+\code{phyDat}, whose names correspond to the labels of any accompanying tree.
+Perhaps load into R using \code{\link[TreeTools]{ReadCharacters}}.}
 
 \item{weight}{Logical specifying whether to weight sites according to the
 number of quartets they are decisive for.}

From 329b0dd564ddbceca0dbe43480eb4c49e66f2a41 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Fri, 14 Feb 2025 11:16:27 +0000
Subject: [PATCH 2/6] Explicit ape link

---
 man-roxygen/treeParam.r         | 2 +-
 man/CharacterLength.Rd          | 2 +-
 man/ConcordantInformation.Rd    | 2 +-
 man/Consistency.Rd              | 2 +-
 man/JackLabels.Rd               | 2 +-
 man/Jackknife.Rd                | 2 +-
 man/NNI.Rd                      | 2 +-
 man/Ratchet.Rd                  | 2 +-
 man/SPR.Rd                      | 2 +-
 man/SiteConcordance.Rd          | 2 +-
 man/SuccessiveApproximations.Rd | 2 +-
 man/cSPR.Rd                     | 2 +-
 12 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/man-roxygen/treeParam.r b/man-roxygen/treeParam.r
index e4b0c68b4..7b04ba8a5 100644
--- a/man-roxygen/treeParam.r
+++ b/man-roxygen/treeParam.r
@@ -1,2 +1,2 @@
-#' @param tree A tree of class \code{\link{phylo}}.
+#' @param tree A tree of class \code{\link[ape]{phylo}}.
 # Defined in TreeTools.  Please propagate any changes there.
diff --git a/man/CharacterLength.Rd b/man/CharacterLength.Rd
index 5f217f6c5..5d60f8ecf 100644
--- a/man/CharacterLength.Rd
+++ b/man/CharacterLength.Rd
@@ -13,7 +13,7 @@ FitchSteps(tree, dataset)
 FastCharacterLength(tree, dataset)
 }
 \arguments{
-\item{tree}{A tree of class \code{\link{phylo}}.}
+\item{tree}{A tree of class \code{\link[ape]{phylo}}.}
 
 \item{dataset}{A phylogenetic data matrix of \pkg{phangorn} class
 \code{phyDat}, whose names correspond to the labels of any accompanying tree.
diff --git a/man/ConcordantInformation.Rd b/man/ConcordantInformation.Rd
index b1d10935d..2dd4cafc5 100644
--- a/man/ConcordantInformation.Rd
+++ b/man/ConcordantInformation.Rd
@@ -13,7 +13,7 @@ Evaluate(tree, dataset)
 ConcordantInfo(tree, dataset)
 }
 \arguments{
-\item{tree}{A tree of class \code{\link{phylo}}.}
+\item{tree}{A tree of class \code{\link[ape]{phylo}}.}
 
 \item{dataset}{A phylogenetic data matrix of \pkg{phangorn} class
 \code{phyDat}, whose names correspond to the labels of any accompanying tree.
diff --git a/man/Consistency.Rd b/man/Consistency.Rd
index 2af757710..1266c8b24 100644
--- a/man/Consistency.Rd
+++ b/man/Consistency.Rd
@@ -11,7 +11,7 @@ Consistency(dataset, tree, compress = FALSE)
 \code{phyDat}, whose names correspond to the labels of any accompanying tree.
 Perhaps load into R using \code{\link[TreeTools]{ReadCharacters}}.}
 
-\item{tree}{A tree of class \code{\link{phylo}}.}
+\item{tree}{A tree of class \code{\link[ape]{phylo}}.}
 
 \item{compress}{Logical specifying whether to retain the compression of a
 \code{phyDat} object or to return a vector specifying to each individual
diff --git a/man/JackLabels.Rd b/man/JackLabels.Rd
index f71912677..731c39b36 100644
--- a/man/JackLabels.Rd
+++ b/man/JackLabels.Rd
@@ -17,7 +17,7 @@ JackLabels(
 )
 }
 \arguments{
-\item{tree}{A tree of class \code{\link{phylo}}.}
+\item{tree}{A tree of class \code{\link[ape]{phylo}}.}
 
 \item{jackTrees}{A list or \code{multiPhylo} object containing trees generated
 by \code{\link[=Jackknife]{Jackknife()}}.}
diff --git a/man/Jackknife.Rd b/man/Jackknife.Rd
index 562ec3caf..49f7f2fcd 100644
--- a/man/Jackknife.Rd
+++ b/man/Jackknife.Rd
@@ -20,7 +20,7 @@ Jackknife(
 )
 }
 \arguments{
-\item{tree}{A tree of class \code{\link{phylo}}.}
+\item{tree}{A tree of class \code{\link[ape]{phylo}}.}
 
 \item{dataset}{a dataset in the format required by \code{TreeScorer()}.}
 
diff --git a/man/NNI.Rd b/man/NNI.Rd
index 732fe13d4..d1e904e7c 100644
--- a/man/NNI.Rd
+++ b/man/NNI.Rd
@@ -24,7 +24,7 @@ RootedNNISwap(
 )
 }
 \arguments{
-\item{tree}{A tree of class \code{\link{phylo}}.}
+\item{tree}{A tree of class \code{\link[ape]{phylo}}.}
 
 \item{edgeToBreak}{In (\code{Rooted})\code{NNI()}, an optional integer specifying the
 index of an edge to bisect/prune, generated randomly if not specified.
diff --git a/man/Ratchet.Rd b/man/Ratchet.Rd
index 3f68fd0e9..d1d92a7d0 100644
--- a/man/Ratchet.Rd
+++ b/man/Ratchet.Rd
@@ -105,7 +105,7 @@ by \code{attr(FunctionName, "stopAtPlateau") <- TRUE}.}
 
 \item{\dots}{further arguments to pass to \code{TreeScorer()}, e.g. \verb{dataset = }.}
 
-\item{tree}{A tree of class \code{\link{phylo}}.}
+\item{tree}{A tree of class \code{\link[ape]{phylo}}.}
 
 \item{dataset}{a dataset in the format required by \code{TreeScorer()}.}
 
diff --git a/man/SPR.Rd b/man/SPR.Rd
index 85261937c..1e892560b 100644
--- a/man/SPR.Rd
+++ b/man/SPR.Rd
@@ -39,7 +39,7 @@ RootedSPRSwap(
 )
 }
 \arguments{
-\item{tree}{A tree of class \code{\link{phylo}}.}
+\item{tree}{A tree of class \code{\link[ape]{phylo}}.}
 
 \item{edgeToBreak}{the index of an edge to bisect, generated randomly if not specified.}
 
diff --git a/man/SiteConcordance.Rd b/man/SiteConcordance.Rd
index fc78c6792..422dec8fe 100644
--- a/man/SiteConcordance.Rd
+++ b/man/SiteConcordance.Rd
@@ -20,7 +20,7 @@ MutualClusteringConcordance(tree, dataset)
 SharedPhylogeneticConcordance(tree, dataset)
 }
 \arguments{
-\item{tree}{A tree of class \code{\link{phylo}}.}
+\item{tree}{A tree of class \code{\link[ape]{phylo}}.}
 
 \item{dataset}{A phylogenetic data matrix of \pkg{phangorn} class
 \code{phyDat}, whose names correspond to the labels of any accompanying tree.
diff --git a/man/SuccessiveApproximations.Rd b/man/SuccessiveApproximations.Rd
index 774dc45b7..275ec3061 100644
--- a/man/SuccessiveApproximations.Rd
+++ b/man/SuccessiveApproximations.Rd
@@ -22,7 +22,7 @@ SuccessiveApproximations(
 SuccessiveWeights(tree, dataset)
 }
 \arguments{
-\item{tree}{A tree of class \code{\link{phylo}}.}
+\item{tree}{A tree of class \code{\link[ape]{phylo}}.}
 
 \item{dataset}{A phylogenetic data matrix of \pkg{phangorn} class
 \code{phyDat}, whose names correspond to the labels of any accompanying tree.
diff --git a/man/cSPR.Rd b/man/cSPR.Rd
index b0467e389..496fb5947 100644
--- a/man/cSPR.Rd
+++ b/man/cSPR.Rd
@@ -7,7 +7,7 @@
 cSPR(tree, whichMove = NULL)
 }
 \arguments{
-\item{tree}{A tree of class \code{\link{phylo}}.}
+\item{tree}{A tree of class \code{\link[ape]{phylo}}.}
 
 \item{whichMove}{Integer specifying which SPR move index to perform.}
 }

From 6c1edcca2b96fbd5116b1b099cfe14aa34af3935 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Fri, 14 Feb 2025 11:19:49 +0000
Subject: [PATCH 3/6] Link [ape]

---
 R/CustomSearch.R                | 2 +-
 R/MaximizeParsimony.R           | 2 +-
 R/TBR.R                         | 2 +-
 R/mpl_visualise.R               | 2 +-
 man-roxygen/treeChild.R         | 2 +-
 man-roxygen/treeNEdge.R         | 2 +-
 man-roxygen/treeNEdgeOptional.R | 2 +-
 man-roxygen/treeParent.r        | 2 +-
 man/AllSPR.Rd                   | 6 +++---
 man/DoubleNNI.Rd                | 4 ++--
 man/MaximizeParsimony.Rd        | 2 +-
 man/MorphyTreeLength.Rd         | 4 ++--
 man/NNI.Rd                      | 4 ++--
 man/RearrangeEdges.Rd           | 4 ++--
 man/SPR.Rd                      | 6 +++---
 man/StopUnlessBifurcating.Rd    | 2 +-
 man/TBR.Rd                      | 6 +++---
 man/TBRWarning.Rd               | 4 ++--
 man/TreeSearch.Rd               | 2 +-
 man/dot-NonDuplicateRoot.Rd     | 6 +++---
 20 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/R/CustomSearch.R b/R/CustomSearch.R
index c680d3dba..272776403 100644
--- a/R/CustomSearch.R
+++ b/R/CustomSearch.R
@@ -99,7 +99,7 @@ EdgeListSearch <- function (edgeList, dataset,
 #' configuring tree search, see the
 #' [package documentation](https://ms609.github.io/TreeSearch/).
 #'  
-#' @param tree A fully-resolved starting tree in \code{\link{phylo}} format, 
+#' @param tree A fully-resolved starting tree in \code{\link[ape]{phylo}} format, 
 #' with the desired outgroup.
 #' Edge lengths are not supported and will be removed.
 #' @template datasetParam
diff --git a/R/MaximizeParsimony.R b/R/MaximizeParsimony.R
index c1c0f4fd0..bad5cefb4 100644
--- a/R/MaximizeParsimony.R
+++ b/R/MaximizeParsimony.R
@@ -30,7 +30,7 @@
 #' 
 #' 
 #' @template datasetParam
-#' @param tree (optional) A bifurcating tree of class \code{\link{phylo}},
+#' @param tree (optional) A bifurcating tree of class \code{\link[ape]{phylo}},
 #' containing only the tips listed in `dataset`, from which the search
 #' should begin.
 #' If unspecified, an [addition tree][AdditionTree()] will be generated from
diff --git a/R/TBR.R b/R/TBR.R
index d4374be58..206f0894f 100644
--- a/R/TBR.R
+++ b/R/TBR.R
@@ -27,7 +27,7 @@ TBRWarning <- function (parent, child, error) {
 #' All nodes in a tree must be bifurcating; [ape::collapse.singles] and
 #' [ape::multi2di] may help.
 #' 
-#' @param tree A bifurcating tree of class \code{\link{phylo}}, with all nodes resolved;
+#' @param tree A bifurcating tree of class \code{\link[ape]{phylo}}, with all nodes resolved;
 #' @template edgeToBreakParam
 #' @template mergeEdgesParam
 #' 
diff --git a/R/mpl_visualise.R b/R/mpl_visualise.R
index e9caafb0b..3ab490068 100644
--- a/R/mpl_visualise.R
+++ b/R/mpl_visualise.R
@@ -24,7 +24,7 @@
 ### #' @description Determine and depict the possible states for a character on a tree under the most parsimonious conditions
 ### #' @usage VisualiseCharacter(tree, dataset, char.no, plot.fun = plot)
 ### #' 
-### #' @param tree a fully-resolved tree in \code{\link{phylo}} format, with the desired outgroup; edge lengths are not supported and will be deleted;
+### #' @param tree a fully-resolved tree in \code{\link[ape]{phylo}} format, with the desired outgroup; edge lengths are not supported and will be deleted;
 ### #' @template datasetParam
 ### #' @param char.no number of the character to be displayed;
 ### #' @param plot.fun a function that plots a tree, \code{\link{plot}} by default.
diff --git a/man-roxygen/treeChild.R b/man-roxygen/treeChild.R
index 043545d9d..9a950b8ce 100644
--- a/man-roxygen/treeChild.R
+++ b/man-roxygen/treeChild.R
@@ -1,3 +1,3 @@
 #' @param child Integer vector corresponding to the second column of the edge
-#' matrix of a tree of class \code{\link{phylo}}, i.e. `tree$edge[, 2]`.
+#' matrix of a tree of class \code{\link[ape]{phylo}}, i.e. `tree$edge[, 2]`.
 # Defined in TreeTools.  Please propagate any changes there.
diff --git a/man-roxygen/treeNEdge.R b/man-roxygen/treeNEdge.R
index 624d39af2..1170799e0 100644
--- a/man-roxygen/treeNEdge.R
+++ b/man-roxygen/treeNEdge.R
@@ -1 +1 @@
-#' @param nEdge integer specifying the number of edges of a tree of class \code{\link{phylo}}, i.e. \code{dim(tree$edge)[1]}
+#' @param nEdge integer specifying the number of edges of a tree of class \code{\link[ape]{phylo}}, i.e. \code{dim(tree$edge)[1]}
diff --git a/man-roxygen/treeNEdgeOptional.R b/man-roxygen/treeNEdgeOptional.R
index f5951842b..f64c9fdec 100644
--- a/man-roxygen/treeNEdgeOptional.R
+++ b/man-roxygen/treeNEdgeOptional.R
@@ -1,3 +1,3 @@
 #' @param nEdge (optional) integer specifying the number of edges of a tree of
-#' class \code{\link{phylo}}, i.e. \code{dim(tree$edge)[1]}
+#' class \code{\link[ape]{phylo}}, i.e. \code{dim(tree$edge)[1]}
 # Defined in TreeTools.  Please propagate any changes there.
diff --git a/man-roxygen/treeParent.r b/man-roxygen/treeParent.r
index 7dc054508..77609f2ea 100644
--- a/man-roxygen/treeParent.r
+++ b/man-roxygen/treeParent.r
@@ -1,3 +1,3 @@
 #' @param parent Integer vector corresponding to the first column of the edge
-#' matrix of a tree of class \code{\link{phylo}}, i.e. `tree$edge[, 1]`.
+#' matrix of a tree of class \code{\link[ape]{phylo}}, i.e. `tree$edge[, 1]`.
 # Defined in TreeTools.  Please propagate any changes there.
diff --git a/man/AllSPR.Rd b/man/AllSPR.Rd
index cbc891ca1..ac718a30f 100644
--- a/man/AllSPR.Rd
+++ b/man/AllSPR.Rd
@@ -8,12 +8,12 @@ AllSPR(parent, child, nEdge, notDuplicateRoot, edgeToBreak)
 }
 \arguments{
 \item{parent}{Integer vector corresponding to the first column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 1]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 1]}.}
 
 \item{child}{Integer vector corresponding to the second column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 2]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 2]}.}
 
-\item{nEdge}{integer specifying the number of edges of a tree of class \code{\link{phylo}}, i.e. \code{dim(tree$edge)[1]}}
+\item{nEdge}{integer specifying the number of edges of a tree of class \code{\link[ape]{phylo}}, i.e. \code{dim(tree$edge)[1]}}
 
 \item{notDuplicateRoot}{logical vector of length \code{nEdge}, specifying for each
 edge whether it is the second edge leading to the root (in which case
diff --git a/man/DoubleNNI.Rd b/man/DoubleNNI.Rd
index 0a286a3aa..22ba4bcfe 100644
--- a/man/DoubleNNI.Rd
+++ b/man/DoubleNNI.Rd
@@ -8,10 +8,10 @@ DoubleNNI(parent, child, edgeToBreak)
 }
 \arguments{
 \item{parent}{Integer vector corresponding to the first column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 1]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 1]}.}
 
 \item{child}{Integer vector corresponding to the second column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 2]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 2]}.}
 
 \item{edgeToBreak}{(optional) integer specifying the index of an edge to bisect/prune,
 generated randomly if not specified.
diff --git a/man/MaximizeParsimony.Rd b/man/MaximizeParsimony.Rd
index 8de3f5d24..e4c65f8c6 100644
--- a/man/MaximizeParsimony.Rd
+++ b/man/MaximizeParsimony.Rd
@@ -50,7 +50,7 @@ EasyTreesy()
 \code{phyDat}, whose names correspond to the labels of any accompanying tree.
 Perhaps load into R using \code{\link[TreeTools]{ReadCharacters}}.}
 
-\item{tree}{(optional) A bifurcating tree of class \code{\link{phylo}},
+\item{tree}{(optional) A bifurcating tree of class \code{\link[ape]{phylo}},
 containing only the tips listed in \code{dataset}, from which the search
 should begin.
 If unspecified, an \link[=AdditionTree]{addition tree} will be generated from
diff --git a/man/MorphyTreeLength.Rd b/man/MorphyTreeLength.Rd
index e23f42be8..c57e29ac3 100644
--- a/man/MorphyTreeLength.Rd
+++ b/man/MorphyTreeLength.Rd
@@ -30,10 +30,10 @@ in the corresponding Morphy object.}
 \code{\link[=PhyDat2Morphy]{PhyDat2Morphy()}}.}
 
 \item{parent}{Integer vector corresponding to the first column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 1]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 1]}.}
 
 \item{child}{Integer vector corresponding to the second column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 2]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 2]}.}
 
 \item{parentOf}{For each node, numbered in postorder, the number of its parent node.}
 
diff --git a/man/NNI.Rd b/man/NNI.Rd
index d1e904e7c..3ba669d06 100644
--- a/man/NNI.Rd
+++ b/man/NNI.Rd
@@ -37,10 +37,10 @@ specifying which internal edge to break.}
 the broken internal edge.}
 
 \item{parent}{Integer vector corresponding to the first column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 1]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 1]}.}
 
 \item{child}{Integer vector corresponding to the second column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 2]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 2]}.}
 
 \item{nTips}{(optional) Number of tips.}
 }
diff --git a/man/RearrangeEdges.Rd b/man/RearrangeEdges.Rd
index ea22701ba..550b82328 100644
--- a/man/RearrangeEdges.Rd
+++ b/man/RearrangeEdges.Rd
@@ -19,10 +19,10 @@ RearrangeEdges(
 }
 \arguments{
 \item{parent}{Integer vector corresponding to the first column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 1]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 1]}.}
 
 \item{child}{Integer vector corresponding to the second column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 2]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 2]}.}
 
 \item{dataset}{Third argument to pass to \code{TreeScorer}.}
 
diff --git a/man/SPR.Rd b/man/SPR.Rd
index 1e892560b..cddf63a4a 100644
--- a/man/SPR.Rd
+++ b/man/SPR.Rd
@@ -46,13 +46,13 @@ RootedSPRSwap(
 \item{mergeEdge}{the index of an edge on which to merge the broken edge.}
 
 \item{parent}{Integer vector corresponding to the first column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 1]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 1]}.}
 
 \item{child}{Integer vector corresponding to the second column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 2]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 2]}.}
 
 \item{nEdge}{(optional) integer specifying the number of edges of a tree of
-class \code{\link{phylo}}, i.e. \code{dim(tree$edge)[1]}}
+class \code{\link[ape]{phylo}}, i.e. \code{dim(tree$edge)[1]}}
 
 \item{nNode}{(optional) Number of nodes.}
 }
diff --git a/man/StopUnlessBifurcating.Rd b/man/StopUnlessBifurcating.Rd
index 5130c7627..73f8e6ec4 100644
--- a/man/StopUnlessBifurcating.Rd
+++ b/man/StopUnlessBifurcating.Rd
@@ -8,7 +8,7 @@ StopUnlessBifurcating(parent)
 }
 \arguments{
 \item{parent}{Integer vector corresponding to the first column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 1]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 1]}.}
 }
 \value{
 Returns \code{NULL}, but will \code{stop} with an error message if a tree
diff --git a/man/TBR.Rd b/man/TBR.Rd
index 7daa03992..8843e8754 100644
--- a/man/TBR.Rd
+++ b/man/TBR.Rd
@@ -37,7 +37,7 @@ RootedTBRSwap(
 )
 }
 \arguments{
-\item{tree}{A bifurcating tree of class \code{\link{phylo}}, with all nodes resolved;}
+\item{tree}{A bifurcating tree of class \code{\link[ape]{phylo}}, with all nodes resolved;}
 
 \item{edgeToBreak}{(optional) integer specifying the index of an edge to bisect/prune,
 generated randomly if not specified.
@@ -51,10 +51,10 @@ sides of \code{edgeToBreak}); if only a single edge is specified,
 the second will be chosen at random}
 
 \item{parent}{Integer vector corresponding to the first column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 1]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 1]}.}
 
 \item{child}{Integer vector corresponding to the second column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 2]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 2]}.}
 
 \item{nEdge}{(optional) Number of edges.}
 }
diff --git a/man/TBRWarning.Rd b/man/TBRWarning.Rd
index a6d271822..44532e4fc 100644
--- a/man/TBRWarning.Rd
+++ b/man/TBRWarning.Rd
@@ -12,10 +12,10 @@ TBRWarning(parent, child, error)
 }
 \arguments{
 \item{parent}{Integer vector corresponding to the first column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 1]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 1]}.}
 
 \item{child}{Integer vector corresponding to the second column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 2]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 2]}.}
 
 \item{error}{error message to report}
 }
diff --git a/man/TreeSearch.Rd b/man/TreeSearch.Rd
index 33b0658ff..31a148938 100644
--- a/man/TreeSearch.Rd
+++ b/man/TreeSearch.Rd
@@ -86,7 +86,7 @@ larger numbers provide more verbose feedback to the user.}
 
 \item{\dots}{further arguments to pass to \code{TreeScorer()}, e.g. \verb{dataset = }.}
 
-\item{tree}{A fully-resolved starting tree in \code{\link{phylo}} format,
+\item{tree}{A fully-resolved starting tree in \code{\link[ape]{phylo}} format,
 with the desired outgroup.
 Edge lengths are not supported and will be removed.}
 
diff --git a/man/dot-NonDuplicateRoot.Rd b/man/dot-NonDuplicateRoot.Rd
index 198eefeb1..1f7d7e089 100644
--- a/man/dot-NonDuplicateRoot.Rd
+++ b/man/dot-NonDuplicateRoot.Rd
@@ -8,13 +8,13 @@
 }
 \arguments{
 \item{parent}{Integer vector corresponding to the first column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 1]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 1]}.}
 
 \item{child}{Integer vector corresponding to the second column of the edge
-matrix of a tree of class \code{\link{phylo}}, i.e. \code{tree$edge[, 2]}.}
+matrix of a tree of class \code{\link[ape]{phylo}}, i.e. \code{tree$edge[, 2]}.}
 
 \item{nEdge}{(optional) integer specifying the number of edges of a tree of
-class \code{\link{phylo}}, i.e. \code{dim(tree$edge)[1]}}
+class \code{\link[ape]{phylo}}, i.e. \code{dim(tree$edge)[1]}}
 }
 \value{
 \code{.NonDuplicateRoot()} returns a logical vector of length \code{nEdge},

From d00c0030234e221f0e0f41903080ad485c5de996 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Fri, 14 Feb 2025 11:29:32 +0000
Subject: [PATCH 4/6] Link package functions

---
 R/MaximizeParsimony.R           | 2 +-
 R/TaxonInfluence.R              | 2 +-
 man-roxygen/labelledTreeParam.R | 6 +++---
 man/AdditionTree.Rd             | 2 +-
 man/MaximizeParsimony.Rd        | 2 +-
 man/MorphyTreeLength.Rd         | 6 +++---
 man/TaxonInfluence.Rd           | 2 +-
 7 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/R/MaximizeParsimony.R b/R/MaximizeParsimony.R
index bad5cefb4..9f8178ee6 100644
--- a/R/MaximizeParsimony.R
+++ b/R/MaximizeParsimony.R
@@ -79,7 +79,7 @@
 #' returned trees will be perfectly compatible with each character in
 #' `constraint`; or a tree of class `phylo`, all of whose nodes will occur
 #' in any output tree.
-#' See [`ImposeConstraint()`] and 
+#' See \link[TreeTools:ImposeConstraint]{`ImposeConstraint()`} and 
 #' [vignette](https://ms609.github.io/TreeSearch/articles/tree-search.html)
 #' for further examples.
 #' @param verbosity Integer specifying level of messaging; higher values give
diff --git a/R/TaxonInfluence.R b/R/TaxonInfluence.R
index 8e601f317..6451ac4fc 100644
--- a/R/TaxonInfluence.R
+++ b/R/TaxonInfluence.R
@@ -52,7 +52,7 @@
 #' `paste0(savePath, droppedTaxonName, ".nex")`; `savePath` should thus contain
 #' a trailing `/` if writing to a directory, which will be created if it does
 #' not exist.  Special characters will be removed from leaf labels when
-#' creating the file path (using [`path_sanitize()`]).
+#' creating the file path (using \link[fs:path_sanitize]{`path_sanitize()`}).
 #' If `NULL`, computed trees will not be saved.
 #' @param useCache Logical vector; if `TRUE`, previous tree search results will
 #' be loaded from the location given by `savePath`, instead of running a fresh
diff --git a/man-roxygen/labelledTreeParam.R b/man-roxygen/labelledTreeParam.R
index ceb56a9c9..b8dbf91a1 100644
--- a/man-roxygen/labelledTreeParam.R
+++ b/man-roxygen/labelledTreeParam.R
@@ -1,3 +1,3 @@
-#' @param tree A tree of class \code{\link[ape:read.tree]{phylo}}, with tip labels in the order generated by 
-#'             \code{\link{RenumberTips}}, i.e. corresponding to the sequence of taxa 
-#'             in the corresponding Morphy object. 
+#' @param tree A tree of class \code{\link[ape:read.tree]{phylo}}, with tip 
+#' labels in the order generated by \code{\link[TreeTools]{RenumberTips}},
+#' i.e. corresponding to the sequence of taxa in the corresponding Morphy object. 
diff --git a/man/AdditionTree.Rd b/man/AdditionTree.Rd
index 88fe9b76c..837d76fe7 100644
--- a/man/AdditionTree.Rd
+++ b/man/AdditionTree.Rd
@@ -25,7 +25,7 @@ approaches
 returned trees will be perfectly compatible with each character in
 \code{constraint}; or a tree of class \code{phylo}, all of whose nodes will occur
 in any output tree.
-See \code{\link[=ImposeConstraint]{ImposeConstraint()}} and
+See \link[TreeTools:ImposeConstraint]{\code{ImposeConstraint()}} and
 \href{https://ms609.github.io/TreeSearch/articles/tree-search.html}{vignette}
 for further examples.}
 
diff --git a/man/MaximizeParsimony.Rd b/man/MaximizeParsimony.Rd
index e4c65f8c6..5c476c19d 100644
--- a/man/MaximizeParsimony.Rd
+++ b/man/MaximizeParsimony.Rd
@@ -110,7 +110,7 @@ in search results, which may improve the accuracy of the consensus tree
 returned trees will be perfectly compatible with each character in
 \code{constraint}; or a tree of class \code{phylo}, all of whose nodes will occur
 in any output tree.
-See \code{\link[=ImposeConstraint]{ImposeConstraint()}} and
+See \link[TreeTools:ImposeConstraint]{\code{ImposeConstraint()}} and
 \href{https://ms609.github.io/TreeSearch/articles/tree-search.html}{vignette}
 for further examples.}
 
diff --git a/man/MorphyTreeLength.Rd b/man/MorphyTreeLength.Rd
index c57e29ac3..1e1816bc0 100644
--- a/man/MorphyTreeLength.Rd
+++ b/man/MorphyTreeLength.Rd
@@ -22,9 +22,9 @@ GetMorphyLength(parentOf, leftChild, rightChild, morphyObj)
 C_MorphyLength(parentOf, leftChild, rightChild, morphyObj)
 }
 \arguments{
-\item{tree}{A tree of class \code{\link[ape:read.tree]{phylo}}, with tip labels in the order generated by
-\code{\link{RenumberTips}}, i.e. corresponding to the sequence of taxa
-in the corresponding Morphy object.}
+\item{tree}{A tree of class \code{\link[ape:read.tree]{phylo}}, with tip
+labels in the order generated by \code{\link[TreeTools]{RenumberTips}},
+i.e. corresponding to the sequence of taxa in the corresponding Morphy object.}
 
 \item{morphyObj}{Object of class \code{morphy}, perhaps created with
 \code{\link[=PhyDat2Morphy]{PhyDat2Morphy()}}.}
diff --git a/man/TaxonInfluence.Rd b/man/TaxonInfluence.Rd
index fdfe41d85..a06bfba9f 100644
--- a/man/TaxonInfluence.Rd
+++ b/man/TaxonInfluence.Rd
@@ -37,7 +37,7 @@ saved (with \code{\link[=write.nexus]{write.nexus()}}). File names will follow t
 \code{paste0(savePath, droppedTaxonName, ".nex")}; \code{savePath} should thus contain
 a trailing \code{/} if writing to a directory, which will be created if it does
 not exist.  Special characters will be removed from leaf labels when
-creating the file path (using \code{\link[=path_sanitize]{path_sanitize()}}).
+creating the file path (using \link[fs:path_sanitize]{\code{path_sanitize()}}).
 If \code{NULL}, computed trees will not be saved.}
 
 \item{useCache}{Logical vector; if \code{TRUE}, previous tree search results will

From d658f15bd07027c90f13fc87eef718ef74321d45 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Fri, 14 Feb 2025 11:36:51 +0000
Subject: [PATCH 5/6] Oustanding package links

---
 R/TaxonInfluence.R           | 7 ++++---
 R/data.R                     | 3 ++-
 man/TaxonInfluence.Rd        | 7 ++++---
 man/inapplicable.datasets.Rd | 3 ++-
 4 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/R/TaxonInfluence.R b/R/TaxonInfluence.R
index 6451ac4fc..1c7bd43a9 100644
--- a/R/TaxonInfluence.R
+++ b/R/TaxonInfluence.R
@@ -44,11 +44,12 @@
 #' If `NULL`, an optimal tree will be sought using parsimony search with 
 #' the parameters provided in \code{\dots}.
 #' @param Distance Function to calculate tree distance; default:
-#' [`ClusteringInfoDistance()`].
+#' \link[TreeDist::ClusteringInfoDistance]{`ClusteringInfoDistance()`}.
 #' @param calcWeighted Logical specifying whether to compute the
 #' distance-weighted mean value.
-#' @param savePath Character giving prefix of path to which reduced trees will be
-#' saved (with [`write.nexus()`]). File names will follow the pattern
+#' @param savePath Character giving prefix of path to which reduced trees will
+#' be saved (with \link[ape:write.nexus]{`write.nexus()`}).
+#' File names will follow the pattern
 #' `paste0(savePath, droppedTaxonName, ".nex")`; `savePath` should thus contain
 #' a trailing `/` if writing to a directory, which will be created if it does
 #' not exist.  Special characters will be removed from leaf labels when
diff --git a/R/data.R b/R/data.R
index fe251ab6c..9057d60ea 100644
--- a/R/data.R
+++ b/R/data.R
@@ -6,7 +6,8 @@
 #' Datasets are sorted into two subsets, each sorted alphabetically;
 #' the first subset comprise simpler datasets with faster processing times.
 #' `inapplicable.datasets` provide the data in the matrix format generated by
-#' [`read.nexus.data()`]; `inapplicable.phyData` are in \code{phyDat} format.
+#' \link[ape:read.nexus.data]{`read.nexus.data()`};
+#' `inapplicable.phyData` are in \code{phyDat} format.
 #' `inapplicable.trees` lists for each dataset a sample of up to 50 trees
 #' obtained by tree search under each inapplicable treatment, named accordingly.
 #' `inapplicable.citations` is a named character vector specifying the source of
diff --git a/man/TaxonInfluence.Rd b/man/TaxonInfluence.Rd
index a06bfba9f..5f8d81a0f 100644
--- a/man/TaxonInfluence.Rd
+++ b/man/TaxonInfluence.Rd
@@ -27,13 +27,14 @@ If \code{NULL}, an optimal tree will be sought using parsimony search with
 the parameters provided in \code{\dots}.}
 
 \item{Distance}{Function to calculate tree distance; default:
-\code{\link[=ClusteringInfoDistance]{ClusteringInfoDistance()}}.}
+\link[TreeDist::ClusteringInfoDistance]{\code{ClusteringInfoDistance()}}.}
 
 \item{calcWeighted}{Logical specifying whether to compute the
 distance-weighted mean value.}
 
-\item{savePath}{Character giving prefix of path to which reduced trees will be
-saved (with \code{\link[=write.nexus]{write.nexus()}}). File names will follow the pattern
+\item{savePath}{Character giving prefix of path to which reduced trees will
+be saved (with \link[ape:write.nexus]{\code{write.nexus()}}).
+File names will follow the pattern
 \code{paste0(savePath, droppedTaxonName, ".nex")}; \code{savePath} should thus contain
 a trailing \code{/} if writing to a directory, which will be created if it does
 not exist.  Special characters will be removed from leaf labels when
diff --git a/man/inapplicable.datasets.Rd b/man/inapplicable.datasets.Rd
index 949a97731..b8383f699 100644
--- a/man/inapplicable.datasets.Rd
+++ b/man/inapplicable.datasets.Rd
@@ -146,7 +146,8 @@ The name of each item corresponds to the datasets listed below.
 Datasets are sorted into two subsets, each sorted alphabetically;
 the first subset comprise simpler datasets with faster processing times.
 \code{inapplicable.datasets} provide the data in the matrix format generated by
-\code{\link[=read.nexus.data]{read.nexus.data()}}; \code{inapplicable.phyData} are in \code{phyDat} format.
+\link[ape:read.nexus.data]{\code{read.nexus.data()}};
+\code{inapplicable.phyData} are in \code{phyDat} format.
 \code{inapplicable.trees} lists for each dataset a sample of up to 50 trees
 obtained by tree search under each inapplicable treatment, named accordingly.
 \code{inapplicable.citations} is a named character vector specifying the source of

From 218fd75560d0603cc4eed7d245ff2d53e3f8cc54 Mon Sep 17 00:00:00 2001
From: RevBayes analysis <1695515+ms609@users.noreply.github.com>
Date: Fri, 14 Feb 2025 13:46:35 +0000
Subject: [PATCH 6/6] =?UTF-8?q?::=E2=86=92:?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 R/TaxonInfluence.R    | 2 +-
 man/TaxonInfluence.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/TaxonInfluence.R b/R/TaxonInfluence.R
index 1c7bd43a9..d7be0e3e3 100644
--- a/R/TaxonInfluence.R
+++ b/R/TaxonInfluence.R
@@ -44,7 +44,7 @@
 #' If `NULL`, an optimal tree will be sought using parsimony search with 
 #' the parameters provided in \code{\dots}.
 #' @param Distance Function to calculate tree distance; default:
-#' \link[TreeDist::ClusteringInfoDistance]{`ClusteringInfoDistance()`}.
+#' \link[TreeDist:ClusteringInfoDistance]{`ClusteringInfoDistance()`}.
 #' @param calcWeighted Logical specifying whether to compute the
 #' distance-weighted mean value.
 #' @param savePath Character giving prefix of path to which reduced trees will
diff --git a/man/TaxonInfluence.Rd b/man/TaxonInfluence.Rd
index 5f8d81a0f..96e708314 100644
--- a/man/TaxonInfluence.Rd
+++ b/man/TaxonInfluence.Rd
@@ -27,7 +27,7 @@ If \code{NULL}, an optimal tree will be sought using parsimony search with
 the parameters provided in \code{\dots}.}
 
 \item{Distance}{Function to calculate tree distance; default:
-\link[TreeDist::ClusteringInfoDistance]{\code{ClusteringInfoDistance()}}.}
+\link[TreeDist:ClusteringInfoDistance]{\code{ClusteringInfoDistance()}}.}
 
 \item{calcWeighted}{Logical specifying whether to compute the
 distance-weighted mean value.}