From b98e40a0779a9f825551eef900731a6246232cd0 Mon Sep 17 00:00:00 2001
From: SMITH <1695515+ms609@users.noreply.github.com>
Date: Mon, 25 Sep 2023 14:33:43 +0100
Subject: [PATCH] Big*

---
 R/BigTreeDist-package.R    | 16 ++++++++--------
 R/median.R                 |  2 +-
 R/plot.R                   |  2 +-
 man/BigTreeDist-package.Rd | 16 ++++++++--------
 man/MSTSegments.Rd         |  2 +-
 man/median.multiPhylo.Rd   |  2 +-
 6 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/R/BigTreeDist-package.R b/R/BigTreeDist-package.R
index b1a1b4c7f..05f6cf306 100644
--- a/R/BigTreeDist-package.R
+++ b/R/BigTreeDist-package.R
@@ -112,21 +112,21 @@
 #' 
 #' @references
 #' 
-#' - \insertRef{Bocker2013}{TreeDist}
+#' - \insertRef{Bocker2013}{BigTreeDist}
 #' 
-#' - \insertRef{Bogdanowicz2012}{TreeDist}
+#' - \insertRef{Bogdanowicz2012}{BigTreeDist}
 #' 
-#' - \insertRef{Kendall2016}{TreeDist}
+#' - \insertRef{Kendall2016}{BigTreeDist}
 #' 
-#' - \insertRef{Li1996}{TreeDist}
+#' - \insertRef{Li1996}{BigTreeDist}
 #' 
-#' - \insertRef{Lin2012}{TreeDist}
+#' - \insertRef{Lin2012}{BigTreeDist}
 #' 
-#' - \insertRef{Nye2006}{TreeDist}
+#' - \insertRef{Nye2006}{BigTreeDist}
 #' 
-#' - \insertRef{SmithDist}{TreeDist}
+#' - \insertRef{SmithDist}{BigTreeDist}
 #' 
-#' - \insertRef{SmithSpace}{TreeDist}
+#' - \insertRef{SmithSpace}{BigTreeDist}
 #' 
 #' @encoding UTF-8
 #' @keywords internal
diff --git a/R/median.R b/R/median.R
index ae1574a23..a01f8a990 100644
--- a/R/median.R
+++ b/R/median.R
@@ -56,7 +56,7 @@
 #' 
 #' @seealso Consensus methods:
 #'   [`ape::consensus()`],
-#'   [`TreeTools::ConsensusWithout()`]
+#'   [`BigTreeTools::ConsensusWithout()`]
 #'   
 #' @importFrom stats median
 #' @family tree space functions
diff --git a/R/plot.R b/R/plot.R
index 20195328f..258781aa7 100644
--- a/R/plot.R
+++ b/R/plot.R
@@ -277,7 +277,7 @@ VisualizeMatching <- function(Func, tree1, tree2, setPar = TRUE,
 #' @param mapping Two-column matrix giving _x_ and _y_ coordinates of plotted
 #' points.
 #' @param mstEnds Two-column matrix identifying rows of `mapping` at end of
-#' each edge of the MST, as output by [`TreeTools::MSTEdges()`].
+#' each edge of the MST, as output by [`BigTreeTools::MSTEdges()`].
 #' @param distances Matrix or `dist` object giving original distances between
 #' each pair of points.
 #' @param palette Vector of colours with which to colour edges.
diff --git a/man/BigTreeDist-package.Rd b/man/BigTreeDist-package.Rd
index 23a2d906a..f12eb8e0a 100644
--- a/man/BigTreeDist-package.Rd
+++ b/man/BigTreeDist-package.Rd
@@ -97,14 +97,14 @@ for a command-line interface.
 
 \references{
 \itemize{
-\item \insertRef{Bocker2013}{TreeDist}
-\item \insertRef{Bogdanowicz2012}{TreeDist}
-\item \insertRef{Kendall2016}{TreeDist}
-\item \insertRef{Li1996}{TreeDist}
-\item \insertRef{Lin2012}{TreeDist}
-\item \insertRef{Nye2006}{TreeDist}
-\item \insertRef{SmithDist}{TreeDist}
-\item \insertRef{SmithSpace}{TreeDist}
+\item \insertRef{Bocker2013}{BigTreeDist}
+\item \insertRef{Bogdanowicz2012}{BigTreeDist}
+\item \insertRef{Kendall2016}{BigTreeDist}
+\item \insertRef{Li1996}{BigTreeDist}
+\item \insertRef{Lin2012}{BigTreeDist}
+\item \insertRef{Nye2006}{BigTreeDist}
+\item \insertRef{SmithDist}{BigTreeDist}
+\item \insertRef{SmithSpace}{BigTreeDist}
 }
 }
 \seealso{
diff --git a/man/MSTSegments.Rd b/man/MSTSegments.Rd
index 276421de8..c63682ba9 100644
--- a/man/MSTSegments.Rd
+++ b/man/MSTSegments.Rd
@@ -19,7 +19,7 @@ StrainCol(
 points.}
 
 \item{mstEnds}{Two-column matrix identifying rows of \code{mapping} at end of
-each edge of the MST, as output by \code{\link[TreeTools:MSTEdges]{TreeTools::MSTEdges()}}.}
+each edge of the MST, as output by \code{\link[BigTreeTools:MSTEdges]{BigTreeTools::MSTEdges()}}.}
 
 \item{\dots}{Additional arguments to \code{\link[=segments]{segments()}}.}
 
diff --git a/man/median.multiPhylo.Rd b/man/median.multiPhylo.Rd
index 1686df7a5..563b50551 100644
--- a/man/median.multiPhylo.Rd
+++ b/man/median.multiPhylo.Rd
@@ -77,7 +77,7 @@ median(structure(treeList, class = "multiPhylo"))
 \seealso{
 Consensus methods:
 \code{\link[ape:consensus]{ape::consensus()}},
-\code{\link[TreeTools:ConsensusWithout]{TreeTools::ConsensusWithout()}}
+\code{\link[BigTreeTools:ConsensusWithout]{BigTreeTools::ConsensusWithout()}}
 
 Other tree space functions: 
 \code{\link{MSTSegments}()},