update to cophylo & minRotate documentation

man/cophylo.Rd

@@ -12,7 +12,7 @@ cophylo(tr1, tr2, assoc=NULL, rotate=TRUE, ...)
 	\item{assoc}{matrix containing the tip labels in \code{tr1} to match to the tip labels in \code{tr2}. Note that not all labels in either tree need to be included; and, furthermore, one label in \code{tr1} can be matched with more than one label in \code{tr2}, or vice versa.}
 	\item{rotate}{logical argument indicating whether nodes on both trees should be rotated to attempt to match in vertical position.}
 	\item{x}{in the case of \code{plot.cophylo}, an object of class \code{"cophylo"} to be plotted.}
-	\item{...}{optional arguments to be passed to \code{\link{tipRotate}}, or, in the case of \code{plot.cophylo}, to the internally used tree plotting function, \code{phylogram}. \code{phylogram} takes similar arguments to \code{\link{plotSimmap}}, such as \code{fsize}, \code{ftype}, \code{lwd}, and \code{pts}, though not all options from \code{plotSimmap} and \code{plotTree} are available. If \code{fsize} is supplied as a vector, different size fonts for the left & right facing trees may be used. In addition, the optional argument \code{scale.bar}, which should be a vector containing the lengths of the scale bars desired for the right & left trees, will add scale bars to the plot when supplied to \code{plot.cophylo}.}
+	\item{...}{optional arguments to be passed to \code{\link{tipRotate}}, or, in the case of \code{plot.cophylo}, to the internally used tree plotting function, \code{phylogram}. \code{phylogram} takes similar arguments to \code{\link{plotSimmap}}, such as \code{fsize}, \code{ftype}, \code{lwd}, and \code{pts}, though not all options from \code{plotSimmap} and \code{plotTree} are available. If \code{fsize} is supplied as a vector, different size fonts for the left & right facing trees may be used. In addition, the optional argument \code{scale.bar}, which should be a vector containing the lengths of the scale bars desired for the right & left trees, will add scale bars to the plot when supplied to \code{plot.cophylo}. If either tree contains polytomies, the \code{cophylo} argument \code{rotate.multi} should be set to \code{TRUE}. If curved linking lines are desired, the \code{plot.cophylo} argument \code{link.type} should be set to \code{"curved"}.}
 }
 \description{
 	This function creates an object of class \code{"cophylo"} or, in the case of \code{plot.cophylo}, plots that object. The function can (optionally) first attempt to rotate the nodes of both trees to optimize vertical matching of tips.

man/minRotate.Rd

@@ -9,7 +9,7 @@ tipRotate(tree, x, ...)
 \arguments{
 	\item{tree}{tree.}
 	\item{x}{numeric vector.}
-	\item{...}{optional arguments to be used by \code{tipRotate}. Presently optional arguments can be \code{fn}, function to be used to compute the distance between the order of the tip labels in \code{tree} and the numeric vector \code{x} (presently \code{fn=function(x) x^2} by default); \code{methods}, the methods of tree traversal (can be \code{"pre"}, \code{"post"}, or \code{c("pre","post")}, for pre-, post-, or both pre- and post-order tree traversal); and \code{print}, a logical argument specifying whether to print the search progress or to behave quietly. Only the option \code{print} is available for \code{minRotate}.}
+	\item{...}{optional arguments to be used by \code{tipRotate}. Presently optional arguments can be \code{fn}, function to be used to compute the distance between the order of the tip labels in \code{tree} and the numeric vector \code{x} (presently \code{fn=function(x) x^2} by default); \code{methods}, the methods of tree traversal (can be \code{"pre"}, \code{"post"}, or \code{c("pre","post")}, for pre-, post-, or both pre- and post-order tree traversal); \code{rotate.multi}, whether to rotate multifurcations in all possible ways using \code{rotate.multi} (defaults to \code{FALSE}); and \code{print}, a logical argument specifying whether to print the search progress or to behave quietly. Only the option \code{print} is available for \code{minRotate}.}
 }
 \description{
 	This function rotates all the nodes of the tree to try and minimize the different between the order of the tips and the rank-order of a numeric vector \code{x} or (in the case of \code{tipRotate} the actual integer vector, \code{x}.