cleaning of C files and update on simulation of OU process

[ape.git] / man / mantel.test.Rd

diff --git a/man/mantel.test.Rd b/man/mantel.test.Rd
index 5364952c46d25a213dfada17557f03203d6f3f98..babb82c194bf783a43de102aeeaedba42790e96c 100644 (file)
--- a/man/mantel.test.Rd
+++ b/man/mantel.test.Rd
@@ -2,7 +2,8 @@
 \alias{mantel.test}
 \title{Mantel Test for Similarity of Two Matrices}
 \usage{
-mantel.test(m1, m2, nperm = 1000, graph = FALSE, ...)
+mantel.test(m1, m2, nperm = 1000, graph = FALSE,
+            alternative = "two.sided",  ...)
 }
 \arguments{
   \item{m1}{a numeric matrix giving a measure of pairwise distances,
@@ -12,34 +13,38 @@ mantel.test(m1, m2, nperm = 1000, graph = FALSE, ...)
   \item{nperm}{the number of times to permute the data.}
   \item{graph}{a logical indicating whether to produce a summary graph
     (by default the graph is not plotted).}
+  \item{alternative}{a character string defining the alternative
+    hypothesis:  \code{"two.sided"} (default),  \code{"less"},
+    \code{"greater"}, or any unambiguous abbreviation of these.}
   \item{\dots}{further arguments to be passed to \code{plot()} (to add a
     title, change the axis labels, and so on).}
 }
 \description{
   This function computes Mantel's permutation test for similarity of two
   matrices. It permutes the rows and columns of the two matrices
-  randomly and calculates a Z-statistic.
+  randomly and calculates a \eqn{Z}-statistic.
 }
 \details{
-  The function calculates a Z-statistic for the Mantel test, equal to
+  The function calculates a \eqn{Z}-statistic for the Mantel test, equal to
   the sum of the  pairwise product of the lower triangles of the
   permuted matrices, for each permutation of rows and columns. It
-  compares the permuted distribution with the Z-statistic observed for
-  the actual data.
+  compares the permuted distribution with the \eqn{Z}-statistic observed
+  for the actual data.
 
   If \code{graph = TRUE}, the functions plots the density estimate of
-  the permutation distribution along with the observed Z-statistic as a
-  vertical line.
+  the permutation distribution along with the observed \eqn{Z}-statistic
+  as a vertical line.
 
-  The \code{...} argument allows the user to give further options to
+  The \code{\dots} argument allows the user to give further options to
   the \code{plot} function: the title main be changed with \code{main=},
   the axis labels with \code{xlab =}, and \code{ylab =}, and so on.
 }
 \value{
-  \item{z.stat}{the Z-statistic (sum of rows*columns of lower triangle)
-    of the data matrices.}
-  \item{p}{P-value (quantile of the observed Z-statistic in the
-    permutation distribution).}
+  \item{z.stat}{the \eqn{Z}-statistic (sum of rows*columns of lower
+    triangle) of the data matrices.}
+  \item{p}{\eqn{P}-value (quantile of the observed \eqn{Z}-statistic in
+    the permutation distribution).}
+  \item{alternative}{the alternative hypothesis.}
 }
 \references{
   Mantel, N. (1967) The detection of disease clustering and a
@@ -49,7 +54,8 @@ mantel.test(m1, m2, nperm = 1000, graph = FALSE, ...)
   Manly, B. F. J. (1986) \emph{Multivariate statistical methods: a primer.}
   London: Chapman & Hall.
 }
-\author{Original code in S by Ben Bolker \email{bolker@zoo.ufl.edu}, ported
+\author{
+  Original code in S by Ben Bolker \email{bolker@zoo.ufl.edu}, ported
   to \R by Julien Claude \email{claude@isem.univ-montp2.fr}
 }
 \examples{