final commit for ape 3.0-8

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

diff --git a/man/mantel.test.Rd b/man/mantel.test.Rd
index 72a6009070cc4c92582d925f4dcc468b3ee769ec..07dfc395858fc259d53c38910f5e04b421298d3d 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{
 \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 = 999, graph = FALSE,
+            alternative = "two.sided",  ...)

 }
 \arguments{
   \item{m1}{a numeric matrix giving a measure of pairwise distances,
 }
 \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{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
   \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{
 }
 \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
   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
 
   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{
   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
 }
 \references{
   Mantel, N. (1967) The detection of disease clustering and a


@@ -49,8 +54,8 @@ mantel.test(m1, m2, nperm = 1000, graph = FALSE, ...)
   Manly, B. F. J. (1986) \emph{Multivariate statistical methods: a primer.}
   London: Chapman & Hall.
 }
   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
-  to R by Julien Claude \email{claude@isem.univ-montp2.fr}
+\author{
+  Original code in S by Ben Bolker, ported to \R by Julien Claude

 }
 \examples{
 q1 <- matrix(runif(36), nrow = 6)
 }
 \examples{
 q1 <- matrix(runif(36), nrow = 6)