[Vegan-commits] r944 - pkg/vegan/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Aug 24 11:43:27 CEST 2009
Author: jarioksa
Date: 2009-08-24 11:43:23 +0200 (Mon, 24 Aug 2009)
New Revision: 944
Modified:
pkg/vegan/man/mantel.correlog.Rd
Log:
formatting (shorter lines)
Modified: pkg/vegan/man/mantel.correlog.Rd
===================================================================
--- pkg/vegan/man/mantel.correlog.Rd 2009-08-23 17:25:04 UTC (rev 943)
+++ pkg/vegan/man/mantel.correlog.Rd 2009-08-24 09:43:23 UTC (rev 944)
@@ -2,88 +2,155 @@
\alias{mantel.correlog}
\alias{print.mantel.correlog}
\alias{plot.mantel.correlog}
-\title{ Mantel correlogram }
+\title{ Mantel Correlogram }
+
\description{
-Function \code{mantel.correlog} computes a multivariate Mantel correlogram. Proposed by Sokal (1986) and Oden and Sokal (1986), the method is also described in Legendre and Legendre (1998, pp. 736-738).
+ Function \code{mantel.correlog} computes a multivariate
+ Mantel correlogram. Proposed by Sokal (1986) and Oden and Sokal
+ (1986), the method is also described in Legendre and Legendre (1998,
+ pp. 736-738).
}
+
\usage{
mantel.correlog(D.eco, D.geo=NULL, XY=NULL, n.class=0, break.pts=NULL,
cutoff=TRUE, r.type="pearson", nperm=999, mult="holm", progressive=TRUE)
-
\method{plot}{mantel.correlog}(x, alpha=0.05, ...)
}
\arguments{
- \item{D.eco}{ An ecological distance matrix, with class either \code{dist} or \code{matrix}. }
- \item{D.geo}{ A geographic distance matrix, with class either \code{dist} or \code{matrix}. Provide either \code{D.geo} or \code{XY}. Default: \code{D.geo=NULL}. }
- \item{XY}{ A file of Cartesian geographic coordinates of the points. Default: \code{XY=NULL}. }
- \item{n.class}{ Number of classes. If \code{n.class=0}, the Sturge equation will be used unless break points are provided. }
- \item{break.pts}{ Vector containing the break points of the distance distribution. Default: \code{break.pts=NULL}. }
- \item{cutoff}{ For the second half of the distance classes, \code{cutoff = TRUE} limits the correlogram to the distance classes that include all points. If \code{cutoff = FALSE}, the correlogram includes all distance classes. }
- \item{r.type}{ Type of correlation in calculation of the Mantel statistic. Default: \code{r.type="pearson"}. Other choices are \code{r.type="spearman"} and \code{r.type="kendall"}, as in functions \code{\link{cor}} and \code{\link{mantel}}. }
- \item{nperm}{ Number of permutations for the tests of significance. Default: \code{nperm=999}. For large data files, permutation tests are rather slow. }
- \item{mult}{ Correct P-values for multiple testing. The correction methods are \code{"holm"} (default), \code{"hochberg"}, \code{"sidak"}, and other methods available in the \code{\link{p.adjust}} function: \code{"bonferroni"} (best known, but not recommended because it is overly conservative), \code{"hommel"}, \code{"BH"}, \code{"BY"}, \code{"fdr"}, and \code{"none"}. }
- \item{progressive}{ Default: \code{progressive=TRUE} for progressive correction of multiple-testing, as described in Legendre and Legendre (1998, p. 721). Test of the first distance class: no correction; second distance class: correct for 2 simultaneous tests; distance class k: correct for k simultaneous tests. \code{progressive=FALSE}: correct all tests for \code{n.class} simultaneous tests. }
+ \item{D.eco}{ An ecological distance matrix, with class
+ either \code{dist} or \code{matrix}. }
+
+ \item{D.geo}{ A geographic distance matrix, with class either
+ \code{dist} or \code{matrix}. Provide either \code{D.geo} or
+ \code{XY}. Default: \code{D.geo=NULL}. }
+
+ \item{XY}{ A file of Cartesian geographic coordinates of the
+ points. Default: \code{XY=NULL}. }
+
+ \item{n.class}{ Number of classes. If \code{n.class=0}, the Sturge
+ equation will be used unless break points are provided. }
+
+ \item{break.pts}{ Vector containing the break points of the distance
+ distribution. Default: \code{break.pts=NULL}. }
+
+ \item{cutoff}{ For the second half of the distance classes,
+ \code{cutoff = TRUE} limits the correlogram to the distance classes
+ that include all points. If \code{cutoff = FALSE}, the correlogram
+ includes all distance classes. }
+
+ \item{r.type}{ Type of correlation in calculation of the Mantel
+ statistic. Default: \code{r.type="pearson"}. Other choices are
+ \code{r.type="spearman"} and \code{r.type="kendall"}, as in functions
+ \code{\link{cor}} and \code{\link{mantel}}. }
+
+ \item{nperm}{ Number of permutations for the tests of
+ significance. Default: \code{nperm=999}. For large data files,
+ permutation tests are rather slow. }
+
+ \item{mult}{ Correct P-values for multiple testing. The correction
+ methods are \code{"holm"} (default), \code{"hochberg"},
+ \code{"sidak"}, and other methods available in the
+ \code{\link{p.adjust}} function: \code{"bonferroni"} (best known, but
+ not recommended because it is overly conservative), \code{"hommel"},
+ \code{"BH"}, \code{"BY"}, \code{"fdr"}, and \code{"none"}. }
+
+ \item{progressive}{ Default: \code{progressive=TRUE} for progressive
+ correction of multiple-testing, as described in Legendre and Legendre
+ (1998, p. 721). Test of the first distance class: no correction;
+ second distance class: correct for 2 simultaneous tests; distance
+ class k: correct for k simultaneous tests. \code{progressive=FALSE}:
+ correct all tests for \code{n.class} simultaneous tests. }
+
\item{x}{ Output of \code{mantel.correlog}. }
- \item{alpha}{ Significance level for the points drawn with black symbols in the correlogram. Default: \code{alpha=0.05}. }
+
+ \item{alpha}{ Significance level for the points drawn with black
+ symbols in the correlogram. Default: \code{alpha=0.05}. }
+
\item{...}{ Other parameters passed from other functions. }
}
-\details{
-A correlogram is a graph in which spatial correlation values are plotted, on the
-ordinate, as a function of the geographic distance classes among the study sites along the abscissa. In a Mantel correlogram, a Mantel correlation (Mantel 1967) is computed between a multivariate (e.g. multi-species) distance matrix of the user's choice and a design matrix representing each of the geographic distance classes in turn. The Mantel statistic is tested through a permutational Mantel test performed by \code{vegan}'s \code{\link{mantel}} function.
+\details{ A correlogram is a graph in which spatial correlation values
+ are plotted, on the ordinate, as a function of the geographic distance
+ classes among the study sites along the abscissa. In a Mantel
+ correlogram, a Mantel correlation (Mantel 1967) is computed between a
+ multivariate (e.g. multi-species) distance matrix of the user's choice
+ and a design matrix representing each of the geographic distance
+ classes in turn. The Mantel statistic is tested through a
+ permutational Mantel test performed by \code{vegan}'s
+ \code{\link{mantel}} function.
-When a correction for multiple testing is applied, more permutations are necessary than in the no-correction case, to obtain significant p-values in the higher correlogram classes.
+ When a correction for multiple testing is applied, more permutations
+ are necessary than in the no-correction case, to obtain significant
+ p-values in the higher correlogram classes.
-The \code{print.mantel.correlog} function prints out the correlogram. See examples.
-}
+ The \code{print.mantel.correlog} function prints out the
+ correlogram. See examples. }
\value{
- \item{mantel.res }{A table with the distance classes as rows and the class indices, number of distances per class, Mantel statistics (computed using Pearson's r, Spearman's r, or Kendall's tau), and p-values as columns. A positive Mantel statistic indicates positive spatial correlation. An additional column with p-values corrected for multiple testing is added unless \code{mult="none"}. }
- \item{n.class }{The number of distance classes. }
- \item{break.pts }{The break points provided by the user or computed by the program. }
- \item{mult }{The name of the correction for multiple testing. No correction: \code{mult="none"}. }
-# \item{progressive }{A logical (\code{TRUE}, \code{FALSE}) value indicating whether or not a progressive correction for multiple testing was requested. }
- \item{n.tests }{The number of distance classes for which Mantel tests have been computed and tested for significance. }
- \item{call }{The function call. }
-}
+ \item{mantel.res }{A table with the distance classes as rows and the
+ class indices, number of distances per class, Mantel statistics
+ (computed using Pearson's r, Spearman's r, or Kendall's tau), and
+ p-values as columns. A positive Mantel statistic indicates positive
+ spatial correlation. An additional column with p-values corrected for
+ multiple testing is added unless \code{mult="none"}. }
+ \item{n.class }{The n umber of distance classes. }
+
+ \item{break.pts }{The break points provided by the user or computed by
+ the program. }
+
+ \item{mult }{The name of the correction for multiple testing. No
+ correction: \code{mult="none"}. } #
+
+ \item{progressive }{A logical (\code{TRUE}, \code{FALSE}) value
+ indicating whether or not a progressive correction for multiple
+ testing was requested. } \item{n.tests }{The number of distance
+ classes for which Mantel tests have been computed and tested for
+ significance. }
+
+\item{call }{The function call. } }
+
\author{ Pierre Legendre, Universite de Montreal }
-\references{
-Legendre, P. and L. Legendre. 1998. Numerical ecology, 2nd English edition. Elsevier Science BV, Amsterdam.
+\references{
-Mantel, N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Res. 27: 209-220.
+ Legendre, P. and L. Legendre. 1998. Numerical ecology, 2nd English
+ edition. Elsevier Science BV, Amsterdam.
-Oden, N. L. and R. R. Sokal. 1986. Directional autocorrelation: an extension of spatial correlograms to two dimensions. Syst. Zool. 35: 608-617.
+ Mantel, N. 1967. The detection of disease clustering and a generalized
+ regression approach. Cancer Res. 27: 209-220.
-Sokal, R. R. 1986. Spatial data analysis and historical processes. 29-43 in: E. Diday et al. [eds.] Data analysis and informatics, IV. North-Holland, Amsterdam.
-}
+ Oden, N. L. and R. R. Sokal. 1986. Directional autocorrelation: an
+ extension of spatial correlograms to two dimensions. Syst. Zool. 35:
+ 608-617.
+ Sokal, R. R. 1986. Spatial data analysis and historical
+ processes. 29-43 in: E. Diday et al. [eds.] Data analysis and
+ informatics, IV. North-Holland, Amsterdam. }
+
\examples{
# Mite data from "vegan"
data(mite)
data(mite.xy)
-mite.hel = decostand(mite, "hellinger")
-mite.hel.D = dist(mite.hel)
+mite.hel <- decostand(mite, "hellinger")
+mite.hel. <- dist(mite.hel)
-mite.correlog = mantel.correlog(mite.hel.D, XY=mite.xy, nperm=99)
+mite.correlog <- mantel.correlog(mite.hel.D, XY=mite.xy, nperm=99)
summary(mite.correlog)
mite.correlog
-# or: print(mite.correlog)
-# or: print.mantel.correlog(mite.correlog)
plot(mite.correlog)
-mite.correlog2 = mantel.correlog(mite.hel.D, XY=mite.xy, cutoff=FALSE,
+mite.correlog2 <- mantel.correlog(mite.hel.D, XY=mite.xy, cutoff=FALSE,
r.type="spearman", nperm=99)
summary(mite.correlog2)
mite.correlog2
plot(mite.correlog2)
-# Mite correlogram after spatially detrending the mite data
+## Mite correlogram after spatially detrending the mite data
mite.h.det <- resid(lm(as.matrix(mite.hel.D) ~ ., data=mite.xy))
-mite.correlog3 = mantel.correlog(mite.h.det, XY=mite.xy, nperm=99)
+mite.correlog3 <- mantel.correlog(mite.h.det, XY=mite.xy, nperm=99)
mite.correlog3
plot(mite.correlog3)
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