[Vegan-commits] r1183 - pkg/vegan/man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sun May 2 08:01:40 CEST 2010


Author: jarioksa
Date: 2010-05-02 08:01:39 +0200 (Sun, 02 May 2010)
New Revision: 1183

Modified:
   pkg/vegan/man/mantel.correlog.Rd
Log:
revert to old mantel.correlog.Rd: new was too badly formatted

Modified: pkg/vegan/man/mantel.correlog.Rd
===================================================================
--- pkg/vegan/man/mantel.correlog.Rd	2010-05-02 05:55:12 UTC (rev 1182)
+++ pkg/vegan/man/mantel.correlog.Rd	2010-05-02 06:01:39 UTC (rev 1183)
@@ -4,89 +4,153 @@
 \alias{plot.mantel.correlog}
 \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).  }
+\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).
+}
 
 \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. Provide (n.class+1) breakpoints, that is, a list with a beginning and an ending point. 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.D <- 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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