[Vegan-commits] r745 - in pkg/vegan: R inst man

[noreply at r-forge.r-project.org]

Author: psolymos
Date: 2009-03-15 17:32:18 +0100 (Sun, 15 Mar 2009)
New Revision: 745

Added:
   pkg/vegan/R/as.mcmc.permat.R
Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/plot.permat.Rd
Log:
new method for permat objects


Added: pkg/vegan/R/as.mcmc.permat.R
===================================================================
--- pkg/vegan/R/as.mcmc.permat.R	                        (rev 0)
+++ pkg/vegan/R/as.mcmc.permat.R	2009-03-15 16:32:18 UTC (rev 745)
@@ -0,0 +1 @@
+`as.mcmc.permat` <- as.mcmc.oecosimu

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-03-15 14:51:51 UTC (rev 744)
+++ pkg/vegan/inst/ChangeLog	2009-03-15 16:32:18 UTC (rev 745)
@@ -4,6 +4,14 @@
 
 Version 1.16-15 (opened Mar 10, 2009)
 
+    * as.mcmc.permat: provides same same functionality for permat
+    objects as as.mcmc.oecosimu for oecosimu objects.
+
+    * burnin and thin in permatswap: same default values (0 and 1,
+    respectively) are set for permatswap and oecosimu functions.
+    Previous defaults for permatswap were in conflict with oecosimu
+    when called by permat.control.
+
     * hiersimu: new function to evaluate a statistic value at different
     levels of a nested hierarchical sampling design. Based on oecosimu
     and null model testing, but with evaluation process similar to adipart.

Modified: pkg/vegan/man/plot.permat.Rd
===================================================================
--- pkg/vegan/man/plot.permat.Rd	2009-03-15 14:51:51 UTC (rev 744)
+++ pkg/vegan/man/plot.permat.Rd	2009-03-15 16:32:18 UTC (rev 745)
@@ -3,6 +3,7 @@
 \alias{plot.permat}
 \alias{lines.permat}
 \alias{as.ts.permat}
+\alias{as.mcmc.permat}
 
 \title{Plotting Methods for Matrix Permutation Algorithms}
 
@@ -13,6 +14,7 @@
     lowess = TRUE, plot = TRUE, text = TRUE, ...)
 \method{lines}{permat}(x, type = "bray", ...)
 \method{as.ts}{permat}(x, type = "bray", ...)
+\method{as.mcmc}{permat}(x)
 }
 \arguments{
   \item{x}{Object of class \code{"permat"} created by the functions \code{\link{permatfull}} and \code{\link{permatswap}}.}
@@ -27,7 +29,7 @@
 The \code{plot} method is useful for graphically testing for trend and independence of permuted matrices. This is especially important when using sequential algorithms (\code{"swap", "tswap", "abuswap"}).
 
 
-The \code{as.ts} method can be used to extract Bray-Curtis dissimilarities or Chi-squared values as time series. This can further used in testing independence (see Examples).
+The \code{as.ts} method can be used to extract Bray-Curtis dissimilarities or Chi-squared values as time series. This can further used in testing independence (see Examples). The method \code{as.mcmc} is useful for accessing diagnostic tool available in the 'code' package.
 }
 
 \value{