[Vegan-commits] r731 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2009-03-08 16:54:41 +0100 (Sun, 08 Mar 2009)
New Revision: 731

Added:
   pkg/vegan/R/as.mcmc.oecosimu.R
Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/oecosimu.Rd
Log:
as.mcmc.oecosimu: translates sequential oecosimu results to mcmc object of the coda package for further analysis of the sequences

Added: pkg/vegan/R/as.mcmc.oecosimu.R
===================================================================
--- pkg/vegan/R/as.mcmc.oecosimu.R	                        (rev 0)
+++ pkg/vegan/R/as.mcmc.oecosimu.R	2009-03-08 15:54:41 UTC (rev 731)
@@ -0,0 +1,10 @@
+`as.mcmc.oecosimu` <-
+    function(x) 
+{
+    x <- as.ts(out)
+    mcpar <- attr(x, "tsp")
+    mcpar[3] <- round(1/mcpar[3])
+    attr(x, "mcpar") <- mcpar
+    class(x) <- "mcmc"
+    x
+}

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-03-08 07:21:28 UTC (rev 730)
+++ pkg/vegan/inst/ChangeLog	2009-03-08 15:54:41 UTC (rev 731)
@@ -4,6 +4,12 @@
 
 Version 1.16-14 (opened Feb 24, 2009)
 
+	* as.mcmc.oecosimu: a new function to translate sequential null
+	models to "mcmc" object of the coda package. The coda package
+	provides a wealthy source of the analysis of things like
+	stationarity, adequate sample size, autocorrelation, length of
+	needed burnin-in etc.
+
 	* density and densityplot: new methods for "oecosimu" objects.
 
 	* as.ts.oecosimu: new function for applying time series methods

Modified: pkg/vegan/man/oecosimu.Rd
===================================================================
--- pkg/vegan/man/oecosimu.Rd	2009-03-08 07:21:28 UTC (rev 730)
+++ pkg/vegan/man/oecosimu.Rd	2009-03-08 15:54:41 UTC (rev 731)
@@ -4,6 +4,7 @@
 \alias{commsimulator}
 \alias{print.oecosimu}
 \alias{as.ts.oecosimu}
+\alias{as.mcmc.oecosimu}
 \alias{density.oecosimu}
 \alias{densityplot.oecosimu}
 
@@ -22,6 +23,7 @@
    statistic = "statistic", control, ...)
 commsimulator(x, method, thin=1)
 \method{as.ts}{oecosimu}(x, ...)
+\method{as.mcmc}{oecosimu}(x)
 \method{density}{oecosimu}(x, ...)
 \method{densityplot}{oecosimu}(x, data, xlab = "Simulated", ...)
 }
@@ -29,7 +31,8 @@
 \arguments{
   \item{comm}{Community data.}
   \item{x}{Community data for \code{commsimulator}, or an \code{oecosimu}
-    result object for \code{as.ts}, \code{density} and \code{densityplot}.}
+    result object for \code{as.ts}, \code{as.mcmc}, \code{density} and 
+    \code{densityplot}.}
   \item{nestfun}{Function to analyse nestedness. Some functions are
   provided in \pkg{vegan}, but any function can be used if it accepts the
   community as the first argument, and returns either a plain number or
@@ -139,7 +142,14 @@
   Function \code{as.ts} transforms the simulated results of sequential
   methods into a time series or a \code{\link{ts}} object. This allows
   using analytic tools for time series in studying the sequences (see
-  examples). Function \code{density} provides an interface to the
+  examples). Function \code{as.mcmc} transformts teh simulated results
+  of sequential mehots into an \code{\link[coda]{mcmc}} object of the
+  \pkg{coda} package. The \pkg{coda} package provides functions for
+  the analysis of stationarity, adequacy of sample size,
+  autocorrelation, need of burn-in and much more for sequential
+  methods. Please consult the documentation of \pkg{coda} package.
+
+  Function \code{density} provides an interface to the
   standard \code{\link{density}} function for the simulated
   values. Function \code{\link{densityplot}} is an interface the
   \code{\link[lattice]{densityplot}} function of the \pkg{lattice}