[Vegan-commits] r917 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2009-08-12 18:00:20 +0200 (Wed, 12 Aug 2009)
New Revision: 917

Added:
   pkg/vegan/R/plot.poolaccum.R
Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/specpool.Rd
Log:
poolaccum: plot methods and more docuentation

Added: pkg/vegan/R/plot.poolaccum.R
===================================================================
--- pkg/vegan/R/plot.poolaccum.R	                        (rev 0)
+++ pkg/vegan/R/plot.poolaccum.R	2009-08-12 16:00:20 UTC (rev 917)
@@ -0,0 +1,14 @@
+`plot.poolaccum` <-
+    function(x, alpha = 0.05, type = c("l","g"), ...)
+{
+    require(lattice) || stop("Needs package 'lattice'")
+    m <- summary(x, alpha = alpha, ...)
+    n <- nrow(m[[1]])
+    Size <- as.vector(sapply(m, function(x) c(x[,1], x[,1], rev(x[,1]))))
+    Richness <- as.vector(sapply(m, function(x) c(x[,2], x[,3], rev(x[,4]))) )
+    indnames <- as.character(sapply(m, function(x) colnames(x[,2, drop=FALSE])))
+    Index <- factor(rep(indnames, each = 3 * n), levels = indnames)
+    lintype <- rep(c(rep("aver", n), rep("envel", 2*n)), length=length(Size))
+    xyplot(Richness ~  Size | Index, as.table = TRUE, groups = lintype,
+           type = type, ...)
+}

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-08-12 09:10:52 UTC (rev 916)
+++ pkg/vegan/inst/ChangeLog	2009-08-12 16:00:20 UTC (rev 917)
@@ -5,7 +5,9 @@
 Version 1.16-23 (opened August 11, 2009)
 
 	* poolaccum: new function to find the extrapolated richness
-	values (or specpool() estimates) for random accumulation of sites.
+	values (or specpool() estimates) for random accumulation of
+	sites (with summary and plot methods). Arguments (indices) still
+	need consistent naming.
 	
 Version 1.16-22 (closed August 11, 2009)
 

Modified: pkg/vegan/man/specpool.Rd
===================================================================
--- pkg/vegan/man/specpool.Rd	2009-08-12 09:10:52 UTC (rev 916)
+++ pkg/vegan/man/specpool.Rd	2009-08-12 16:00:20 UTC (rev 917)
@@ -4,6 +4,7 @@
 \alias{poolaccum}
 \alias{print.poolaccum}
 \alias{summary.poolaccum}
+\alias{plot.poolaccum}
 \alias{estimateR}
 \alias{estimateR.default}
 \alias{estimateR.matrix}
@@ -18,19 +19,26 @@
 }
 \usage{
 specpool(x, pool)
+estimateR(x, ...)
 specpool2vect(X, index = c("Jack.1","Jack.2", "Chao", "Boot","Species"))
 poolaccum(x, permutations = 100, minsize = 3)
-estimateR(x, ...)
+\method{summary}{poolaccum}(object, display, alpha = 0.05, ...)
+\method{plot}{poolaccum}(x, alpha = 0.05, type = c("l","g"), ...)
 }
 
 \arguments{
-  \item{x}{Data frame or matrix with species data.}
+  \item{x}{Data frame or matrix with species data or the analysis result 
+    for \code{plot} function.}
   \item{pool}{A vector giving a classification for pooling the sites in
     the species data. If missing, all sites are pooled together.}
-  \item{X}{A \code{specpool} result object.}
+  \item{X, object}{A \code{specpool} result object.}
   \item{index}{The selected index of extrapolated richness.}
   \item{permutations}{Number of permutations of sampling order of sites.}
   \item{minsize}{Smallest number of sampling units reported.}
+  \item{display}{Indices to be displayed.}
+  \item{alpha}{Level of quantiles shown. This proportion will be left outside
+    symmetric limits.}
+  \item{type}{Type of graph produced in \code{\link[lattice]{xyplot}}.}
   \item{...}{Other parameters (not used).}
 }
 \details{
@@ -67,6 +75,13 @@
   Function \code{poolaccum} is similar to \code{\link{specaccum}}, but
   it estimates all extrapolated richness values of \code{specpool} in
   addition to number of species for random ordering of sampling units.
+  The function has \code{summary} and \code{plot} methods. The
+  \code{summary} returns quantile envilopes of permutations
+  corresponding the given level of \code{alpha} and standard deviation
+  of permutations for each sample size. The \code{plot} function shows
+  the mean and envelope of permutations with given \code{alpha} for
+  models. The selection of models can be restricted and order changes
+  using the \code{display} argument in \code{summary} or \code{plot}.
 
     The abundance-based estimates in \code{estimateR} use counts (frequencies) of
     species in a single site. If called for a matrix or data frame, the
@@ -166,6 +181,11 @@
  border="cyan3", notch=TRUE)
 par(op)
 data(BCI)
+## Accumulation model
+pool <- poolaccum(BCI)
+summary(pool, display = "chao")
+plot(pool)
+## Quantitative model
 estimateR(BCI[1:5,])
 }
 \keyword{ univar }