[Picante-commits] r96 - in branches/gsoc: R man

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

Author: mrhelmus
Date: 2008-06-11 05:57:39 +0200 (Wed, 11 Jun 2008)
New Revision: 96

Added:
   branches/gsoc/R/specaccum.PSR.R
   branches/gsoc/man/specaccum.PSR.Rd
Removed:
   branches/gsoc/R/specaccum.PSR.r
Log:
Documentation for specaccum.PSR

Added: branches/gsoc/R/specaccum.PSR.R
===================================================================
--- branches/gsoc/R/specaccum.PSR.R	                        (rev 0)
+++ branches/gsoc/R/specaccum.PSR.R	2008-06-11 03:57:39 UTC (rev 96)
@@ -0,0 +1,43 @@
+specaccum.PSR<-function (samp, tree, permutations = 100, method = "random", ...)
+{
+
+#function adapted from the vegan package specaccum
+
+  x <- as.matrix(samp)
+  n <- nrow(x)
+  p <- ncol(x)
+  if (p == 1)
+  {
+    x <- t(x)
+    n <- nrow(x)
+    p <- ncol(x)
+  }
+  accumulator <- function(x,ind,tree)
+  {
+    n <- nrow(x)
+    p <- ncol(x)
+    xx<-x
+    xx[1:n,1:p]<-0
+    xx[apply(x[ind, ], 2, cumsum)>0]<-1
+    PSV<-PSVcalc(xx,tree,compute.var=FALSE)
+    PSV[,1]*PSV[,2]
+  }
+  METHODS <- c("collector", "random", "exact", "rarefaction",
+        "coleman")
+    method <- match.arg(method, METHODS)
+
+  specaccum <- sdaccum <- sites <- perm <- NULL
+  perm <- array(dim = c(n, permutations))
+  for (i in 1:permutations)
+  {
+    r.x=0
+    while(length(r.x)<n){r.x <- accumulator(x, sample(n),tree)}
+    perm[, i]<-r.x
+  }
+  sites <- 1:n
+  specaccum <- apply(perm, 1, mean)
+  sdaccum <- apply(perm, 1, sd)
+  out <- list(call = match.call(), method = method, sites = sites, richness = specaccum, sd = sdaccum, perm = perm)
+  class(out) <- "specaccum"
+  out
+}
\ No newline at end of file

Deleted: branches/gsoc/R/specaccum.PSR.r
===================================================================
--- branches/gsoc/R/specaccum.PSR.r	2008-06-11 01:55:42 UTC (rev 95)
+++ branches/gsoc/R/specaccum.PSR.r	2008-06-11 03:57:39 UTC (rev 96)
@@ -1,43 +0,0 @@
-specaccum.PSR<-function (samp, Cmatrix, permutations = 100, method = "random", ...)
-{
-
-#function adapted from the vegan package specaccum
-
-  x <- as.matrix(samp)
-  n <- nrow(x)
-  p <- ncol(x)
-  if (p == 1)
-  {
-    x <- t(x)
-    n <- nrow(x)
-    p <- ncol(x)
-  }
-  accumulator <- function(x,ind,Cmatrix)
-  {
-    n <- nrow(x)
-    p <- ncol(x)
-    xx<-x
-    xx[1:n,1:p]<-0
-    xx[apply(x[ind, ], 2, cumsum)>0]<-1
-    PSV<-PSVcalc(xx,Cmatrix,compute.var=FALSE)
-    PSV[,1]*PSV[,2]
-  }
-  METHODS <- c("collector", "random", "exact", "rarefaction",
-        "coleman")
-    method <- match.arg(method, METHODS)
-
-  specaccum <- sdaccum <- sites <- perm <- NULL
-  perm <- array(dim = c(n, permutations))
-  for (i in 1:permutations)
-  {
-    r.x=0
-    while(length(r.x)<n){r.x <- accumulator(x, sample(n),Cmatrix)}
-    perm[, i]<-r.x
-  }
-  sites <- 1:n
-  specaccum <- apply(perm, 1, mean)
-  sdaccum <- apply(perm, 1, sd)
-  out <- list(call = match.call(), method = method, sites = sites, richness = specaccum, sd = sdaccum, perm = perm)
-  class(out) <- "specaccum"
-  out
-}
\ No newline at end of file

Added: branches/gsoc/man/specaccum.PSR.Rd
===================================================================
--- branches/gsoc/man/specaccum.PSR.Rd	                        (rev 0)
+++ branches/gsoc/man/specaccum.PSR.Rd	2008-06-11 03:57:39 UTC (rev 96)
@@ -0,0 +1,37 @@
+\name{specaccum.PSR}
+\alias{specaccum.PSR}
+
+\title{ Phylogenetic Species Richness Sample-Based Rarefaction Curve }
+\description{
+  Finds a sample-based rarefaction curve for phylogentic species richness for a set of samples.
+}
+\usage{
+specaccum.PSR(samp, tree, permutations = 100, method = "random", ...)
+}
+
+\arguments{
+  \item{samp}{ Community data matrix }
+  \item{tree}{ A phylo tree object or a phylogenetic covariance matrix}
+  \item{permutations}{ Number of permutations with method method= "random" }
+  \item{method} { Species accumulation method, currently only "random" is supported which add samples in random order. }
+  \item{...}{ Other parameters to functions }
+}
+
+\value{
+The function returns an object of class "specaccum" with items:
+
+\item{call}{ Function call. }
+\item{method}{ Accumulator method. }
+\item{sites}{ Number of sites/samples. For method = "rarefaction" this is the average number of sites corresponding to a certain number of individuals.}
+\item{richness}{ The phylogenetic species richness corresponding to number of sites/samples. With method = "collector" this is the observed phylogenetic species richness, for other methods the average or expected phylogenetic species richness. }
+\item{sd}{ The standard deviation of phylogenetic apecies accumulation curve (or its standard error). This is NULL in method = "collector", and it is estimated from permutations in method = "random", and from analytic equations in other methods. }
+\item{perm}{ Permutation results with method = "random" and NULL in other cases. Each column in perm holds one permutation. }
+}
+
+\references{ Gotelli N.J. & Colwell R.K. (2001) Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecology Letters, 4, 379-391\cr
+              Helmus M.R., Bland T.J., Williams C.K. & Ives A.R. (2007) Phylogenetic measures of biodiversity. American Naturalist, 169, E68-E83 }
+\author{ Matthew Helmus \email{mrhelmus at gmail.com}
+ }
+\seealso{ \code{\link{calcPSR}}, \code{\link{specaccum}}}
+
+\keyword{univar}