[Picante-commits] r74 - branches/gsoc/R

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

Author: mrhelmus
Date: 2008-05-28 22:57:35 +0200 (Wed, 28 May 2008)
New Revision: 74

Added:
   branches/gsoc/R/specaccum.PSR.r
Log:
Working code to calculate sample-based rarefaction for PSR. Calls function PSVcalc, and for plotting functions requires library vegan.

Added: branches/gsoc/R/specaccum.PSR.r
===================================================================
--- branches/gsoc/R/specaccum.PSR.r	                        (rev 0)
+++ branches/gsoc/R/specaccum.PSR.r	2008-05-28 20:57:35 UTC (rev 74)
@@ -0,0 +1,41 @@
+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)
+  {
+    perm[, i] <- accumulator(x, sample(n),Cmatrix)
+  }
+  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
+}
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