[Vegan-commits] r1522 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2011-03-06 10:03:07 +0100 (Sun, 06 Mar 2011)
New Revision: 1522

Modified:
   pkg/vegan/R/rrarefy.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/diversity.Rd
Log:
add drarefy: occurrence probabilities in a rarefied community

Modified: pkg/vegan/R/rrarefy.R
===================================================================
--- pkg/vegan/R/rrarefy.R	2011-03-06 06:21:20 UTC (rev 1521)
+++ pkg/vegan/R/rrarefy.R	2011-03-06 09:03:07 UTC (rev 1522)
@@ -1,5 +1,7 @@
-rrarefy <-
-function(x, sample)
+### Random rarefied subsample: sample without replacement
+
+`rrarefy` <-
+    function(x, sample)
 {
     if (length(sample) > 1 && length(sample) != nrow(x))
         stop("length of 'sample' and number of rows of 'x' do not match")
@@ -15,3 +17,22 @@
     }
     x
 }
+
+### Probabilities that species occur in a rarefied 'sample'
+
+`drarefy` <-
+    function(x, sample)
+{
+    if (length(sample) > 1)
+        stop(gettextf("only scalar 'sample' is accepted"))
+    x <- drop(as.matrix(x))
+    dfun <- function(x, sample) {
+        J <- sum(x)
+        sample <- min(sample, J)
+        1 - exp(lchoose(J - x, sample) - lchoose(J, sample))
+    }
+    if (length(dim(x) > 1))
+        t(apply(x, 1, dfun, sample = sample))
+    else
+        dfun(x, sample)
+}

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-03-06 06:21:20 UTC (rev 1521)
+++ pkg/vegan/inst/ChangeLog	2011-03-06 09:03:07 UTC (rev 1522)
@@ -23,6 +23,10 @@
 	concern cca(); rda() and capscale() are only changed after (and
 	if) this change appears sensible and correct in cca().
 
+	* drarefy: a new function to return the probabilities that a
+	species occurs in a rarefied sample (= sampled without
+	replacement) of a given size.
+
 Version 1.18-23 (closed February 28, 2011)
 
 	* opened with the release of 1.17-7 based on version 1.18-22 on

Modified: pkg/vegan/man/diversity.Rd
===================================================================
--- pkg/vegan/man/diversity.Rd	2011-03-06 06:21:20 UTC (rev 1521)
+++ pkg/vegan/man/diversity.Rd	2011-03-06 09:03:07 UTC (rev 1522)
@@ -3,6 +3,7 @@
 \alias{diversity}
 \alias{rarefy}
 \alias{rrarefy}
+\alias{drarefy}
 \alias{fisher.alpha}
 \alias{specnumber}
 
@@ -13,13 +14,10 @@
 
 \usage{
 diversity(x, index = "shannon", MARGIN = 1, base = exp(1))
-
 rarefy(x, sample, se = FALSE, MARGIN = 1)
-
 rrarefy(x, sample)
-
+drarefy(x, sample)
 fisher.alpha(x, MARGIN = 1, se = FALSE, ...)
-
 specnumber(x, MARGIN = 1)
 }
 
@@ -64,6 +62,13 @@
   that the variance of rarefied communities is rather related to
   rarefaction proportion than to to the size of the \code{sample}.  
 
+  Function \code{drarefy} returns probabilities that species occur in
+  a rarefied community of size \code{sample}. Only a single scalar of
+  \code{sample} size is accepted. If \code{x} is a single site, the
+  function returns a vector of species occurrence probabilities. If
+  \code{x} is a data frame or a matrix, a matrix of probabilities for
+  each row is returned.
+
   \code{fisher.alpha} estimates the \eqn{\alpha} parameter of
   Fisher's logarithmic series (see \code{\link{fisherfit}}). 
   The estimation is possible only for genuine