[Vegan-commits] r326 - in pkg: R man

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

Author: jarioksa
Date: 2008-04-23 13:07:09 +0200 (Wed, 23 Apr 2008)
New Revision: 326

Modified:
   pkg/R/rarefy.R
   pkg/man/diversity.Rd
Log:
rarefy accepts now a vector of sample sizes

Modified: pkg/R/rarefy.R
===================================================================
--- pkg/R/rarefy.R	2008-04-23 10:39:47 UTC (rev 325)
+++ pkg/R/rarefy.R	2008-04-23 11:07:09 UTC (rev 326)
@@ -1,4 +1,4 @@
-"rarefy" <-
+`rarefy` <-
     function (x, sample, se = FALSE, MARGIN = 1) 
 {
     x <- as.matrix(x)
@@ -28,9 +28,18 @@
         }
         out
     }
-    S.rare <- apply(x, MARGIN, rarefun, sample = sample)
-    if (se) 
-        rownames(S.rare) <- c("S", "se")
+    if (length(sample) > 1) {
+        S.rare <- sapply(sample, function(n) apply(x, MARGIN, rarefun, sample = n))
+        colnames(S.rare) <- paste("N", sample, sep="")
+        if (se) {
+            dn <- unlist(dimnames(x)[MARGIN])
+            rownames(S.rare) <- paste(rep(dn, each=2), c("S","se"), sep=".")
+        }
+    } else {
+        S.rare <- apply(x, MARGIN, rarefun, sample = sample)
+        if (se) 
+            rownames(S.rare) <- c("S", "se")
+    }
     attr(S.rare, "Subsample") <- sample
     S.rare
 }

Modified: pkg/man/diversity.Rd
===================================================================
--- pkg/man/diversity.Rd	2008-04-23 10:39:47 UTC (rev 325)
+++ pkg/man/diversity.Rd	2008-04-23 11:07:09 UTC (rev 326)
@@ -26,7 +26,8 @@
     \code{"simpson"} or \code{"invsimpson"}.}
   \item{MARGIN}{Margin for which the index is computed. }
   \item{base}{ The logarithm \code{base} used in \code{shannon}.}
-  \item{sample}{Subsample size for rarefying community.}
+  \item{sample}{Subsample size for rarefying community, either a single
+    value or a vector.}
   \item{se}{Estimate standard errors.}
   \item{...}{Parameters passed to \code{\link{nlm}}}
 }
@@ -46,7 +47,9 @@
   subsamples of size \code{sample} from the community. The size of
   \code{sample} should be smaller than total community size, but the
   function will  silently work for larger \code{sample} as well and
-  return non-rarefied species richness (and standard error = 0).
+  return non-rarefied species richness (and standard error = 0). If
+  \code{sample} is a vector, rarefaction is performed for each sample
+  size separately.
   Rarefaction can be performed only with genuine counts of individuals.
   The function \code{rarefy} is based on Hurlbert's (1971) formulation,
   and the standard errors on Heck et al. (1975).  
@@ -79,9 +82,13 @@
 
 \value{
   A vector of diversity indices or rarefied species richness values. With
-  option \code{se = TRUE}, function \code{rarefy} returns a 2-row matrix
+  a single \code{sample} and \code{se = TRUE}, function \code{rarefy}
+  returns a 2-row matrix 
   with rarefied richness (\code{S}) and its standard error
-  (\code{se}).
+  (\code{se}). If \code{sample} is a vector in \code{rarefy}, the
+  function returns a matrix with a column for each \code{sample} size,
+  and if \code{se = TRUE}, rarefied richness and its standard error are
+  on consecutive lines.
   With option \code{se = TRUE}, function \code{fisher.alpha} returns a
   data frame with items for \eqn{\alpha} (\code{alpha}), its approximate
   standard errors (\code{se}), residual degrees of freedom