[Vegan-commits] r949 - in branches/1.15: R inst man

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

Author: jarioksa
Date: 2009-08-25 20:24:54 +0200 (Tue, 25 Aug 2009)
New Revision: 949

Added:
   branches/1.15/R/indpower.R
   branches/1.15/man/indpower.Rd
Modified:
   branches/1.15/inst/ChangeLog
   branches/1.15/man/beals.Rd
Log:
copied indpower to branches/1.15

Copied: branches/1.15/R/indpower.R (from rev 948, pkg/vegan/R/indpower.R)
===================================================================
--- branches/1.15/R/indpower.R	                        (rev 0)
+++ branches/1.15/R/indpower.R	2009-08-25 18:24:54 UTC (rev 949)
@@ -0,0 +1,22 @@
+indpower <-
+function(x, type=0)
+{
+    x <- as.matrix(x)
+    x <- ifelse(x > 0, 1, 0)
+    if (NCOL(x) < 2)
+        stop("provide at least 2 columns for 'x'")
+    if (!(type %in% 0:2))
+        stop("'type' must be in c(0, 1, 2)")
+    n <- nrow(x)
+    j <- t(x) %*% x
+    ip1 <- sweep(j, 1, diag(j), "/")
+    ip2 <- 1 - sweep(-sweep(j, 2, diag(j), "-"), 1, n - diag(j), "/")
+    ip <- sqrt(ip1 * ip2)
+    out <- switch(as.character(type),
+        "0" = ip,
+        "1" = ip1,
+        "2" = ip2)
+    colnames(out) <- paste("t", colnames(out), sep=".")
+    rownames(out) <- paste("i", rownames(out), sep=".")
+    out
+}

Modified: branches/1.15/inst/ChangeLog
===================================================================
--- branches/1.15/inst/ChangeLog	2009-08-25 10:32:38 UTC (rev 948)
+++ branches/1.15/inst/ChangeLog	2009-08-25 18:24:54 UTC (rev 949)
@@ -41,6 +41,8 @@
 
 	* radlattice copied from pkg/ and merged doc changes r551, 553.
 
+	* copied indpower (with rev948 for beals.Rd).
+
 Version 1.15-3 (released June 17, 2009)
 
 	* merged revs 866 to 868: changed the way capscale displays

Modified: branches/1.15/man/beals.Rd
===================================================================
--- branches/1.15/man/beals.Rd	2009-08-25 10:32:38 UTC (rev 948)
+++ branches/1.15/man/beals.Rd	2009-08-25 18:24:54 UTC (rev 949)
@@ -106,7 +106,8 @@
 
 \seealso{\code{\link{decostand}} for proper standardization methods,
   \code{\link{specpool}} for an attempt to assess the size of species
-  pool. }
+  pool. Function \code{\link{indpower}} assesses the power of each species
+  to estimate the probabilities predicted by \code{beals}. }
 \examples{
 data(dune)
 ## Default

Copied: branches/1.15/man/indpower.Rd (from rev 948, pkg/vegan/man/indpower.Rd)
===================================================================
--- branches/1.15/man/indpower.Rd	                        (rev 0)
+++ branches/1.15/man/indpower.Rd	2009-08-25 18:24:54 UTC (rev 949)
@@ -0,0 +1,62 @@
+\encoding{UTF-8}
+\name{indpower}
+\alias{indpower}
+
+\title{Indicator Power of Species}
+
+\description{ Indicator power calculation of Halme et al.  (2009)
+  or the congruence between indicator and target species.  
+}
+
+\usage{
+indpower(x, type = 0)
+}
+\arguments{
+  \item{x}{Community data frame or matrix. }
+  \item{type}{The type of
+  statistic to be returned. See Details for explanation.}  
+}
+\details{
+
+  Halme et al. (2009) described an index of indicator power defined as
+  \eqn{IP_I = \sqrt{a \times  b}}{IP_I = sqrt(a*b)}, where \eqn{a = S / O_I} and
+  \eqn{b = 1 - (O_T - S) / (N - O_I)}. 
+  \eqn{N} is the number of sites,
+  \eqn{S} is the number of shared occurrences of the indicator (\eqn{I})
+  and the target (\eqn{T}) species. \eqn{O_I} and \eqn{O_T} are number
+  of occurrences of the indicator and target species. The \code{type}
+  argument in the function call enables to choose which statistic to
+  return. \code{type = 0} returns \eqn{IP_I}, \code{type = 1} returns 
+  \eqn{a}, \code{type = 2} returns \eqn{b}.
+  Total indicator power (TIP) of an indicator species is the column mean
+  (without its own value, see examples).  
+  Halme et al. (2009) explain how to calculate confidence
+  intervals for these statistics.
+}
+\value{
+  A matrix with indicator species as rows and
+  target species as columns (this is indicated by the first letters of the
+  row/column names).
+}
+\references{
+Halme, P., \enc{Mönkkönen}{Monkkonen}, M., Kotiaho, J. S, 
+\enc{Ylisirniö}{Ylisirnio}, A-L. 2009. Quantifying the indicator power
+of an indicator species. \emph{Conservation Biology} 23: 1008--1016.
+}
+\author{Peter Solymos}
+
+\seealso{ \code{\link[labdsv]{duleg}} (package \pkg{labdsv}) for the
+indicator species analysis of \enc{Dufrêne}{Dufrene} & Legendre. 
+Function \code{\link{beals}} estimates individual cell probabilities
+of species occurrences. }
+
+\examples{
+data(dune)
+## IP values
+ip <- indpower(dune)
+## and TIP values
+diag(ip) <- NA
+rowMeans(ip, na.rm=TRUE)
+}
+\keyword{ multivariate }
+