[Esm-commits] r41 - pkg/ESM/R

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

Author: timotheepoisot
Date: 2011-01-14 12:15:47 +0100 (Fri, 14 Jan 2011)
New Revision: 41

Modified:
   pkg/ESM/R/functions.r
Log:


Modified: pkg/ESM/R/functions.r
===================================================================
--- pkg/ESM/R/functions.r	2010-10-07 17:11:09 UTC (rev 40)
+++ pkg/ESM/R/functions.r	2011-01-14 11:15:47 UTC (rev 41)
@@ -9,6 +9,16 @@
 	return(out)
 }
 
+Rpdi <- function(fit)
+{
+	fit <- fit[fit>0]
+	if(length(fit)==1){return(1)}
+	fit <- sort(as.vector(fit),decreasing=TRUE)
+	test <- fit[2:length(fit)]
+	out <- sum(fit[1]-test)/length(test)
+	return(out)
+}
+
 rr <- function(fit)
 {
 	N <- length(fit)
@@ -39,7 +49,7 @@
 	return(SSI)
 }
 
-getspe <- function(mat,measure=pdi,normal='whole',...)
+getspe <- function(mat,measure=pdi,normal='species',...)
 {
 	mat <- fixmat(mat)
 	if(normal=='species'){mat <- t(apply(mat,1,function(x)x/max(x)))}
@@ -71,43 +81,4 @@
 		nm[(cl[i]<m)&(m<=cl[(i+1)])] <- cl[i]
 	}
 	return(scale(nm,0,1))
-}
-
-Overlap = function(mat)
-{
-	for(i in 1:nrow(mat))
-	{
-		mat[i,] <- mat[i,]/sum(mat[i,])
-	}
-	out <- matrix(0,nrow=nrow(mat),ncol=nrow(mat))
-	colnames(out) <- rownames(mat)
-	rownames(out) <- rownames(mat)
-	for(i in 1:(nrow(mat)-1))
-	{
-		for(j in (i+1):nrow(mat))
-		{
-			out[i,j] <- 1-1/2*sum(abs(mat[i,]-mat[j,]))
-		}
-	}
-	diag(out) <- rep(1,length(diag(out)))
-	return(out)
-}
-
-getOLsp = function(OLmat,id)
-{
-	byR <- OLmat[id,]
-	byC <- OLmat[,id]
-	OlSP <- c(byR[c((id+1):length(byR))],byC[c(1:(id-1))])
-	return(OlSP)
-}
-
-getOLvec = function(net)
-{
-	net <- empty(net)
-	net <- net/max(net)
-	OLmat <- Overlap(net)
-	l <- c(1:nrow(OLmat))
-	OL <- lapply(l,function(x)getOLsp(OLmat,id=x))
-	if(!is.null(rownames(OLmat))){names(OL)<-rownames(OLmat)}
-	return(OL)
 }
\ No newline at end of file