[Esm-commits] r43 - in pkg/ESM: . R

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

Author: timotheepoisot
Date: 2011-01-17 22:41:45 +0100 (Mon, 17 Jan 2011)
New Revision: 43

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


Modified: pkg/ESM/DESCRIPTION
===================================================================
--- pkg/ESM/DESCRIPTION	2011-01-14 16:59:54 UTC (rev 42)
+++ pkg/ESM/DESCRIPTION	2011-01-17 21:41:45 UTC (rev 43)
@@ -1,6 +1,6 @@
 Package: ESM
-Version: 2.0.0-01
-Date: 2011-01-14
+Version: 2.0.2-01
+Date: 2011-01-17
 Title: Ecological Specificity Measures
 Author: Timothee Poisot <tpoisot at um2.fr>
 Maintainer: Timothee Poisot <tpoisot at um2.fr>

Modified: pkg/ESM/R/functions.r
===================================================================
--- pkg/ESM/R/functions.r	2011-01-14 16:59:54 UTC (rev 42)
+++ pkg/ESM/R/functions.r	2011-01-17 21:41:45 UTC (rev 43)
@@ -1,5 +1,26 @@
 fixmat = function(mat) mat[rowSums(mat)>0,colSums(mat)>0]
+subsamp = function(mat,nc=5,nr=5) fixmat(mat[sample(c(1:nrow(mat)),nr,replace=FALSE),sample(c(1:ncol(mat)),nc,replace=FALSE)])
 
+entropy = function(vec)
+{
+	uns <- unique(vec)
+	ps <- NULL
+	for(i in 1:length(uns))
+	{
+		ps <- c(ps,sum(vec==uns[i])/length(vec))
+	}
+	ENT = -sum(ps*log(ps))
+	INF = ENT/log(length(uns))
+	return(as.data.frame(list(E=ENT,I=INF)))
+}
+
+simpson = function(fit)
+{
+	fit <- round(fit*1000,0)
+	Simp <- sum(fit*(fit-1))/(sum(fit)*(sum(fit)-1))
+	return(Simp)
+}
+
 pdi <- function(fit)
 {
 	if(length(fit)==1){return(1)}
@@ -38,7 +59,7 @@
 	return(1-shannon)
 }
 
-ssi = function(fit)
+ssi <- function(fit)
 { # Normalized and using quantitative data
 	if (length(fit) == 1) {
         return(1)