[Vegan-commits] r2082 - in branches/2.0: R inst man

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

Author: jarioksa
Date: 2012-02-11 08:53:27 +0100 (Sat, 11 Feb 2012)
New Revision: 2082

Modified:
   branches/2.0/R/indpower.R
   branches/2.0/R/permutest.betadisper.R
   branches/2.0/inst/ChangeLog
   branches/2.0/man/indpower.Rd
   branches/2.0/man/renyi.Rd
Log:
merge r2060 (broken url), 2071,2 (indpower fix), 2079 (do not use .Internal)

Modified: branches/2.0/R/indpower.R
===================================================================
--- branches/2.0/R/indpower.R	2012-02-10 10:34:19 UTC (rev 2081)
+++ branches/2.0/R/indpower.R	2012-02-11 07:53:27 UTC (rev 2082)
@@ -11,12 +11,15 @@
     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,
+        "0" = sqrt(ip1 * ip2),
         "1" = ip1,
         "2" = ip2)
-    colnames(out) <- paste("t", colnames(out), sep=".")
-    rownames(out) <- paste("i", rownames(out), sep=".")
+    cn <- if (is.null(colnames(out)))
+        1:ncol(out) else colnames(out)
+    rn <- if (is.null(rownames(out)))
+        1:ncol(out) else rownames(out)
+    colnames(out) <- paste("t", cn, sep=".")
+    rownames(out) <- paste("i", rn, sep=".")
     out
 }

Modified: branches/2.0/R/permutest.betadisper.R
===================================================================
--- branches/2.0/R/permutest.betadisper.R	2012-02-10 10:34:19 UTC (rev 2081)
+++ branches/2.0/R/permutest.betadisper.R	2012-02-11 07:53:27 UTC (rev 2082)
@@ -4,10 +4,10 @@
     t.statistic <- function(x, y) {
         m <- length(x)
         n <- length(y)
-        xbar <- .Internal(mean(x))
-        ybar <- .Internal(mean(y))
-        xvar <- .Internal(cov(x, NULL, 1, FALSE))
-        yvar <- .Internal(cov(y, NULL, 1, FALSE))
+        xbar <- mean(x) ## .Internal(mean(x))
+        ybar <- mean(y) ## .Internal(mean(y))
+        xvar <- var(x)  ## .Internal(cov(x, NULL, 1, FALSE))
+        yvar <- var(y)  ## .Internal(cov(y, NULL, 1, FALSE))
         pooled <- sqrt(((m-1)*xvar + (n-1)*yvar) / (m+n-2))
         (xbar - ybar) / (pooled * sqrt(1/m + 1/n))
     }

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2012-02-10 10:34:19 UTC (rev 2081)
+++ branches/2.0/inst/ChangeLog	2012-02-11 07:53:27 UTC (rev 2082)
@@ -4,6 +4,9 @@
 
 Version 2.0-3 (opened November 13, 2011)
 
+	* merge r2079: do not use .Internal().
+	* merge r2071,2: dimnames fix in indopower & expand example.
+	* merge r2068: broken url in renyi.Rd.
 	* merge r2060: adonis tells terms were added sequentially.
 	* mrege r2057: add .Rinstignore to silense R 2.15.0 checks.
 	* merge r2056: use inconsolata fonts in vignettes.

Modified: branches/2.0/man/indpower.Rd
===================================================================
--- branches/2.0/man/indpower.Rd	2012-02-10 10:34:19 UTC (rev 2081)
+++ branches/2.0/man/indpower.Rd	2012-02-11 07:53:27 UTC (rev 2082)
@@ -31,7 +31,7 @@
   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.
+  intervals for these statistics, see Examples.
 }
 \value{
   A matrix with indicator species as rows and
@@ -56,7 +56,29 @@
 ip <- indpower(dune)
 ## and TIP values
 diag(ip) <- NA
-rowMeans(ip, na.rm=TRUE)
+(TIP <- rowMeans(ip, na.rm=TRUE))
+
+## p value calculation for a species
+## from Halme et al. 2009
+## i is ID for the species
+i <- 1
+fun <- function(x, i) indpower(x)[i,-i]
+## 'c0' randomizes species occurrences
+os <- oecosimu(dune, fun, "c0", i=i, nsimul=99)
+## get z values from oecosimu output
+z <- os$oecosimu$z
+## p-value
+(p <- sum(z) / sqrt(length(z)))
+## 'heterogeneity' measure
+(chi2 <- sum((z - mean(z))^2))
+pchisq(chi2, df=length(z)-1)
+## Halme et al.'s suggested output
+out <- c(TIP=TIP[i], 
+    significance=p,
+    heterogeneity=chi2,
+    minIP=min(fun(dune, i=i)),
+    varIP=sd(fun(dune, i=i)^2))
+out
 }
 \keyword{ multivariate }
 

Modified: branches/2.0/man/renyi.Rd
===================================================================
--- branches/2.0/man/renyi.Rd	2012-02-10 10:34:19 UTC (rev 2081)
+++ branches/2.0/man/renyi.Rd	2012-02-11 07:53:27 UTC (rev 2082)
@@ -87,7 +87,7 @@
   replaced with individual permutation results. 
 }
 \references{
-  \url{http://www.worldagroforestry.org/treesandmarkets/tree_diversity_analysis.asp}
+  \url{http://www.worldagroforestry.org/resources/databases/tree-diversity-analysis}
 
   Hill, M.O. (1973). Diversity and evenness: a unifying notation and its
    consequences. \emph{Ecology} 54, 427--473.