[Vegan-commits] r2369 - in pkg/vegan: R inst

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

Author: psolymos
Date: 2013-01-14 19:49:04 +0100 (Mon, 14 Jan 2013)
New Revision: 2369

Modified:
   pkg/vegan/R/clamtest.R
   pkg/vegan/inst/ChangeLog
Log:
clamtest fixes: dimnames bug and solution for an extreme case.

Modified: pkg/vegan/R/clamtest.R
===================================================================
--- pkg/vegan/R/clamtest.R	2013-01-14 08:32:50 UTC (rev 2368)
+++ pkg/vegan/R/clamtest.R	2013-01-14 18:49:04 UTC (rev 2369)
@@ -19,7 +19,7 @@
         stop("number of groups must be 2")
     glabel <- as.character(unique(groups))
     if (is.null(colnames(comm)))
-        colnames(comm) <- paste("Species", 1:nrow(comm), sep=".")
+        colnames(comm) <- paste("Species", 1:ncol(comm), sep=".")
     if (any(colSums(comm) <= 0))
         stop("'comm' contains zero sum columns")
     spp <- colnames(comm)
@@ -73,14 +73,28 @@
     ## finding Xmin and Ymin values for Xseq and Yseq
     Xmins <- sapply(Yseq, function(z) rootfun(z, C1, C2, n, m, upper=max(X)))
     Ymins <- sapply(Xseq, function(z) rootfun(z, C2, C1, m, n, upper=max(Y)))
+
+    ## needed to tweak original set of rules (extreme case reported
+    ## by Richard Telford failed here)
+    if (all(is.na(Xmins)))
+        Xmins[1] <- 1
+    if (all(is.na(Ymins)))
+        Ymins[1] <- 1
+
     minval <- list(data.frame(x=Xseq[!is.na(Ymins)], y=Ymins[!is.na(Ymins)]),
         data.frame(x=Xmins[!is.na(Xmins)], y=Yseq[!is.na(Xmins)]))
+
     ## shared but too rare
     Ymin <- Ymins[1]
     Xmin <- Xmins[1]
     sr <- X < Xmin & Y < Ymin
-    tmp1 <- approx(c(Xmin, 1), c(1, Ymin), xout=1:Xmin)
-    tmp2 <- approx(c(1, Ymin), c(Xmin, 1), xout=1:Ymin)
+
+    ## consequence of manually setting Xmin/Ymin resolved here
+    tmp1 <- if (Xmin==1)
+        list(x=1, y=Xmin) else approx(c(Xmin, 1), c(1, Ymin), xout=1:Xmin)
+    tmp2 <- if (Ymin==1)
+        list(x=1, y=Ymin) else approx(c(1, Ymin), c(Xmin, 1), xout=1:Ymin)
+
     for (i in 1:S) {
         if (X[i] %in% tmp1$x)
             sr[i] <- Y[i] < tmp1$y[which(X[i]==tmp1$x)]

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2013-01-14 08:32:50 UTC (rev 2368)
+++ pkg/vegan/inst/ChangeLog	2013-01-14 18:49:04 UTC (rev 2369)
@@ -4,6 +4,14 @@
 
 Version 2.1-23 (opened January 8, 2013)
 
+	* clamtest: Richard Telford reported an extreme case 
+	{rbind(a=c(1,0,5,10,4),b=c(0,10,5,2,1))} where
+	clamtest failed due to inadequately setting up minimum
+	abundance thresholds for rare species. The issue is solved
+	by hard coding the minimum values to be 1 when no suitable 
+	solution is found. Also, clamtest failed when the community matrix 
+	had no column names, this is now fixed.
+
 	* capscale: It was wrongly assumed that eigenvalues could be used
 	in normalization of species scores, but this worked only with
 	Euclidean distances. Now normalization is done explicitly with