[Vegan-commits] r2543 - in pkg/vegan: R inst man

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

Author: gsimpson
Date: 2013-07-08 05:19:38 +0200 (Mon, 08 Jul 2013)
New Revision: 2543

Modified:
   pkg/vegan/R/permutest.betadisper.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/permutest.betadisper.Rd
Log:
adds a permutations argument

Modified: pkg/vegan/R/permutest.betadisper.R
===================================================================
--- pkg/vegan/R/permutest.betadisper.R	2013-07-08 03:18:51 UTC (rev 2542)
+++ pkg/vegan/R/permutest.betadisper.R	2013-07-08 03:19:38 UTC (rev 2543)
@@ -1,5 +1,6 @@
 `permutest.betadisper` <- function(x, pairwise = FALSE,
-                                   control = how(nperm = 999), ...)
+                                   control = how(nperm = 999),
+                                   permutations = NULL, ...)
 {
     t.statistic <- function(x, y) {
         m <- length(x)
@@ -11,7 +12,7 @@
         pooled <- sqrt(((m-1)*xvar + (n-1)*yvar) / (m+n-2))
         (xbar - ybar) / (pooled * sqrt(1/m + 1/n))
     }
-    
+
     if(!inherits(x, "betadisper"))
         stop("Only for class \"betadisper\"")
     ## will issue error if only a single group
@@ -22,20 +23,29 @@
     p <- mod.Q$rank
     resids <- qr.resid(mod.Q, x$distances)
 
+    N <- nrow(x) ## number of observations
+
     ## extract groups
     group <- x$group
-    
-    ## get set of permutations - shuffleSet checks design
-    perms <- shuffleSet(length(group), control = control)
 
+    ## If permutations is NULL, work with control
+    if(is.null(permutations)) {
+        permutations <- shuffleSet(length(group), control = control)
+    } else {
+        permutations <- as.matrix(permutations)
+        if (ncol(permutations) != N)
+            stop(gettextf("'permutations' have %d columns, but data have %d observations",
+                          ncol(permutations), N))
+    }
+
     ## number of permutations being performed, possibly adjusted after
     ## checking in shuffleSet
-    nperm <- nrow(perms)
+    nperm <- nrow(permutations)
 
     ## set-up objects to hold permuted results
     res <- numeric(length = nperm + 1)
     res[1] <- summary(mod)$fstatistic[1]
-    
+
     ## pairwise comparisons
     if(pairwise) {
         ## unique pairings
@@ -49,7 +59,7 @@
 
     ## begin loop over shuffleSet perms
     for(i in seq_len(nperm)) {
-        perm <- perms[i,] ## take current permutation from set
+        perm <- permutations[i,] ## take current permutation from set
         perm.resid <- resids[perm] ## permute residuals
         f <- qr.fitted(mod.Q, perm.resid) ## create new data
         mss <- sum((f - mean(f))^2)
@@ -58,7 +68,7 @@
         rdf <- nobs - p
         resvar <- rss / rdf
         res[i+1] <- (mss / (p - 1)) / resvar
-        
+
         ## pairwise comparisons
         if(pairwise) {
             for(j in seq_len(n.pairs)) {
@@ -71,7 +81,7 @@
 
     ## compute permutation p-value
     pval <- sum(res >= res[1]) / length(res)
-    
+
     if(pairwise) {
         df <- apply(combin, 2, function(z) {
             length(x$distances[group == z[1]]) +
@@ -84,7 +94,7 @@
     } else {
         pairwise <- NULL
     }
-    
+
     retval <- cbind(mod.aov[, 1:4], c(nperm, NA), c(pval, NA))
     dimnames(retval) <- list(c("Groups", "Residuals"),
                              c("Df", "Sum Sq", "Mean Sq", "F", "N.Perm",

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2013-07-08 03:18:51 UTC (rev 2542)
+++ pkg/vegan/inst/ChangeLog	2013-07-08 03:19:38 UTC (rev 2543)
@@ -8,7 +8,9 @@
 	later.
 
 	* betadisper, permutest.betadisper: Modified to use the new
-	permute package API (from version 0.7-3 onwards).
+	permute package API (from version 0.7-3 onwards). The `permutest`
+	method gains a new argument `permutations`, which takes a matrix
+	of permutations to be used.
 
 	* protest: modified to use the new permute API. Gains argument
 	`control` which describes the design. As a result, `strata`
@@ -47,7 +49,7 @@
 	* stressplot: metaMDS and monoMDS stressplot() use now
 	expression(R^2) instead of ascii R2.  The stressplot.monoMDS()
 	function returns the plotting structures in the original input
-	order. 
+	order.
 
 	* vignettes: Brian Ripley urged as to remove
 	\usepackage{inconsolota} as this package is on the way to be

Modified: pkg/vegan/man/permutest.betadisper.Rd
===================================================================
--- pkg/vegan/man/permutest.betadisper.Rd	2013-07-08 03:18:51 UTC (rev 2542)
+++ pkg/vegan/man/permutest.betadisper.Rd	2013-07-08 03:19:38 UTC (rev 2543)
@@ -10,7 +10,8 @@
 }
 \usage{
 \method{permutest}{betadisper}(x, pairwise = FALSE,
-         control = how(nperm = 999), \dots)
+         control = how(nperm = 999), permutations = NULL,
+         \dots)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{
@@ -18,7 +19,9 @@
     call to \code{betadisper}.}
   \item{pairwise}{logical; perform pairwise comparisons of group means?}
   \item{control}{a list of control values for the permutations
-    as returned by the function \code{\link[permute]{how}}}
+    as returned by the function \code{\link[permute]{how}}.}
+  \item{permutations}{A permutation matrix where each row gives the
+    permuted indices. If this is supplied, \code{control} is ignored.}
   \item{\dots}{Arguments passed to other methods.}
 }
 \details{