[Vegan-commits] r2745 - in pkg/vegan: R man

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

Author: gsimpson
Date: 2013-11-22 18:59:51 +0100 (Fri, 22 Nov 2013)
New Revision: 2745

Modified:
   pkg/vegan/R/permutest.betadisper.R
   pkg/vegan/R/print.permutest.betadisper.R
   pkg/vegan/man/permutest.betadisper.Rd
Log:
update permutest method to the new permute API

Modified: pkg/vegan/R/permutest.betadisper.R
===================================================================
--- pkg/vegan/R/permutest.betadisper.R	2013-11-22 17:59:07 UTC (rev 2744)
+++ pkg/vegan/R/permutest.betadisper.R	2013-11-22 17:59:51 UTC (rev 2745)
@@ -1,6 +1,6 @@
 `permutest.betadisper` <- function(x, pairwise = FALSE,
-                                   control = how(nperm = 999),
-                                   permutations = NULL, ...)
+                                   permutations = how(nperm = 999),
+                                   ...)
 {
     t.statistic <- function(x, y) {
         m <- length(x)
@@ -17,27 +17,31 @@
         stop("Only for class \"betadisper\"")
     ## will issue error if only a single group
     mod.aov <- anova(x)
-    nobs <- length(x$distances)
+    nobs <- length(x$distances) ## number of observations
     mod <- lm(x$distances ~ x$group)
     mod.Q <- mod$qr
     p <- mod.Q$rank
     resids <- qr.resid(mod.Q, x$distances)
 
-    N <- nrow(x) ## number of observations
-
     ## extract groups
     group <- x$group
+    ## permutations is either a single number, a how() structure or a
+    ## permutation matrix
+    if (length(permutations) == 1) {
+        nperm <- permutations
+        permutations <- how(nperm = nperm)
+    }
 
-    ## 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))
+    ## permutations is either a single number, a how() structure or a
+    ## permutation matrix
+    if (length(permutations) == 1) {
+        nperm <- permutations
+        permutations <- how(nperm = nperm)
     }
-
+    ## now permutations is either a how() structure or a permutation
+    ## matrix. Make it to a matrix if it is "how"
+    if (inherits(permutations, "how"))
+        permutations <- shuffleSet(nobs, control = permutations)
     ## number of permutations being performed, possibly adjusted after
     ## checking in shuffleSet
     nperm <- nrow(permutations)
@@ -45,7 +49,6 @@
     ## set-up objects to hold permuted results
     res <- numeric(length = nperm + 1)
     res[1] <- summary(mod)$fstatistic[1]
-
     ## pairwise comparisons
     if(pairwise) {
         ## unique pairings
@@ -95,12 +98,13 @@
         pairwise <- NULL
     }
 
-    retval <- cbind(mod.aov[, 1:4], c(nperm, NA), c(pval, NA))
+    retval <- cbind(mod.aov[, 1:4], c(nperm + 1, NA), c(pval, NA))
     dimnames(retval) <- list(c("Groups", "Residuals"),
                              c("Df", "Sum Sq", "Mean Sq", "F", "N.Perm",
                                "Pr(>F)"))
     retval <- list(tab = retval, pairwise = pairwise,
-                   groups = levels(group), control = control)
+                   groups = levels(group),
+                   control = attr(permutations, "control"))
     class(retval) <- "permutest.betadisper"
     retval
 }

Modified: pkg/vegan/R/print.permutest.betadisper.R
===================================================================
--- pkg/vegan/R/print.permutest.betadisper.R	2013-11-22 17:59:07 UTC (rev 2744)
+++ pkg/vegan/R/print.permutest.betadisper.R	2013-11-22 17:59:51 UTC (rev 2745)
@@ -21,7 +21,7 @@
         zap.i <- zap.i[!(zap.i %in% i)]
     if (length(i <- grep("N.Perm$", cn)))
         zap.i <- zap.i[!(zap.i %in% i)]
-    cat("Response: Distances", sep = "\n")
+    cat("\nResponse: Distances", sep = "\n")
     printCoefmat(x$tab, digits = digits,
                  signif.stars = getOption("show.signif.stars"),
                  has.Pvalue = has.P, P.values = has.P, cs.ind = NULL,

Modified: pkg/vegan/man/permutest.betadisper.Rd
===================================================================
--- pkg/vegan/man/permutest.betadisper.Rd	2013-11-22 17:59:07 UTC (rev 2744)
+++ pkg/vegan/man/permutest.betadisper.Rd	2013-11-22 17:59:51 UTC (rev 2745)
@@ -10,18 +10,18 @@
 }
 \usage{
 \method{permutest}{betadisper}(x, pairwise = FALSE,
-         control = how(nperm = 999), permutations = NULL,
-         \dots)
+          permutations = how(nperm = 999),
+          \dots)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{x}{an object of class \code{"betadisper"}, the result of a
     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}}.}
-  \item{permutations}{A permutation matrix where each row gives the
-    permuted indices. If this is supplied, \code{control} is ignored.}
+  \item{permutations}{a list of control values for the permutations
+    as returned by the function \code{\link[permute]{how}}, or the
+    number of permutations required, or a permutation matrix where each
+    row gives the permuted indices.}
   \item{\dots}{Arguments passed to other methods.}
 }
 \details{
@@ -82,7 +82,7 @@
 anova(mod)
 
 ## Permutation test for F
-permutest(mod, pairwise = TRUE)
+permutest(mod, permutations = 99, pairwise = TRUE)
 
 ## Tukey's Honest Significant Differences
 (mod.HSD <- TukeyHSD(mod))