[Vegan-commits] r1650 - in pkg/vegan: R man

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

Author: gsimpson
Date: 2011-06-21 21:42:44 +0200 (Tue, 21 Jun 2011)
New Revision: 1650

Modified:
   pkg/vegan/R/permutest.betadisper.R
   pkg/vegan/man/simulate.rda.Rd
   pkg/vegan/man/vegan-internal.Rd
Log:
final few tweaks to get vegan to pass R CMD check, remove references to permuted.index2 which now point to shuffle, permutest.betadisper now uses shuffle temporarily

Modified: pkg/vegan/R/permutest.betadisper.R
===================================================================
--- pkg/vegan/R/permutest.betadisper.R	2011-06-21 18:57:28 UTC (rev 1649)
+++ pkg/vegan/R/permutest.betadisper.R	2011-06-21 19:42:44 UTC (rev 1650)
@@ -33,7 +33,8 @@
                         x$distances[x$group == z[2]])})
     }
     for(i in seq(along = res[-1])) {
-        perm <- permuted.index2(nobs, control = control)
+        ##perm <- permuted.index2(nobs, control = control)
+        perm <- shuffle(nobs, control = control)
         perm.resid <- resids[perm]
         f <- qr.fitted(mod.Q, perm.resid)
         mss <- sum((f - mean(f))^2)

Modified: pkg/vegan/man/simulate.rda.Rd
===================================================================
--- pkg/vegan/man/simulate.rda.Rd	2011-06-21 18:57:28 UTC (rev 1649)
+++ pkg/vegan/man/simulate.rda.Rd	2011-06-21 19:42:44 UTC (rev 1650)
@@ -23,7 +23,7 @@
     \code{\link{simulate}} for details. }
   \item{indx}{Index of residuals added to the fitted values, such as
     produced by  \code{\link{permuted.index}},
-    \code{\link{permuted.index2}} or \code{\link{sample}}. The index can
+    \code{\link{shuffle}} or \code{\link{sample}}. The index can
     have duplicate entries so that bootstrapping is allowed. If null,
     parametric simulation is used and Gaussian error is added to the
     fitted values.}

Modified: pkg/vegan/man/vegan-internal.Rd
===================================================================
--- pkg/vegan/man/vegan-internal.Rd	2011-06-21 18:57:28 UTC (rev 1649)
+++ pkg/vegan/man/vegan-internal.Rd	2011-06-21 19:42:44 UTC (rev 1650)
@@ -69,8 +69,8 @@
   \code{permuted.index} creates permuted index of length \code{n}
   possibly stratified within \code{strata}. This is the basic \pkg{vegan}
   permutation function that should be replaced with more powerful
-  \code{permuted.index2} in the future releases of \pkg{vegan}, and all
-  new functions should use \code{\link{permuted.index2}}.
+  \code{\link{shuffle}} in the future releases of \pkg{vegan}, and all
+  new functions should use \code{\link{shuffle}}.
 
   \code{pasteCall} prints the function call so that it is nicely wrapped
   in \code{\link[utils]{Sweave}} output.