[Vegan-commits] r846 - pkg/vegan/R

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

Author: jarioksa
Date: 2009-06-01 10:30:55 +0200 (Mon, 01 Jun 2009)
New Revision: 846

Modified:
   pkg/vegan/R/adonis.R
   pkg/vegan/R/anosim.R
   pkg/vegan/R/factorfit.R
   pkg/vegan/R/mantel.R
   pkg/vegan/R/vectorfit.R
Log:
remove patronizing if(permutations %% 100 == 0) permutations <- permutations - 1

Modified: pkg/vegan/R/adonis.R
===================================================================
--- pkg/vegan/R/adonis.R	2009-05-31 17:59:08 UTC (rev 845)
+++ pkg/vegan/R/adonis.R	2009-06-01 08:30:55 UTC (rev 846)
@@ -8,11 +8,6 @@
     ## variables.  data is the data frame from which A, B, and C would
     ## be drawn.
     TOL <- 1e-7
-    ## Set no. of permutations to x-1 if x is an even hundred
-    if (permutations %% 100 == 0) {
-        permutations <- permutations - 1
-        warning("Setting no. of permutations to ", permutations)
-    }
     Terms <- terms(formula, data = data)
     lhs <- formula[[2]]
     lhs <- eval(lhs, data, parent.frame()) # to force evaluation 

Modified: pkg/vegan/R/anosim.R
===================================================================
--- pkg/vegan/R/anosim.R	2009-05-31 17:59:08 UTC (rev 845)
+++ pkg/vegan/R/anosim.R	2009-06-01 08:30:55 UTC (rev 846)
@@ -28,8 +28,6 @@
     cl.vec[within] <- levels(grouping)[grouping[take]]
     cl.vec <- factor(cl.vec, levels = c("Between", levels(grouping)))
     if (permutations) {
-        if (permutations %% 100 == 0)
-            permutations <- permutations - 1
         perm <- rep(0, permutations)
         for (i in 1:permutations) {
             take <- permuted.index(N, strata)

Modified: pkg/vegan/R/factorfit.R
===================================================================
--- pkg/vegan/R/factorfit.R	2009-05-31 17:59:08 UTC (rev 845)
+++ pkg/vegan/R/factorfit.R	2009-06-01 08:30:55 UTC (rev 846)
@@ -33,8 +33,6 @@
         r.this <- 1 - invar/totvar
         r <- c(r, r.this)
         if (permutations) {
-            if (permutations %% 100 == 0)
-                permutations <- permutations - 1
             A <- as.integer(P[[i]])
             NL <- nlevels(P[[i]])
             tmp <- rep(NA, permutations)

Modified: pkg/vegan/R/mantel.R
===================================================================
--- pkg/vegan/R/mantel.R	2009-05-31 17:59:08 UTC (rev 845)
+++ pkg/vegan/R/mantel.R	2009-06-01 08:30:55 UTC (rev 846)
@@ -8,8 +8,6 @@
     statistic <- as.numeric(tmp$estimate)
     variant <- tmp$method
     if (permutations) {
-        if (permutations %% 100 == 0)
-            permutatoins <- permutations - 1
         N <- attributes(xdis)$Size
         perm <- rep(0, permutations)
         for (i in 1:permutations) {

Modified: pkg/vegan/R/vectorfit.R
===================================================================
--- pkg/vegan/R/vectorfit.R	2009-05-31 17:59:08 UTC (rev 845)
+++ pkg/vegan/R/vectorfit.R	2009-06-01 08:30:55 UTC (rev 846)
@@ -29,8 +29,6 @@
         colnames(heads) <- paste("Dim", 1:nc, sep = "")
     else colnames(heads) <- colnames(X)
     if (permutations) {
-        if (permutations %% 100 == 0)
-            permutations <- permutations - 1
         nr <- nrow(X)
         permstore <- matrix(nrow = permutations, ncol = ncol(P))
         for (i in 1:permutations) {