[Vegan-commits] r2791 - pkg/vegan/R

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

Author: jarioksa
Date: 2013-12-01 18:07:03 +0100 (Sun, 01 Dec 2013)
New Revision: 2791

Modified:
   pkg/vegan/R/anovacca.R
   pkg/vegan/R/howHead.R
Log:
howHead returns no. of permutations, and we use that in anova display instead of N.perm column

Modified: pkg/vegan/R/anovacca.R
===================================================================
--- pkg/vegan/R/anovacca.R	2013-12-01 16:44:30 UTC (rev 2790)
+++ pkg/vegan/R/anovacca.R	2013-12-01 17:07:03 UTC (rev 2791)
@@ -77,14 +77,12 @@
     Fval <- c(tst$F.0, NA)
     Pval <- (sum(tst$F.perm >= tst$F.0) + 1)/(tst$nperm + 1)
     Pval <- c(Pval, NA)
-    nperm <- c(tst$nperm, NA)
-    table <- data.frame(tst$df, tst$chi, Fval, nperm, Pval)
+    table <- data.frame(tst$df, tst$chi, Fval, Pval)
     is.rda <- inherits(object, "rda")
     colnames(table) <- c("Df", ifelse(is.rda, "Var", "Chisq"), 
-                         "F", "N.Perm", "Pr(>F)")
+                         "F", "Pr(>F)")
     head <- paste0("Permutation test for ", tst$method, " under ", 
-                  tst$model, " model\n", howHead(control),
-                   "Number of permutations: ", tst$nperm, "\n")
+                  tst$model, " model\n", howHead(control))
     mod <- paste("Model:", c(object$call))
     structure(table, heading = c(head, mod), Random.seed = seed,
               control = control,

Modified: pkg/vegan/R/howHead.R
===================================================================
--- pkg/vegan/R/howHead.R	2013-12-01 16:44:30 UTC (rev 2790)
+++ pkg/vegan/R/howHead.R	2013-12-01 17:07:03 UTC (rev 2791)
@@ -46,6 +46,6 @@
         head <- paste0(head, sprintf(ngettext(nc, " %d column",
                                              " %d columns"), nc))
     }
-    head <- paste0(head, "\n")
+    head <- paste0(head, "\nNumber of permutations: ", getNperm(x),  "\n")
     head
 }