[Vegan-commits] r2100 - pkg/vegan/R

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

Author: jarioksa
Date: 2012-02-20 20:18:39 +0100 (Mon, 20 Feb 2012)
New Revision: 2100

Modified:
   pkg/vegan/R/simper.R
Log:
fix print.summary.simper

Modified: pkg/vegan/R/simper.R
===================================================================
--- pkg/vegan/R/simper.R	2012-02-19 19:33:15 UTC (rev 2099)
+++ pkg/vegan/R/simper.R	2012-02-20 19:18:39 UTC (rev 2100)
@@ -117,7 +117,7 @@
     function(x, digits = attr(x, "digits"), ...)
 {
     signif.stars <- getOption("show.signif.stars") && attr(x, "permutations") > 0
-    starprint <- function(z, ...) {
+    starprint <- function(z) {
         if (signif.stars && any(z$p < 0.1)) {
             stars <- symnum(z$p, cutpoints = c(0, 0.001, 0.01, 0.05, 0.1, 1),
                             symbols = c("***", "**", "*", ".", " "))
@@ -125,8 +125,11 @@
         }
         z
     }
-    out <- lapply(x, starprint, digits = digits, ...)
-    print(out)
+    out <- lapply(x, starprint)
+    for (nm in names(out)) {
+        cat("\nContrast:", nm, "\n\n")
+        print(out[[nm]], digits = digits, ...)
+    }
     if (signif.stars && any(sapply(x, function(z) z$p) < 0.1)) {
         leg <- attr(symnum(1, cutpoints = c(0, 0.001, 0.01, 0.05, 0.1, 1),
                             symbols = c("***", "**", "*", ".", " ")), "legend")
@@ -136,4 +139,3 @@
         cat("P-values based on", np, "permutations\n")
     invisible(x)
 }
-