[Vegan-commits] r2050 - in branches/2.0: R inst

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

Author: jarioksa
Date: 2012-01-20 13:27:11 +0100 (Fri, 20 Jan 2012)
New Revision: 2050

Modified:
   branches/2.0/R/anova.ccabymargin.R
   branches/2.0/R/capscale.R
   branches/2.0/R/ordistep.R
   branches/2.0/inst/ChangeLog
Log:
2043,44,49: ordinations robust for zeroed effects

Modified: branches/2.0/R/anova.ccabymargin.R
===================================================================
--- branches/2.0/R/anova.ccabymargin.R	2012-01-20 12:06:30 UTC (rev 2049)
+++ branches/2.0/R/anova.ccabymargin.R	2012-01-20 12:27:11 UTC (rev 2050)
@@ -41,7 +41,8 @@
         assign(".Random.seed", seed, envir = .GlobalEnv)
     }
     ## Put RNG at the end of the longest simulation
-    assign(".Random.seed", bigseed, envir = .GlobalEnv)
+    if (bigperm > 0)
+        assign(".Random.seed", bigseed, envir = .GlobalEnv)
     rownames(sol)[1:ntrms] <- trms
     head <- attr(sol, "heading")
     head[1] <- paste(head[1], "Marginal effects of terms\n", sep="")

Modified: branches/2.0/R/capscale.R
===================================================================
--- branches/2.0/R/capscale.R	2012-01-20 12:06:30 UTC (rev 2049)
+++ branches/2.0/R/capscale.R	2012-01-20 12:27:11 UTC (rev 2050)
@@ -147,6 +147,8 @@
         rs <- rowSums(sol$CCA$centroids^2)
         sol$CCA$centroids <- sol$CCA$centroids[rs > 1e-04, , 
                                                drop = FALSE]
+        if (nrow(sol$CCA$centroids) == 0)
+            sol$CCA$centroids <- NULL
     }
     sol$call <- match.call()
     sol$terms <- terms(formula, "Condition", data = data)

Modified: branches/2.0/R/ordistep.R
===================================================================
--- branches/2.0/R/ordistep.R	2012-01-20 12:06:30 UTC (rev 2049)
+++ branches/2.0/R/ordistep.R	2012-01-20 12:27:11 UTC (rev 2050)
@@ -53,7 +53,7 @@
                 cat("\n")
                 print(aod)
             }
-            if (aod[1,5] > Pout) {
+            if (is.na(aod[1,5]) || aod[1,5] > Pout) {
                 anotab <- rbind(anotab, aod[1,])
                 change <- rownames(aod)[1]
                 object <- eval.parent(update(object, paste("~  .", change)))
@@ -77,7 +77,7 @@
                 cat("\n")
                 print(aod)
             }
-            if (aod[1,5] <= Pin) {
+            if (!is.na(aod[1,5]) && aod[1,5] <= Pin) {
                 anotab <- rbind(anotab, aod[1,])
                 change <- rownames(aod)[1]
                 object <- eval.parent(update(object, paste( "~  .",change)))

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2012-01-20 12:06:30 UTC (rev 2049)
+++ branches/2.0/inst/ChangeLog	2012-01-20 12:27:11 UTC (rev 2050)
@@ -3,7 +3,10 @@
 VEGAN RELEASE VERSIONS at http://cran.r-project.org/
 
 Version 2.0-3 (opened November 13, 2011)
-
+	
+	* merge r2049: capscale robust for zeroed centroids.
+	* merge r2044: ordistep robust for complete aliasing.
+	* merge r2043: anova.ccabymargin robust for zero effects.
 	* merge r2035,6,7: more robust plot.cca.
 	* merge r2030: resurrect old ChangeLog entries.
 	* merge r2027,28,33: tweak oecosimu printed output.