[Vegan-commits] r1364 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2010-11-11 09:28:23 +0100 (Thu, 11 Nov 2010)
New Revision: 1364

Modified:
   pkg/vegan/R/ordiParseFormula.R
   pkg/vegan/inst/ChangeLog
Log:
na.action failed in capscale (reported by Nevil Amos)

Modified: pkg/vegan/R/ordiParseFormula.R
===================================================================
--- pkg/vegan/R/ordiParseFormula.R	2010-11-10 20:00:05 UTC (rev 1363)
+++ pkg/vegan/R/ordiParseFormula.R	2010-11-11 08:28:23 UTC (rev 1364)
@@ -8,6 +8,8 @@
     flapart <- fla <- formula <- formula(Terms, width.cutoff = 500)
     specdata <- formula[[2]]
     X <- eval.parent(specdata, n = envdepth)
+    ## X is usually a matrix, but it is "dist" with capscale():
+    X <- as.matrix(X)
     indPartial <- attr(Terms, "specials")$Condition
     zmf <- ymf <- Y <- Z <- NULL
     formula[[2]] <- NULL

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-11-10 20:00:05 UTC (rev 1363)
+++ pkg/vegan/inst/ChangeLog	2010-11-11 08:28:23 UTC (rev 1364)
@@ -4,6 +4,12 @@
 
 Version 1.18-16 (opened November 9, 20109
 
+	* capscale: failed with na.action -- fix in ordiParseFormula().
+	na.action was introduced in rev1002 (Sept 11, 2009), and then
+	ruined with a change in ordiParseFormula() in rev1007 (Sept 15,
+	2009) so it lived four days and was broken when released. The
+	problem was reported by Nevil Amos.
+
 	* SSgleason: a new SS-species-area-model.
 
 	* SSlomolino: improved starting values for 'xmid' (and