[Vegan-commits] r810 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2009-04-21 15:08:47 +0200 (Tue, 21 Apr 2009)
New Revision: 810

Modified:
   pkg/vegan/R/ordilattice.getEnvfit.R
   pkg/vegan/R/ordixyplot.R
   pkg/vegan/inst/ChangeLog
Log:
ordixyplot failed in constrained ordination -- broken in r108 in Nov 2007

Modified: pkg/vegan/R/ordilattice.getEnvfit.R
===================================================================
--- pkg/vegan/R/ordilattice.getEnvfit.R	2009-04-21 09:54:57 UTC (rev 809)
+++ pkg/vegan/R/ordilattice.getEnvfit.R	2009-04-21 13:08:47 UTC (rev 810)
@@ -1,7 +1,7 @@
 `ordilattice.getEnvfit` <-
     function(formula, object, envfit, choices = 1:3,  ...)
 {
-    if (!missing(envfit))
+    if (!missing(envfit) && !is.null(envfit))
         object <- envfit
     bp <- scores(object, display = "bp", choices = choices)
     cn <- scores(object, display = "cn",  choices = choices)

Modified: pkg/vegan/R/ordixyplot.R
===================================================================
--- pkg/vegan/R/ordixyplot.R	2009-04-21 09:54:57 UTC (rev 809)
+++ pkg/vegan/R/ordixyplot.R	2009-04-21 13:08:47 UTC (rev 810)
@@ -15,6 +15,8 @@
       formula <- as.formula(paste(v[2], "~", v[1]))
     }
   if ("biplot" %in% type && (!is.null(x$CCA) || !missing(envfit))) {
+    if (missing(envfit))
+      envfit <- NULL
     env <- localOrdilattice.getEnvfit(formula, x, envfit, choices, ...)
     if (!is.null(env$arrows)) {
       mul <- apply(p[,colnames(env$arrows)], 2, range)/apply(env$arrows, 2, range)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-04-21 09:54:57 UTC (rev 809)
+++ pkg/vegan/inst/ChangeLog	2009-04-21 13:08:47 UTC (rev 810)
@@ -4,6 +4,9 @@
 
 Version 1.16-18 (opened April 21, 2009)
 
+	* ordixyplot: failed in constrained ordination (cca, rda,
+	capscale). Was broken in rev108 on Nov 7, 2007(!). 
+
 	* RsquareAdj: defined as generic function. The old RsquareAdj is
 	now the "default" method, and there are specific methods for
 	"rda", "cca" (= NA), "lm" and "glm" objects. Not yet documented,