[Vegan-commits] r1608 - in pkg/vegan: R inst

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

Author: jarioksa
Date: 2011-05-27 09:59:48 +0200 (Fri, 27 May 2011)
New Revision: 1608

Modified:
   pkg/vegan/R/capscale.R
   pkg/vegan/inst/ChangeLog
Log:
make species scores NA if no 'comm' was defined in capscale

Modified: pkg/vegan/R/capscale.R
===================================================================
--- pkg/vegan/R/capscale.R	2011-05-26 13:28:31 UTC (rev 1607)
+++ pkg/vegan/R/capscale.R	2011-05-27 07:59:48 UTC (rev 1608)
@@ -128,6 +128,11 @@
             sol$CA$v <- sweep(sol$CA$v.eig, 2, sqrt(sol$CA$eig[1:poseig]), 
                               "/")
         }
+    } else {
+        ## input data were dissimilarities, and no 'comm' defined:
+        ## species scores make no sense and are made NA
+        sol$CA$v.eig <- sol$CA$v <- sol$CCA$v <- sol$CCA$v.eig <- NA
+        sol$colsum <- NA
     }
     if (!is.null(sol$CCA)) 
         sol$CCA$centroids <- centroids.cca(sol$CCA$wa, d$modelframe)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2011-05-26 13:28:31 UTC (rev 1607)
+++ pkg/vegan/inst/ChangeLog	2011-05-27 07:59:48 UTC (rev 1608)
@@ -4,6 +4,11 @@
 
 Version 1.18-31 (opened May 26, 2011)
 
+	* capscale: species scores will be NA if input data were
+	dissimilarities and no 'comm' was given. (BTW, if input data were
+	dissimilarities, update() will fail! -- I don't know why, but
+	anybody can fix this.)
+
 	* oecosimu: reverted r1557 of version 1.18-26, or splitting tied
 	values. This was introduced because Chase et al. (Ecosphere 2011,
 	http://www.esajournals.org/doi/pdf/10.1890/ES10-00117.1) used this