[Vegan-commits] r1300 - in pkg/vegan/inst: . doc

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

Author: jarioksa
Date: 2010-09-09 10:29:24 +0200 (Thu, 09 Sep 2010)
New Revision: 1300

Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/inst/doc/FAQ-vegan.texi
Log:
FAQ on ade4:cca name clash

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-09-08 10:13:55 UTC (rev 1299)
+++ pkg/vegan/inst/ChangeLog	2010-09-09 08:29:24 UTC (rev 1300)
@@ -7,6 +7,9 @@
 	* diversity: example says that rarefy(x, 2) - 1 is the same as
 	unbiased Simpson of a true random sample of Hurlbert (1971,
 	eq. 5). Added after several wishes to have this function.
+
+	* FAQ: entry on ade4:cca name clash triggered by an invalid bug
+	report #1066 and queries in r-sig-ecology.
 	
 Version 1.18-10 (closed August 31, 2010)
 

Modified: pkg/vegan/inst/doc/FAQ-vegan.texi
===================================================================
--- pkg/vegan/inst/doc/FAQ-vegan.texi	2010-09-08 10:13:55 UTC (rev 1299)
+++ pkg/vegan/inst/doc/FAQ-vegan.texi	2010-09-09 08:29:24 UTC (rev 1300)
@@ -313,6 +313,7 @@
 * Can you analyse binary or cover class data?::  
 * Why dissimilarities in vegan differ from other sources?::  
 * Zero dissimilarities in isoMDS::  
+* cca fails with ``data.frame expected'' or ``"site.env" missing''::  
 * Variance explained by ordination axes::  
 * Is it possible to have passive points in ordination?::  
 * Class variables and dummies::  
@@ -357,7 +358,7 @@
 Another reason may be that indices indeed are defined differently,
 because people use same names for different indices.
 
- at node Zero dissimilarities in isoMDS, Variance explained by ordination axes, Why dissimilarities in vegan differ from other sources?, Ordination
+ at node Zero dissimilarities in isoMDS, cca fails with ``data.frame expected'' or ``"site.env" missing'', Why dissimilarities in vegan differ from other sources?, Ordination
 @section Zero dissimilarities in isoMDS
 
 You can use argument @code{zerodist = "add"} in @code{metaMDS} or
@@ -370,7 +371,17 @@
 zero dissimilarity, and you have to resort to the kluge (or work
 harder with your data).
 
- at node Variance explained by ordination axes, Is it possible to have passive points in ordination?, Zero dissimilarities in isoMDS, Ordination
+ at node cca fails with ``data.frame expected'' or ``"site.env" missing'', Variance explained by ordination axes, Zero dissimilarities in isoMDS, Ordination
+ at section cca fails with ``data.frame expected'' or ``"site.env" missing''
+
+This is not a vegan error message, but it comes from the @code{cca}
+function in the ade4 package. There is an unfortunate name clash, and if
+you have loaded ade4 after vegan, the ade4 version of @code{cca} will
+mask the vegan version. You can use the vegan version using command
+ at code{vegan:cca()}. If you do not need package ade4, you can detach it
+with command @code{detach(package:ade4)}. 
+
+ at node Variance explained by ordination axes, Is it possible to have passive points in ordination?, cca fails with ``data.frame expected'' or ``"site.env" missing'', Ordination
 @section Variance explained by ordination axes.
 
 In general, vegan does not directly give any statistics on the