[Vegan-commits] r1244 - in pkg/vegan/inst: . doc

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

Author: jarioksa
Date: 2010-07-21 10:51:48 +0200 (Wed, 21 Jul 2010)
New Revision: 1244

Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/inst/doc/FAQ-vegan.texi
Log:
FAQ updates: non-numeric data, new functions for R2 in ordination

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2010-07-21 07:32:57 UTC (rev 1243)
+++ pkg/vegan/inst/ChangeLog	2010-07-21 08:51:48 UTC (rev 1244)
@@ -4,18 +4,21 @@
 
 Version 1.18-8 (opened July 19, 2010)
 
-	DEPENDENCE: does not suggest package 'ellipse'.
+	* DEPENDENCE: does not suggest package 'ellipse'.
 
-	plot.MOStest: uses veganCovEllipse instead of
-	ellipse:::ellipse.glm. 
+	* FAQ: new entry on negative or non-numeric data, and updates of
+	variance explained by ordination.
 
-	ordiellipse: failed to plot labels with filled polygons, since the
-	same colour was used for polygon filling and labels. Now uses
+	* plot.MOStest: uses veganCovEllipse instead of
+	ellipse:::ellipse.glm.
+
+	* ordiellipse: failed to plot labels with filled polygons, since
+	the same colour was used for polygon filling and labels. Now uses
 	ordilabel() with draw == "polygon" (but still text() with draw ==
-	"lines"). 
+	"lines").
 
-	decorana: change order of data checks so that non-numeric data is
-	detected (by rowSums()) before checking negative data entries. 
+	* decorana: change order of data checks so that non-numeric data
+	is detected (by rowSums()) before checking negative data entries.
 
 Version 1.18-7 (closed July 19, 2010)
 

Modified: pkg/vegan/inst/doc/FAQ-vegan.texi
===================================================================
--- pkg/vegan/inst/doc/FAQ-vegan.texi	2010-07-21 07:32:57 UTC (rev 1243)
+++ pkg/vegan/inst/doc/FAQ-vegan.texi	2010-07-21 08:51:48 UTC (rev 1244)
@@ -3,7 +3,7 @@
 @setfilename FAQ-vegan.info
 @settitle vegan FAQ
 @setchapternewpage on
- at set FAQ_YEAR 2008
+ at set FAQ_YEAR 2010
 @afourpaper
 @c %**end of header
 
@@ -311,6 +311,7 @@
 @chapter Ordination
 
 @menu
+* I have only numeric and positive data but vegan still complaints::  
 * Can you analyse binary or cover class data?::  
 * Why dissimilarities in vegan differ from other sources?::  
 * Zero dissimilarities in isoMDS::  
@@ -325,7 +326,17 @@
 * How to avoid cluttered ordination graphs?::  
 @end menu
 
- at node Can you analyse binary or cover class data?, Why dissimilarities in vegan differ from other sources?, Ordination, Ordination
+ at node  I have only numeric and positive data but vegan still complaints, Can you analyse binary or cover class data?, Ordination, Ordination
+ at comment  node-name,  next,  previous,  up
+ at section I have only numeric and positive data but vegan still complaints
+
+You are wrong! Computers are painfully pedantic, and if they find
+non-numeric ore negative data entries, you really have them. Check your
+data. Most common reasons for non-numeric data are that row names were
+read as a non-numeric variable instead of being used as row
+names. Another is that you had empty cells in your input data.
+
+ at node Can you analyse binary or cover class data?, Why dissimilarities in vegan differ from other sources?, I have only numeric and positive data but vegan still complaints, Ordination
 @section Can you analyse binary or cover class data?
 
 Yes. Most vegan methods can handle binary data or cover abundance data.
@@ -393,11 +404,14 @@
 @item Eigenvector methods:
 Functions @code{rda}, @code{cca} and @code{capscale} give the variation
 of conditional (partialled), constrained (canonical) and residual
-components, but you must calculate the proportions by hand. The
- at code{summary} gives the contributions of the axes. 
-Function @code{goodness} gives the same statistics for individual
-species or sites (species are unavailable with @code{capscale}). In
-addition, there is a special function 
+components, but you must calculate the proportions by hand.  Function
+ at code{eigenvals} extracts the eigenvalues, and
+ at code{eigenvals(summary(ord))} reports the proportions explained in the
+result object @code{ord}.  Function @code{RsquareAdj} gives the
+R-squared and adjusted R-squared (if available) for constrained
+components.  Function @code{goodness} gives the same statistics for
+individual species or sites (species are unavailable with
+ at code{capscale}). In addition, there is a special function
 @code{varpart} for unbiased partitioning of variance between up to four
 separate components in redundancy analysis.