[Vegan-commits] r865 - branches/1.15/inst

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

Author: jarioksa
Date: 2009-06-11 18:27:09 +0200 (Thu, 11 Jun 2009)
New Revision: 865

Modified:
   branches/1.15/inst/NEWS
Log:
NEWS about coming 1.15-3 release

Modified: branches/1.15/inst/NEWS
===================================================================
--- branches/1.15/inst/NEWS	2009-06-10 20:12:07 UTC (rev 864)
+++ branches/1.15/inst/NEWS	2009-06-11 16:27:09 UTC (rev 865)
@@ -3,6 +3,62 @@
 			VEGAN RELEASE VERSIONS 
 		       	======================
 
+
+			CHANGES IN VEGAN 1.15-3
+
+    - anosim, mantel, mrpp, protest, envfit: did not include the
+      observed statistic among permutations. Functions adonis and
+      permutest.cca did this correctly, but did not print results
+      neatly. 
+      
+    - anova.cca: name clash if data were indexed with 'i'.
+
+    - capscale: fixed handling of negative eigenvalues with
+      non-Euclidean distances. The negative eigenvalues are subtracted
+      from the total and unconstrained inertia, and the rank of the
+      unconstrained component is the number of all non-zero
+      eigenvalues, including negative ones. The procedure is based on
+      Gower, Linear Algebra and its Applications 67, 81-97 (1985).
+      New argument 'sqrt.dist' takes square root of the internally
+      calculated dissimilarities which avoids negative eigenvalues
+      with some indices, such as vegan Jaccard and Bray-Curtis.
+
+    - eigenvals: a new function to extract eigenvalues from rda, cca,
+      capscale, wcmdscale, prcomp, princomp, svd or eigen. If the
+      result object contains squareroots of eigenvalues, they are
+      squared. The summary method also finds proportions and
+      cumulative proportions explained. Function summary.cca now uses
+      this to display eigenvalues.
+
+    - kendall.global: could get wrong counts of ties in large data
+      sets. 
+
+    - meandist: new sister function to 'mrpp' that finds mean
+      within-group and between-group dissimilarities. The summary
+      function finds overall averages of these, and returns all three
+      MRPP variants plus classification strength. The plot method
+      draws a dendrogram based on the mean dissimilarity matrix, with
+      leaves hanging to within-groups dissimilarity. The functions
+      follow Sickle, J. Agric. Biol. Envir. Stat. 2, 370-388 (1997). 
+
+    - ordisurf: fits now linear or quadratic trend surfaces if 
+      'knots' argument is set to 0, 1, or 2. 
+
+    - orditkplot: copes with NA and NaN scores.
+
+    - ordixyplot: mixed x and y axes for biplot arrows and class
+      centroids. Function failed in constrained ordination. 
+
+    - tsallis: gained argument 'hill' to find results analogous to
+      Hill numbers in renyi(), or the species number equivalents of
+      indices.  
+
+    - wcmdscale: removes now zero eigenvalues instead of the last
+      eigenvalue. The bug was copied from cmdscale(), which still has
+      the bug in R 2.9.0 (plus another that was not copied to
+      wcmdscale).
+
+
 		       CHANGES IN VEGAN 1.15-2
     
     - adonis: adds one to numerator and denominator of permutation