[Vegan-commits] r970 - in branches/1.15: . inst

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

Author: jarioksa
Date: 2009-09-01 08:33:03 +0200 (Tue, 01 Sep 2009)
New Revision: 970

Modified:
   branches/1.15/DESCRIPTION
   branches/1.15/inst/ChangeLog
   branches/1.15/inst/NEWS
Log:
packing up 1.15-4 for the release to CRAN

Modified: branches/1.15/DESCRIPTION
===================================================================
--- branches/1.15/DESCRIPTION	2009-09-01 05:50:20 UTC (rev 969)
+++ branches/1.15/DESCRIPTION	2009-09-01 06:33:03 UTC (rev 970)
@@ -1,7 +1,7 @@
 Package: vegan
 Title: Community Ecology Package
 Version: 1.15-4
-Date: August 22, 2009
+Date: September 1, 2009
 Author: Jari Oksanen, Roeland Kindt, Pierre Legendre, Bob O'Hara, Gavin L. Simpson, 
    Peter Solymos, M. Henry H. Stevens, Helene Wagner  
 Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>

Modified: branches/1.15/inst/ChangeLog
===================================================================
--- branches/1.15/inst/ChangeLog	2009-09-01 05:50:20 UTC (rev 969)
+++ branches/1.15/inst/ChangeLog	2009-09-01 06:33:03 UTC (rev 970)
@@ -3,7 +3,7 @@
 
 VEGAN STABLE VERSIONS
 
-Version 1.15-4 (working from August 20, 2009)
+Version 1.15-4 (released September 1, 2009)
 
 	* merged r874: rrarefy.
 

Modified: branches/1.15/inst/NEWS
===================================================================
--- branches/1.15/inst/NEWS	2009-09-01 05:50:20 UTC (rev 969)
+++ branches/1.15/inst/NEWS	2009-09-01 06:33:03 UTC (rev 970)
@@ -3,25 +3,21 @@
 			VEGAN RELEASE VERSIONS 
 		       	======================
 
-			  CHANGES IN 1.15-4
+		       CHANGES IN VEGAN 1.15-4
 
     - Changed package dependence: vegan does not depend on 'ellipse'.
 
-    - anosim: user interface identical to 'mrpp'. Most importantly,
-      accepts now data matrix and finds dissimilarities within the
-      function instead of accepting only dissimilarities.
+    - anosim: user interface identical to 'mrpp' -- accepts now data
+      matrix and finds dissimilarities within the function instead of
+      accepting only dissimilarities.
 
-    - betadisper: fix removing zero eigenvalues with non-Euclidean
+    - betadisper: fix removal of zero eigenvalues with non-Euclidean
       distances. This may change the results slightly, but in most
       cases the effects are minor or none.
 
     - capscale: has now 'fitted' and 'residual' methods, and 'predict'
       works with 'type = "response"'. These return dissimilarities
-      that produce the same ordination as the original data. However,
-      with non-Euclidean distances the dissimilarities of constrained
-      and unconstrained components are not additive as the imaginary
-      axes with negative eigenvalues are not used in estimating the
-      unconstrained dissimilarities.
+      that produce the same ordination as the original data. 
 
     - indpower: new function to find the indicator power of species to
       predict presence of other species (Halme et al., Conservation
@@ -32,15 +28,14 @@
       correlograms (Legendre & Legendre, Numerical Ecology, section
       13.1.5; 1998). 
 
-    - metaMDS: accepts user-supplied dissimilarities instead of
-      calculating dissimilarities in the function. Species scores,
+    - metaMDS: accepts user-supplied dissimilarities. Species scores,
       data transformation, step-across and half-change scaling are
       unavailable with user-supplied dissimilarities, but random
       starts, PC rotation and scaling to original range of input
-      dissimilarities work. 
+      dissimilarities work.
 
     - nestedtemp: row and column labels can be turned on/off
-      independently. 
+      independently in plot.
 
     - ordihull & ordiellipse: new argument 'label' to plot group names
       for hulls or ellipses. Return (invisibly) the data for plotted
@@ -49,9 +44,7 @@
       centre data for ellipses. New 'summary' methods find the centres
       and areas of plotted hulls or ellipses. Argument 'draw' has new
       option "none" that suppresses all drawing so that only the data
-      for summary can be extracted without plotting. This feature was
-      added so that it is easier to develop permutation tests for
-      hulls and ellipses
+      for summary can be extracted without plotting.
 
     - orditorp: works with reversed axes, like with 'xlim = c(3, -3)'.
 
@@ -67,17 +60,13 @@
       function. In particular, this concerned rda where 'scaling' and
       'const' arguments could not be used within these functions.
 
-    - radfit: has new function 'radlattice' for a lattice alternative
-      to simple plot function for single site.
+    - radfit: new function 'radlattice' for a lattice plots of fitted
+      models for single site.
 
     - rrarefy: a new function to generate random rarefied communities.
 
-    - RsquareAdj: now a generic function with special cases to 'rda',
-      'cca', 'lm' and 'glm'. The specific functions directly estimate
-      the adjusted R-squared from the ordination or regression result
-      of the previous methods, and the default function estimates the
-      adjusted R-squared from the unadjusted R-squared, number of
-      model df, and number of observations. 
+    - RsquareAdj: now a generic function to find adjusted R squared
+      with special cases to 'rda', 'cca', 'lm' and 'glm'. 
 
     - summary.cca: cleaner output.