[Vegan-commits] r798 - branches/1.15/inst

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

Author: jarioksa
Date: 2009-04-07 08:05:49 +0200 (Tue, 07 Apr 2009)
New Revision: 798

Modified:
   branches/1.15/inst/NEWS
Log:
NEWS about upcoming release 1.15-2

Modified: branches/1.15/inst/NEWS
===================================================================
--- branches/1.15/inst/NEWS	2009-04-07 04:46:41 UTC (rev 797)
+++ branches/1.15/inst/NEWS	2009-04-07 06:05:49 UTC (rev 798)
@@ -3,6 +3,82 @@
 			VEGAN RELEASE VERSIONS 
 		       	======================
 
+		       CHANGES IN VEGAN 1.15-2
+    
+    - adonis: adds one to numerator and denominator of permutation
+      tests, the default number of iterations was raised from 5 to
+      999, and the result object got a 'terms' component.
+
+    - anova.cca: anova(..., by = "axis") gained new keyword 'cutoff'
+      to stop permutation tests after exceeding the given cut-off
+      level of significance. The second term of anova(..., by =
+      "margin") used different random numbers than other terms.
+    
+    - beals: Completely rewritten by Miquel de Caceres.  Knows now
+      also the cross validated version of Beals smoothing and other
+      choices described by De Caceres & Legendre, Oecologia 156,
+      657-669; 2008.
+
+    - cca/rda: cleaner output of summary() in unconstrained models.
+
+    - commsimulator: simulated result retains original row and column
+      names. 
+
+    - betadisper: handles missing values both in dissimilarities and
+      grouping. 
+
+    - contribdiv: new function for contribution diversity (Lu et al.,
+      Basic and Applied Ecology 8, 1-12; 2007).
+
+    - decostand: gained dots in argument list, so that
+      stressplot(metaMDS(x, dist = "gower", trymax = 40)) works.
+
+    - dispindmorisita: new function for the Morisita index of
+      dispersion. See Krebs, Ecological Methodology; 1999.
+
+    - kendall.global and kendall.post: new functions for Kendall's
+      coefficient of concordance. In ecology these can be used to
+      identify significant species associations (Legendre, J Agric
+      Biol Environm Stat 10, 226-245; 2005).
+
+    - metaMDS: more robust with distances like Euclidean and Manhattan
+      which have no upper limit. The stepacross works correctly for
+      these, but gives a warning that stepacross may not be
+      sensible. There is a better heuristics to avoid half-change
+      scaling with these indices. The 'halfchange' argument is now
+      honoured when given in metaMDS() call.
+
+    - mrpp: returns within-class dissimilarities. Evaluates
+      classification strength (Van Sickle, Biological and
+      Environmental Statistics, 2, 370-388; 1997) if weight.type = 3
+      was used.
+
+    - ordirgl: no more superfluous warnings with type = "t". 
+
+    - ordisurf: gained an argument 'bubble' to draw bubble plots, or
+      vary point sizes according the value of the observed variable.
+      The (invisible) return object now has an item 'grid' for the
+      fitted value and grid values.
+
+    - nestednodf: new nestedness function of overlap and decreasing
+      fill (Almeida-Neto et al., Oikos 117, 1227-1239; 2008). Coding
+      by Gustava Carvalho.
+
+    - orditkplot: can produce TIFF graphics, if the R installation has
+      this capability.
+
+    - procrustes: new text() function.
+
+    - radfit: broken-stick model (function rad.null) failed with
+      Gaussian and Gamma error families. The plot.radfit command
+      gains argument log = "y", which allows using arithmetic scales
+      or double-log scales where Zipf model is a straight line.
+
+    - spantree: retains names and uses labels in plot.
+
+    - help files updated, and do not raise errors or warnings with the
+      Rd parser version 2 in R 2.9.0.
+
 		       CHANGES IN VEGAN 1.15-1
 
     - betadisper and related functions now work when the 'group'