[Vegan-commits] r1089 - branches/1.17/inst

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

Author: jarioksa
Date: 2010-01-02 16:18:54 +0100 (Sat, 02 Jan 2010)
New Revision: 1089

Modified:
   branches/1.17/inst/NEWS
Log:
update NEWS in branches/1.17

Modified: branches/1.17/inst/NEWS
===================================================================
--- branches/1.17/inst/NEWS	2010-01-02 14:01:15 UTC (rev 1088)
+++ branches/1.17/inst/NEWS	2010-01-02 15:18:54 UTC (rev 1089)
@@ -3,6 +3,87 @@
 			VEGAN RELEASE VERSIONS 
 		       	======================
 
+	       CHANGES AND NEW FEATURES IN VEGAN 1.17-0
+
+    - adipart: new function for additive partitioning of
+      diversity. New function hiersimu() performs hierarchical null
+      model testing for evaluating the adipart() components of alpha,
+      beta and gamma diversity.
+
+    - as.ts.oecosimu: 
+
+    - calibrate: calibrate is now a generic function with a new method
+      calibrate.ordisurf() in addition to the old calibrate.cca. These
+      find the estimates of environmental variables from ordination.
+
+    - model.matrix.cca & model.frame.cca: new functions to reconstruct
+      the model frame and model matrix of constraints used in
+      ordination methods cca(), rda() and capscale().
+
+    - MOStest: Mithcell-Olds & Shaw test to evaluate the probability
+      that a quadratic response has its extreme value (top or bottom)
+      at the given interval. 
+
+    - multipart: multiplicative partitioning of diversity into alpha,
+      beta and gamma components.
+
+    - ordistep: stepwise selection of terms in constrained ordination
+      (cca, rda and capscale) using permutation tests instead of
+      pseudo-AIC that is used by the standard step() function.
+
+    - pcnm: finds weighted principal coordinates of neighbour matrix
+      (PCNM) from distances between points. These are typically used
+      for spatial filtering in constrained ordination. The function
+      does weighted analysis and can therefore produce PCNM for
+      correspondence analysis in addition to PCA and RDA.
+
+    - simulate.cca & simulate.cca: simulate the community (response)
+      data from the result of cca() or rda() under alternative
+      hypothesis. Error is added to the fitted values from
+      ordination. The function uses either Gaussian error or permutes
+      residuals and adds these to fitted values. Function is intended
+      for advanced users.
+
+    - spandepth: a new function to find the depth of each node in the
+      minimum spanning tree produced by spantree(). 
+
+    - treedist: undocumented (alias in treedive.Rd) --- REMOVE!
+
+    - alias.cca: gained argument names.only.
+
+    - betadisper: can use spatial medians which are the recommended
+      method.
+
+    - decostand & vegdist: new transformation 'log' which implements
+      Marti Anderson's scaling log(x) + 1 for x>0 (which is not at all
+      the same as log(x+1)), and vegdist has alternative Gower
+      function that skips double zeros. Together these implement
+      the "modified Gower" distance of Anderson et al. (Ecology
+      Letters 9, 683-693; 2006).
+ 
+    - metaMDSrotate: a new function to rotate metaMDS so that first
+      axis is parallel to an environmental variable. (KEEP or DROP?)
+
+    - msoplot: uses standard legend. 
+
+    - nesteddisc: new method that tries to find the smallest possible
+      value of the statistic in tied data. Slow, but fixes the
+      problems of the published method.
+
+    - oecosimu: rewritten to handle a simple case of quantitative null
+      models. Gained keyword 'alternative' for "two-sided", or "less"
+      and "greater" one-sided tests. More robust with degenerate
+      solutions. The 'method' can now be a user-supplied function. 
+
+    - contribdiv: gained a plot method. 
+
+    - rarefy: failed with one site and many sample sizes like
+      rarefy(rpois(10, 2), sample=2:3).
+
+    - meandist: plot can draw histograms as an alternative to
+      dendrograms. 
+
+
 		       CHANGES IN VEGAN 1.15-4
 
     - Changed package dependence: vegan does not depend on 'ellipse'.