[Vegan-commits] r1413 - branches/1.17/inst

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

Author: jarioksa
Date: 2010-12-13 14:45:41 +0100 (Mon, 13 Dec 2010)
New Revision: 1413

Modified:
   branches/1.17/inst/NEWS
Log:
edit release NEWS

Modified: branches/1.17/inst/NEWS
===================================================================
--- branches/1.17/inst/NEWS	2010-12-13 13:13:52 UTC (rev 1412)
+++ branches/1.17/inst/NEWS	2010-12-13 13:45:41 UTC (rev 1413)
@@ -4,34 +4,47 @@
 		       	======================
 
 	      NEW FEATURES AND BUG FIXES IN VEGAN 1.17-5				   		    	    
-    
     - anova.cca: Empty models with no constrained component have
       correct degrees of freedom. Tests 'by = "axis"' are really
       marginal for all axes (first axis used to be non-marginal to
       latter axes).
 
     - as.mlm.cca/rda, intersetcor, vif.cca: avoid bug in qr.X in R
-      2.12.0 and older to use wrong variable names in aliased models
-      (fixed also in R 2.12.1). 
+      2.12.0 which use wrong variable names in aliased models (fixed
+      also in R 2.12.1).
 
     - betadisper: plot did not allow selecting axes. Reported by Sarah
       Goslee. 
 
     - capscale: failed with NA action (reported by Nevil Amos). Total
       inertia is defined as the sum of absolute values of all
-      eigenvalues consistently with cmdscale (from R 2.12.1 but not
-      older) and other vegan functions.
+      eigenvalues consistently with cmdscale (from R 2.12.1) and other
+      vegan functions.
 
-    - cca/rda/capscale: print proportional inertia components. 
+    - cca/rda/capscale: print proportions of inertia components. 
 
     - decorana: Fortran code prints warnings of failed convergence.
+      Default plot() uses points if items have no name labels to be
+      plotted.
 
+    - deviance.cca/rda: return 0 (instead of NA) for models with no
+      constrained component.
+
     - eigenvals: uses sum of absolute values of eigenvalues in models
       that may have negative eigenvalues (cmdscale, wcmdscale,
       capscale). Can extract eigenvalues of pcnm() and cmdscale() of R
-      2.12.1 (not older). Uses zapsmall() to print near-zero
+      2.12.1. Uses zapsmall() to print near-zero
       eigenvalues.
 
+    - mantel.correlog: P-values were slightly off, because function
+      added 1 to the numerator and denumerator, although this
+      correction was already done in mantel(). (The correction was not
+      done in older version of mantel(), but the mantel.correlog() was
+      not changed after fixing mantel()).
+
+    - metaMDS: metaMDSdist() is more verbose about connectivity and
+      handles NA values in dissimiliraties.
+   
     - nestednodf: Gustavo Carvalho's new version that also implements
       a new quantitative method of Almeida-Neto & Ulrich (Env Mod
       Software, in press; 2010).
@@ -49,26 +62,25 @@
       capscale() based on adjusted R2 following the recommendations of
       Blanchet, Legendre & Borcard (Ecology 89, 2623-2632; 2008).
 
-    - ordistep: corrected a name clash when the fitted model had term
-      or item called 'mod'. Reported by Richard Telford (Bergen,
-      Norway).
+    - ordistep: correct a name clash when the fitted model had term or
+      item called 'mod'. Reported by Richard Telford (Bergen, Norway).
 
     - pcnm: returns the truncated distanced matrix with argument
       'dist.ret'.
       
     - prc: rewritten by Cajo ter Braak with a fix to scaling of
-      coefficients for full compatibility with Canoco.
+      coefficients for full compatibility with Canoco. 
 
     - procrustes: Fixed translation following the report and fix by
       Christian Dudel (Bochum, Germany). New predict() method to
       rotate 'newdata' points to the target. Graphics with plot()
       select the direction of arrows with new argument 'to.target',
-      and use ordilabel() to display the labels of with 'type = "t"'.
+      and use ordilabel() to display the labels with 'type = "t"'.
 
     - rankindex: can take a list of dissimilarity functions as the
       argument to allow the use of other dissimilarity functions than
       vegdist() of vegan.
-
+ 
     - rda/capscale: the scores() can take two scaling constants
       ('const'). One is used for species, second for WA and LC scores
       of sites. This allows using scalings of prcomp(), princomp() or
@@ -86,28 +98,15 @@
     - treedive: handles trivial cases of zero (diversity NA) or one
       species (diversity 0).
 
+    - vegdist: help page gives now binary variants of the indices
+      using designdist() notation.
+
     - vif.cca: can handle models with aliased terms.
 
     - wcmdscale: returns goodness of fit statistic (item GOF) and
       handles negative eigenvalues consistently with cmdscale() and
       capscale().
 
-    - Small changes that may not be needed, but are put here
-      temporarily for the record and consideration:
-
-      o isomap returns only axes related to positive eigenvalues
-      o mantel.correlog tried to fix an order statistic (add +1 to
-        both sides) although this was already fixed in mantel()
-        earlier.
-      o CCorA: biplot() resests parameters it sets internally. 
-      o deviance.cca/rda: now zero for models with no constrained
-        component (used to be NA).
-      o metaMDSdist is more verbose and handles NA values in
-        dissimiliraties (but isoMDS in MASS 7.3.9 does not handle 
-	them correctly). 
-      o plot.decorana switches to type = "p" if points have no
-        labels. 
-
 	      NEW FEATURES AND BUG FIXES IN VEGAN 1.17-4
 
     - MOStest: a new set of functions to implement generalized