[Vegan-commits] r1406 - branches/1.17/inst

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

Author: jarioksa
Date: 2010-12-09 21:44:58 +0100 (Thu, 09 Dec 2010)
New Revision: 1406

Modified:
   branches/1.17/inst/NEWS
Log:
not now & other edits

Modified: branches/1.17/inst/NEWS
===================================================================
--- branches/1.17/inst/NEWS	2010-12-09 14:08:15 UTC (rev 1405)
+++ branches/1.17/inst/NEWS	2010-12-09 20:44:58 UTC (rev 1406)
@@ -5,32 +5,31 @@
 
 	      NEW FEATURES AND BUG FIXES IN VEGAN 1.17-5				   		    	    
     
-    - anova.cca: Empty models with no constrained component have now
-      correct degrees of freedom. Tests 'by = "axis"' are now really
+    - 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
-      (fix also in R 2.12.1). 
+      (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 now defined as the sum of absolute values of all
+      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.
 
-    - cca/rda/capscale: print now proportional inertia components. 
+    - cca/rda/capscale: print proportional inertia components. 
 
-    - decorana: Fortran code prints now warnings of failed
-      convergence. 
+    - decorana: Fortran code prints warnings of failed convergence.
 
     - eigenvals: uses sum of absolute values of eigenvalues in models
       that may have negative eigenvalues (cmdscale, wcmdscale,
-      capscale). Can now extract eigenvalues of pcnm() and cmdscale()
-      of R 2.12.1 (not older). Uses zapsmall() to print near-zero
+      capscale). Can extract eigenvalues of pcnm() and cmdscale() of R
+      2.12.1 (not older). Uses zapsmall() to print near-zero
       eigenvalues.
 
     - nestednodf: Gustavo Carvalho's new version that also implements
@@ -39,11 +38,10 @@
 
     - oecosimu: takes care that the statistic is evalutaed with binary
       data when null models are binary (regression introduced in vegan
-      1.17-0). Can now handle NA values in permutations (as na.rm =
-      TRUE). 
+      1.17-0). Can handle NA values in permutations (as na.rm = TRUE).
 
     - ordilabel: gained new argument 'col' to set the text colour of
-      the labels separately from 'border', Function ordiellipse() uses
+      the labels separately from 'border'. Function ordiellipse() uses
       this in filled polygons to set the colour of labels to that of
       borders or foreground instead of the colour of the fill.
 
@@ -51,28 +49,27 @@
       capscale() based on adjusted R2 following the recommendations of
       Blanchet, Legendre & Borcard (Ecology 89, 2623-2632; 2008).
 
-    - ordistep: corrected a name clash if the fitted model had term or
-      item called 'mod'. Reported by Richard Telford (Bergen,
-      Norway). 
+    - ordistep: corrected a name clash when the fitted model had term
+      or item called 'mod'. Reported by Richard Telford (Bergen,
+      Norway).
 
-    - pcnm: returns now the truncated distanced matrix with argument
-      'dist.ret'. 
+    - 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.
 
     - procrustes: Fixed translation following the report and fix by
       Christian Dudel (Bochum, Germany). New predict() method to
-      rotate new points to the target. Graphics with plot() can now
+      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 points with 'type =
-      "t"'.
+      and use ordilabel() to display the labels of with 'type = "t"'.
 
-    - rankindex: can now take a list of dissimilarity functions as the
+    - rankindex: can take a list of dissimilarity functions as the
       argument to allow the use of other dissimilarity functions than
-      vegdist() of vegan. 
+      vegdist() of vegan.
 
-    - rda/capscale: the scores() can now take two scaling constant
+    - 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
       Canoco like documented in the design decisions vignette.
@@ -80,20 +77,20 @@
     - swan: disconnected data caused infinite loop. Now zeros are left
       to the result with disconnected data.
 
-    - treedist: can now handle empty or one-node trees. Gained new
+    - treedist: can handle empty or one-node trees. Gained new
       argument 'relative' (defaults TRUE): if FALSE, finds raw
-      dissimilarities of tree heights.  Help page now tells that
-      relative tree distances are in range 0..2 instead of 0..1, since
+      dissimilarities of tree heights.  Help page tells that relative
+      tree distances are in range 0..2 instead of 0..1, since
       combining two trees may add a new common root.
 
     - treedive: handles trivial cases of zero (diversity NA) or one
       species (diversity 0).
 
-    - vif.cca: can now handle models with aliased terms.
+    - vif.cca: can handle models with aliased terms.
 
-    - wcmdscale: returns now goodness of fit statistic (item GOF) and
+    - wcmdscale: returns goodness of fit statistic (item GOF) and
       handles negative eigenvalues consistently with cmdscale() and
-      capscale(). 
+      capscale().
 
     - Small changes that may not be needed, but are put here
       temporarily for the record and consideration: