[Vegan-commits] r2147 - pkg/vegan/inst

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

Author: jarioksa
Date: 2012-04-24 12:12:45 +0200 (Tue, 24 Apr 2012)
New Revision: 2147

Modified:
   pkg/vegan/inst/ChangeLog
Log:
reorder and edit ChangeLog

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2012-04-24 10:12:20 UTC (rev 2146)
+++ pkg/vegan/inst/ChangeLog	2012-04-24 10:12:45 UTC (rev 2147)
@@ -2,31 +2,10 @@
 
 VEGAN DEVEL VERSIONS at http://r-forge.r-project.org/
 
+Version 2.1-15 (opened April 24, 2012)
+	
 Version 2.1-14 (opened March 9, 2012)
 
-	* multipart and hiersimu: permutation tests assumed constant 
-	full gamma diversity in all simulations even when the null model 
-	could produce variable gamma diversities. The default method 
-	("r2dtable") had constant gamma diversity.
-
-	* adipart, multipart, hiersimu: these are now generic functions
-	with default and formula methods. The formula method is 
-	identical to the previous function, the default method
-	can take two matrices as input, but the second argument
-	describing the hierarchy can be missing. In this case
-	a trivial two-level hierarchy will be assumed (each row
-	is a seperate group, all rows are in same group).
-
-	* scoverage: new function for sample coverage based 
-	correction for calculation of relative frequencies in count
-	community matrices (Good 1953, Biometrika 40, 237--264).
-
-	* clamtest: wrongly used frequencies instead of the counts
-	when calculating sample coverage to test x < coverage.limit. 
-	No detectable differences were produced when rerunning 
-	examples from Chazdon et al. 2011 (Ecology, 92, 1332--1343)
-	and vegan help page.
-
 	* Opened a new version with the CRAN release of vegan 2.0-3 on
 	March 3, 2012.
 
@@ -34,23 +13,37 @@
 	paper where the analysed the confusion of location (differences
 	between groups) and dispersion (variability within groups) in
 	dissimilarity-based analyses.  We have warned on this for long in
-	vegan, but now we can get support from this paper. Warnings added
-	to anosim, mrpp, simper (where this worst) and adonis (where this
-	was already analysed by Marti Anderson when introducing the
-	method).
+	vegan, but now we can get support from this paper. Explicit
+	arnings added to anosim, mrpp, simper (where this is worst) and
+	adonis (where this was already analysed by Marti Anderson when
+	introducing the method).
 
-	* adipart: permutation tests assumed constant full gamma diversity
-	in all simulations even when the null model could produce variable
-	gamma diversities. The default method ("r2dtable") had constant
-	gamma diversity.
+	* adipart, multipart, hiersimu: permutation tests assumed constant
+	full gamma diversity in all simulations even when the null model
+	could produce variable gamma diversities. The default method
+	("r2dtable") had constant gamma diversity.
 
+	* adipart, multipart, hiersimu: these are now generic functions
+	with default and formula methods. The formula method is identical
+	to the previous function, the default method can take two matrices
+	as input, but the second argument describing the hierarchy can be
+	missing. In this case a trivial two-level hierarchy will be
+	assumed (each row is a seperate group, all rows are in same
+	group).
+
 	* anova of prc() objects by "axis", "terms" or "margin" failed due
 	to NAMESPACE issues. Reported as issue #7 by Eduard Szöcs in
 	github.com.
 
+	* clamtest: wrongly used frequencies instead of the counts
+	when calculating sample coverage to test x < coverage.limit. 
+	No detectable differences were produced when rerunning 
+	examples from Chazdon et al. 2011 (Ecology, 92, 1332--1343)
+	and vegan help page.
+
 	* envfit: failed if some of the environmental variables were
-	factor with unused factor levels. Fixed in centroids.cca. Reported
-	as issue #8 in github.com by Eduard Szöcs.
+	factors with unused factor levels. Fixed in centroids.cca.
+	Reported as issue #8 in github.com by Eduard Szöcs.
 
 	* msoplot: expose 'ylim' as an argument. Previously, 'ylim' was
 	set internally and user could not change it setting, although
@@ -58,6 +51,10 @@
 	outside the plot, and legend covered lines. The default setting of
 	'ylim' was improved, and the function follows R idiom more
 	closely. Reported in a private email to J.O. by Ricardo Pita.
+
+	* scoverage: new function for sample coverage based correction for
+	calculation of relative frequencies in count community matrices
+	(Good 1953, Biometrika 40, 237--264).
 	
 Version 2.1-13 (closed March 9, 2012)