[Vegan-commits] r223 - branches/1.11-0/inst

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sun Feb 17 08:47:16 CET 2008 

Author: jarioksa
Date: 2008-02-17 08:47:16 +0100 (Sun, 17 Feb 2008)
New Revision: 223

Modified:
   branches/1.11-0/inst/NEWS
Log:
Tweaking NEWS

Modified: branches/1.11-0/inst/NEWS
===================================================================
--- branches/1.11-0/inst/NEWS	2008-02-17 07:02:50 UTC (rev 222)
+++ branches/1.11-0/inst/NEWS	2008-02-17 07:47:16 UTC (rev 223)
@@ -1,7 +1,8 @@
-											-*-Text-*-
-VEGAN RELEASE VERSIONS 
+-*-Text-*-
+
+			VEGAN RELEASE VERSIONS 
 	
-			 VEGAN VERSION 1.11-0
+			     VEGAN 1.11-0
 
 - Based on devel version 1.10-13 (rev. 205 at R-Forge).
 
@@ -12,10 +13,10 @@
 NEW FUNCTIONS
 
 - betadisper: new functions for Marti Anderson's analysis of
-  homogeneity of multivariate dispersions.  
+   homogeneity of multivariate dispersions.
 
 - biplot.rda: biplot function for PCA run with rda. Arrows are used
-  instead of points. 
+  instead of points.
 
 - CCorA: Canonical correlation analysis with a robust algorithm, with
   permutation test and plot function.
@@ -31,31 +32,31 @@
   such as chisq.test.
 
 - ordiresids: similar diagnostic plots as in plot.lm for constrained
-  ordination: Residuals ~  Fitted, sqrt(abs(Residuals)) ~ Fitted, and
-  qqmath(~ Residuals) using Lattice grahcis.
+  ordination: Residuals ~ Fitted, sqrt(abs(Residuals)) ~ Fitted, and
+  qqmath(~ Residuals) using Lattice graphics.
 
 - orditkplot: interactive and editable plotting function. Function
   displays one set of points (species, sites) using both points and
-  labels (text). The points are fixed, but the user can drag labels to
+  labels (text). The points are fixed, but labels can be dragged to
   better positions with mouse. The edited plots can be saved as EPS,
   exported to various graphical formats (EPS, PDF, PNG, JPEG, BMP,
   XFIG depending on the system) or dumped back to the R session for
   plotting and further processing.
 
-- ordixyplot: a set of function for Lattice graphics of ordination
+- ordixyplot: a set of functions for Lattice graphics of ordination
   results. Includes ordixyplot for 2D graphics, ordisplom for pairs
   plots, and ordicloud for 3D graphics. All can be subsetted and
   formatted in the usual Lattice way.
 
 - permuted.index2: New version of permuted.index() that now allows
-   restricted permutations. Can produce permutations for time-series
-   or line transects and for spatial grids. These can also be nested
-   within 'strata'. permuted.series() and permuted.grid() are the
-   relevant workhorse functions. Permutation options are set by new
-   function permControl(). Plan to migrate vegan functions to
-   permuted.index2() in the devel version, and will eventually replace
-   the current permuted.index(). With support function permCheck for
-   checking permutation schemes.
+  restricted permutations. Can produce permutations for time-series or
+  line transects and for spatial grids. These can also be nested
+  within 'strata'. permuted.series() and permuted.grid() are the
+  relevant workhorse functions. Permutation options are set by new
+  function permControl(). Currently used only in betadisper, but we
+  plan to migrate vegan functions to permuted.index2() in the devel
+  version, and will eventually replace the current permuted.index().
+  With support function permCheck for checking permutation schemes.
 
 NEW DATA SETS
 
@@ -65,27 +66,27 @@
 
 - adonis: accepts any 'dist' object as input.
 
-- as.mlm.cca, as.mlm.rda: use now correct names for variables in
+- as.mlm.cca, as.mlm.rda use now correct names for variables in
   aliased models. The data were pivoted correctly in R, but the labels
-  were not. 
+  were not.
 
-- anova.cca: can now analyse marginal effects of individual terms
+- anova.cca can now analyse marginal effects of individual terms
   (which are similar to Type III effects). Defined with argument by =
-  "margin". 
+  "margin".
 
-- anova.cca: assesses now P value as (hits+1)/(tries+1). 
+- anova.cca assesses now P value as (hits+1)/(tries+1).
 
 - anova.cca: anova(..., by = "axis") failed when fitted model had
   terms like poly(x,2) or log(x).
 
-- bgdispersal: uses now a more powerful statistic for the McNemar test
+- bgdispersal uses now a more powerful statistic for the McNemar test
   (in terms of Type 1 error rate).
 
-- calibrate.cca: does correct pivoting in aliased models.
+- calibrate.cca does correct pivoting in aliased models.
 
 - capscale: negative scaling in plot works similarly as in rda.
 
-- decorana: deos not crash R when called with NULL row data, such as
+- decorana does not crash R when called with NULL row data, such as
   decorana(dune[FALSE,]). Method predict(..., type="sites") works
   correctly with downweighted analysis.
 
@@ -93,31 +94,31 @@
   fitted values and residuals used internally in calculation (in cca()
   these are weigthed and Chi-square standardized values).
 
-- isomap: check that input data are dissimilarities or can be changed
+- isomap checks that input data are dissimilarities or can be changed
   into dissimilarities without warnings.
 
-- metaMDS: gains argument wascores (defaults TRUE) to suppress
-  calculation of species scores. 
+- metaMDS gains argument wascores (defaults TRUE) to suppress
+  calculation of species scores.
 
-- orditorp: now handles "..." more cleanly.
+- orditorp now handles "..." more cleanly.
 
-- scores.cca, scores.rda accept display = c("species", "sites"). 
+- scores.cca, scores.rda accept display = c("species", "sites").
 
-- summary.prc honours  argument 'axis'.
+- summary.prc honours argument 'axis'.
 
 - taxa2dist issues now a warning if called with 'check = FALSE' and
-  there are zero distances, typically meaning that basal taxa
-  (species) were not coded. 
+  some distances == 0, typically meaning that basal taxa (species)
+  were not coded.
 
-- varpart: failed if there were unused levels in factors.
+- varpart failed if there were unused levels in factors.
 
-- wascores: return now NA for missing (all zero) species instead of
-  failing. 
+- wascores returns now NA for missing (all zero) species instead of
+  failing.
 
-Documentation
+DOCUMENTS
 
 - new documents: FAQ, a simple introduction to ordination in vegan, a
-  detailed explanation of diversity methods.
+  detailed explanation of diversity methods. New formatting.
 
 			    OLDER VERSIONS

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