[Vegan-commits] r1903 - branches/2.0/inst

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

Author: jarioksa
Date: 2011-09-27 16:18:50 +0200 (Tue, 27 Sep 2011)
New Revision: 1903

Modified:
   branches/2.0/inst/NEWS.Rd
Log:
update NEWS

Modified: branches/2.0/inst/NEWS.Rd
===================================================================
--- branches/2.0/inst/NEWS.Rd	2011-09-27 13:22:42 UTC (rev 1902)
+++ branches/2.0/inst/NEWS.Rd	2011-09-27 14:18:50 UTC (rev 1903)
@@ -3,9 +3,37 @@
 \encoding{UTF-8}
 
 \section{Changes in version 2.0-1}{
+  \subsection{NEW FUNCTIONS}{
+    \itemize{
+  
+      \item \code{clamtest}: new function for the to classify species
+      as generalists and specialists in two distinct habitats (CLAM
+      test of Chazdon et al., \emph{Ecology} 92, 1332--1343; 2011).
+      The test is based on multinomial distribution of individuals in
+      two habitat types or sampling units, and is applicable only to
+      count data with no over-dispersion.
+
+      \item \code{raupcrick}: new function to implement Raup-Crick
+      dissimilarity as a probability of number of co-occurring species
+      with occurrence probabilities proportional to species
+      frequencies.  \pkg{Vegan} has Raup-Crick index as a choice in
+      \code{vegdist}, but it uses equal sampling probabilities for
+      species and exact analytic equations. The new \code{raupcrick}
+      function uses simulation with \code{oecosimu}. The function
+      follows Chase et al. (2011) \emph{Ecoshpere} 2:art24
+      [doi:10.1890/ES10-00117.1], and was developed with the
+      consultation of Brian Inouye.
+
+    }
+  } % end NEW FUNCTIONS
+
   \subsection{BUG FIXES}{
     \itemize{
 
+      \item Function \code{meandist} could randomly permute items,
+      especially when the \code{grouping} was numerical. The problem
+      was reported by Dr Miguel Alvarez (Univ. Bonn).
+
       \item Function \code{permatswap} for community null models using
       quantitative swap never swapped items in a \eqn{2 \times 2}{2x2}
       submatrix if all cells were filled.