[Vegan-commits] r307 - in branches/1.11-0/inst: . doc

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

Author: jarioksa
Date: 2008-04-08 10:32:12 +0200 (Tue, 08 Apr 2008)
New Revision: 307

Modified:
   branches/1.11-0/inst/ChangeLog
   branches/1.11-0/inst/doc/diversity-vegan.Rnw
Log:
merged r301 (R\'{e}nyi fix)

Modified: branches/1.11-0/inst/ChangeLog
===================================================================
--- branches/1.11-0/inst/ChangeLog	2008-04-08 08:14:49 UTC (rev 306)
+++ branches/1.11-0/inst/ChangeLog	2008-04-08 08:32:12 UTC (rev 307)
@@ -11,7 +11,9 @@
 	* anova.cca: merged Rev 288 (no. perms could exceed perm.max)
 
 	* plot.procrustes: merged Rev 278 (fails with two identical
-	configs). 
+	configs).
+
+	* diversity.Rnw: merged Rev 301 (portable spelling R\'{e}nyi). 
 	
 Version 1.11-2 (March 20, 2008)
 

Modified: branches/1.11-0/inst/doc/diversity-vegan.Rnw
===================================================================
--- branches/1.11-0/inst/doc/diversity-vegan.Rnw	2008-04-08 08:14:49 UTC (rev 306)
+++ branches/1.11-0/inst/doc/diversity-vegan.Rnw	2008-04-08 08:32:12 UTC (rev 307)
@@ -76,21 +76,21 @@
 where \texttt{specnumber} is a simple \texttt{vegan} function to find
 the numbers of species.
 
-\texttt{Vegan} also can estimate Rényi diversities of order $a$:
+\texttt{Vegan} also can estimate R\'{e}nyi diversities of order $a$:
 \begin{equation}
 H_a = \frac{1}{1-a} \log \sum_{i=1}^S p_i^a
 \end{equation}
 or the corresponding Hill numbers $N_a = \exp(H_a)$.  Many common
 diversity indices are special cases of Hill numbers: $N_0 = S$, $N_1 =
 \exp(H')$, $N_2 = D_2$, and $N_\infty = 1/(\max p_i)$. The
-correspoding Rényi diversities are $H_0 = \log(S)$, $H_1 = H'$, $H_2 =
+correspoding R\'{e}nyi diversities are $H_0 = \log(S)$, $H_1 = H'$, $H_2 =
 - \log(\sum p_i^2)$, and $H_\infty = - \log(\max p_i)$.  We select a
-random subset of five sites for Rényi diversities:
+random subset of five sites for R\'{e}nyi diversities:
 <<>>=
 k <- sample(nrow(BCI), 6)
 R <- renyi(BCI[k,])
 @
-We can really regard a site more diverse if all of its Rényi
+We can really regard a site more diverse if all of its R\'{e}nyi
 diversities are higher than in another site.  We can inspect this
 graphically using the standard \texttt{plot} function for the
 \texttt{renyi} result (Fig. \ref{fig:renyi}).
@@ -101,7 +101,7 @@
 <<fig=true,echo=false>>=
 print(plot(R))
 @
-\caption{Rényi diversities in six randomly selected plots. The plot
+\caption{R\'{e}nyi diversities in six randomly selected plots. The plot
   uses Trellis graphics with a separate panel for each site. The dots
   show the values for sites, and the lines the extremes and median in
   the data set.}