[Vegan-commits] r1627 - in branches/1.17: inst man

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

Author: jarioksa
Date: 2011-06-08 21:45:06 +0200 (Wed, 08 Jun 2011)
New Revision: 1627

Modified:
   branches/1.17/inst/ChangeLog
   branches/1.17/man/anova.cca.Rd
   branches/1.17/man/vegdist.Rd
Log:
merged r1624:6: doc updates

Modified: branches/1.17/inst/ChangeLog
===================================================================
--- branches/1.17/inst/ChangeLog	2011-06-08 09:54:35 UTC (rev 1626)
+++ branches/1.17/inst/ChangeLog	2011-06-08 19:45:06 UTC (rev 1627)
@@ -4,6 +4,11 @@
 
 Version 1.17-11 (opened April 29, 2011)
 
+	* merger r1625,6: Ref to our MEE paper in anova.cca.Rd.
+	
+	* merged r1624: doc vegdist(..., "raup") not using unequal
+	sampling probabilities for species.
+
 	* merged r1622: document zeroed components in cca.object.Rd. 
 
 	* merged r1620: print.cca does not show "Proportions" in

Modified: branches/1.17/man/anova.cca.Rd
===================================================================
--- branches/1.17/man/anova.cca.Rd	2011-06-08 09:54:35 UTC (rev 1626)
+++ branches/1.17/man/anova.cca.Rd	2011-06-08 19:45:06 UTC (rev 1627)
@@ -109,7 +109,8 @@
   significance tests for each constrained axis.  All previous
   constrained axes will be used as conditions (\dQuote{partialled
   out}) and a test for the first constrained eigenvalues is
-  performed. You can stop permutation tests after exceeding a given
+  performed (Legendre et al. 2011). 
+  You can stop permutation tests after exceeding a given
   significance level with argument \code{cutoff} to speed up
   calculations in large models. Setting \code{by = "terms"} will
   perform separate significance test for each term (constraining
@@ -150,8 +151,12 @@
   only when \code{model = "direct"}.  
 }
 \references{
-  Legendre, P. and Legendre, L. (1998). \emph{Numerical Ecology}. 2nd English
-  ed. Elsevier.
+  Legendre, P. and Legendre, L. (1998). \emph{Numerical Ecology}. 2nd
+  English ed. Elsevier.
+
+  Legendre, P., Oksanen, J. and ter Braak, C.J.F. (2011). Testing the
+  significance of canonical axes in redundancy analysis. 
+  \emph{Methods in Ecology and Evolution} 2, 269--277.
 }
 \author{Jari  Oksanen}
 \seealso{\code{\link{cca}}, \code{\link{rda}}, \code{\link{capscale}}

Modified: branches/1.17/man/vegdist.Rd
===================================================================
--- branches/1.17/man/vegdist.Rd	2011-06-08 09:54:35 UTC (rev 1626)
+++ branches/1.17/man/vegdist.Rd	2011-06-08 19:45:06 UTC (rev 1627)
@@ -149,22 +149,24 @@
   are divided by \eqn{\log(2)}{log(2)} so that the results will be in
   the conventional range \eqn{0 \dots 1}.
 
-  Raup--Crick dissimilarity (\code{method = "raup"}) is a probabilistic
-  index based on presence/absence data.  It is defined as \eqn{1 - prob(j)},
-  or based on the probability of observing at least \eqn{j} 
-  species in shared in compared communities.  Legendre & Legendre (1998)
-  suggest
-  using simulations to assess the probability, but the current function
-  uses analytic result from hypergeometric distribution
-  (\code{\link{phyper}}) instead.  This probability (and the index) is
-  dependent on the number of species missing in both sites, and adding
-  all-zero species to the data or removing missing species from the data
-  will influence the index.  The probability (and the index) may be
-  almost zero or almost one for a wide range of parameter values.  The
-  index is nonmetric: two
-  communities with no shared species may have a dissimilarity slightly
-  below one, and two identical communities may have dissimilarity
-  slightly above zero.
+  Raup--Crick dissimilarity (\code{method = "raup"}) is a
+  probabilistic index based on presence/absence data.  It is defined
+  as \eqn{1 - prob(j)}, or based on the probability of observing at
+  least \eqn{j} species in shared in compared communities.  Legendre &
+  Legendre (1998) suggest using simulations to assess the probability,
+  but the current function uses analytic result from hypergeometric
+  distribution (\code{\link{phyper}}) instead.  This probability (and
+  the index) is dependent on the number of species missing in both
+  sites, and adding all-zero species to the data or removing missing
+  species from the data will influence the index.  The probability
+  (and the index) may be almost zero or almost one for a wide range of
+  parameter values.  The index is nonmetric: two communities with no
+  shared species may have a dissimilarity slightly below one, and two
+  identical communities may have dissimilarity slightly above
+  zero. Please note that this index does not implement the Raup--Crick
+  dissimilarity as discussed by Chase et al. (2011): the current index
+  uses equal probabilities for all species, but the probabilities
+  should be inequal and based on species frequencies.
   
   Chao index tries to take into account the number of unseen species
   pairs, similarly as in \code{method = "chao"} in
@@ -226,6 +228,11 @@
   Chao, A., Chazdon, R. L., Colwell, R. K. and Shen, T. (2005). A new
   statistical approach for assessing similarity of species composition
   with incidence and abundance data. \emph{Ecology Letters} 8, 148--159.
+
+  Chase, J.M., Kraft, N.J.B., Smith, K.G., Vellend, M. and Inouye,
+  B.D. (2011). Using null models to disentangle variation in community
+  dissimilarity from variation in \eqn{\alpha}{alpha}-diversity.
+  \emph{Ecosphere} 2:art24 [doi:10.1890/ES10-00117.1]
    
   Faith, D. P, Minchin, P. R. and Belbin, L. (1987).
   Compositional dissimilarity as a robust measure of ecological