[Vegan-commits] r1233 - branches/1.17/man

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

Author: gsimpson
Date: 2010-06-16 08:24:15 +0200 (Wed, 16 Jun 2010)
New Revision: 1233

Modified:
   branches/1.17/man/adonis.Rd
   branches/1.17/man/anosim.Rd
   branches/1.17/man/envfit.Rd
   branches/1.17/man/mantel.Rd
Log:
links to ?permutations

Modified: branches/1.17/man/adonis.Rd
===================================================================
--- branches/1.17/man/adonis.Rd	2010-06-15 22:13:19 UTC (rev 1232)
+++ branches/1.17/man/adonis.Rd	2010-06-16 06:24:15 UTC (rev 1233)
@@ -93,7 +93,9 @@
 intact for a particular hypothesis test where one does not want to
 permute the data among particular groups. For instance, \code{strata =
 B} causes permutations among levels of \code{A} but retains data within
-levels of \code{B} (no permutation among levels of \code{B}).
+levels of \code{B} (no permutation among levels of \code{B}). See
+\code{\link{permutations}} for additional details on permutation tests
+in Vegan.
 
 The default \code{\link{contrasts}} are different than in \R in
 general. Specifically, they use \dQuote{sum} contrasts, sometimes known

Modified: branches/1.17/man/anosim.Rd
===================================================================
--- branches/1.17/man/anosim.Rd	2010-06-15 22:13:19 UTC (rev 1232)
+++ branches/1.17/man/anosim.Rd	2010-06-16 06:24:15 UTC (rev 1233)
@@ -53,7 +53,9 @@
 
   The statistical significance of observed \eqn{R} is assessed by
   permuting the grouping vector to obtain the empirical
-  distribution of \eqn{R} under null-model.
+  distribution of \eqn{R} under null-model.  See
+  \code{\link{permutations}} for additional details on permutation tests
+  in Vegan.
 
   The function has \code{summary} and \code{plot} methods.  These both
   show valuable information to assess the validity of the method:  The

Modified: branches/1.17/man/envfit.Rd
===================================================================
--- branches/1.17/man/envfit.Rd	2010-06-15 22:13:19 UTC (rev 1232)
+++ branches/1.17/man/envfit.Rd	2010-06-16 06:24:15 UTC (rev 1233)
@@ -100,7 +100,9 @@
   The goodness of fit statistic is squared correlation coefficient
   (\eqn{r^2}).
   For factors this is defined as \eqn{r^2 = 1 - ss_w/ss_t}, where
-  \eqn{ss_w} and \eqn{ss_t} are within-group and total sums of squares.
+  \eqn{ss_w} and \eqn{ss_t} are within-group and total sums of
+  squares. See \code{\link{permutations}} for additional details on
+  permutation tests in Vegan.
 
   User can supply a vector of prior  weights \code{w}. If the ordination
   object has weights, these will be used. In practise this means that

Modified: branches/1.17/man/mantel.Rd
===================================================================
--- branches/1.17/man/mantel.Rd	2010-06-15 22:13:19 UTC (rev 1232)
+++ branches/1.17/man/mantel.Rd	2010-06-16 06:24:15 UTC (rev 1233)
@@ -34,7 +34,9 @@
   related).  However, the significance cannot be directly assessed,
   because there are \eqn{N(N-1)/2} entries for just \eqn{N} observations.
   Mantel developed asymptotic test, but here we use permutations of
-  \eqn{N} rows and columns of dissimilarity matrix.
+  \eqn{N} rows and columns of dissimilarity matrix.  See
+  \code{\link{permutations}} for additional details on permutation tests
+  in Vegan.
 
   Partial Mantel statistic uses partial correlation
   conditioned on the third matrix. Only the first matrix is permuted so