[Vegan-commits] r2310 - in branches/2.0: inst man

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

Author: jarioksa
Date: 2012-10-07 11:04:20 +0200 (Sun, 07 Oct 2012)
New Revision: 2310

Modified:
   branches/2.0/inst/ChangeLog
   branches/2.0/man/anova.cca.Rd
Log:
merge r2309: anova.cca.Rd tweaks

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2012-09-30 06:28:38 UTC (rev 2309)
+++ branches/2.0/inst/ChangeLog	2012-10-07 09:04:20 UTC (rev 2310)
@@ -4,6 +4,7 @@
 
 Version 2.0-5 (opened June 18, 2012)
 
+	* merge r2309: anova.cca.Rd edits.
 	* merge r2307: no line breaks within \code{} in Rd.
 	* merge r2305: proofread Rd files a..b.
 	* merge r2299: fix broken \link{}s in docs. 

Modified: branches/2.0/man/anova.cca.Rd
===================================================================
--- branches/2.0/man/anova.cca.Rd	2012-09-30 06:28:38 UTC (rev 2309)
+++ branches/2.0/man/anova.cca.Rd	2012-10-07 09:04:20 UTC (rev 2310)
@@ -15,7 +15,7 @@
   The function performs an ANOVA like permutation test for Constrained
   Correspondence Analysis (\code{\link{cca}}), Redundancy Analysis
   (\code{\link{rda}}) or distance-based Redundancy Analysis
-  (\code{\link{capscale}}) to assess the significance of constraints.
+  (dbRDA, \code{\link{capscale}}) to assess the significance of constraints.
 }
 \usage{
 \method{anova}{cca}(object, alpha=0.05, beta=0.01, step=100, perm.max=9999,
@@ -106,18 +106,18 @@
   fixed number of permutations will be used, and this is given by
   argument \code{permutations}, or if this is missing, by \code{step}.
   
-  Community data are permuted with choice \code{model = "direct"},
-  residuals after partial CCA/RDA/CAP with choice \code{model = "reduced"} 
-  (default), and residuals after CCA/RDA/CAP under choice
-  \code{model = "full"}.  If there is no partial CCA/RDA/CAP stage,
-  \code{model = "reduced"} simply permutes the data and is equivalent to
-  \code{model = "direct"}.  The test statistic is ``pseudo-\eqn{F}'',
+  Community data are permuted with choice \code{model="direct"},
+  residuals after partial CCA/ RDA/ dbRDA with choice \code{model="reduced"} 
+  (default), and residuals after CCA/ RDA/ dbRDA under choice
+  \code{model="full"}.  If there is no partial CCA/ RDA/ dbRDA stage,
+  \code{model="reduced"} simply permutes the data and is equivalent to
+  \code{model="direct"}.  The test statistic is \dQuote{pseudo-\eqn{F}},
   which is the ratio of constrained and unconstrained total Inertia
   (Chi-squares, variances or something similar), each divided by their
   respective ranks.  If there are no conditions (\dQuote{partial}
   terms), the sum of all eigenvalues remains constant, so that
   pseudo-\eqn{F} and eigenvalues would give equal results.  In partial
-  CCA/RDA/CAP, the effect of conditioning variables
+  CCA/ RDA/ dbRDA, the effect of conditioning variables
   (\dQuote{covariables}) is removed before permutation, and these
   residuals are added to the non-permuted fitted values of partial CCA
   (fitted values of \code{X ~ Z}).  Consequently, the total Chi-square