[Vegan-commits] r2420 - pkg/vegan/man

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

Author: jarioksa
Date: 2013-02-07 18:39:54 +0100 (Thu, 07 Feb 2013)
New Revision: 2420

Modified:
   pkg/vegan/man/capscale.Rd
   pkg/vegan/man/cca.Rd
   pkg/vegan/man/cca.object.Rd
Log:
add cross references to cca methods so that people do not request features that already are there

Modified: pkg/vegan/man/capscale.Rd
===================================================================
--- pkg/vegan/man/capscale.Rd	2013-02-07 16:20:38 UTC (rev 2419)
+++ pkg/vegan/man/capscale.Rd	2013-02-07 17:39:54 UTC (rev 2420)
@@ -213,7 +213,14 @@
 
 \seealso{\code{\link{rda}}, \code{\link{cca}}, \code{\link{plot.cca}},
   \code{\link{anova.cca}}, \code{\link{vegdist}},
-  \code{\link{dist}}, \code{\link{cmdscale}}.}
+  \code{\link{dist}}, \code{\link{cmdscale}}.
+
+  The function returns similar result object as \code{\link{rda}} (see
+  \code{\link{cca.object}}). This section for \code{\link{rda}} gives a
+  more complete list of functions that can be used to access and
+  analyse \code{capscale} results.
+
+}
 \examples{
 data(varespec)
 data(varechem)

Modified: pkg/vegan/man/cca.Rd
===================================================================
--- pkg/vegan/man/cca.Rd	2013-02-07 16:20:38 UTC (rev 2419)
+++ pkg/vegan/man/cca.Rd	2013-02-07 17:39:54 UTC (rev 2420)
@@ -194,25 +194,61 @@
 }
 
 \seealso{
-  There is a special documentation for \code{\link{plot.cca}} and
-  \code{\link{summary.cca}} functions
-  with their helper functions (\code{\link{text.cca}},
-  \code{\link{points.cca}}, \code{\link{scores.cca}}).
-  Function \code{\link{anova.cca}} provides an ANOVA like permutation
-  test for the ``significance'' of constraints. Automatic model building
-  (dangerous!) is discussed in \code{\link{deviance.cca}}.  Diagnostic
-  tools, prediction and adding new points in ordination are discussed in
-  \code{\link{goodness.cca}} and \code{\link{predict.cca}}.
-  Function  \code{\link[ade4]{cca}} (library \pkg{ade4}) provide alternative
-  implementations of CCA (these are internally quite
-  different). Function \code{\link{capscale}} is a non-Euclidean generalization of
-  \code{rda}. The result object is described in
-  \code{\link{cca.object}}.
-  You can use \code{\link{as.mlm}} to refit ordination result as a
-  multiple response linear model to find some descriptive statistics.
-  Design decisions are explained in
-  \code{\link{vignette}} \file{decision-vegan} which also can be accessed
-  with \code{\link{vegandocs}}.  
+  
+  This help page describes two constrained ordination functions,
+  \code{cca} and \code{rda}.  A related method, distance-based
+  redundancy analysis (dbRDA) is described separately
+  (\code{\link{capscale}}). All these function return similar objects
+  (described in \code{\link{cca.object}}). There are numerous support
+  functions that can used to access the result object. In the list
+  below, functions of type \code{cca} will handle all ordination
+  objects, and functions of \code{rda} only handle \code{rda} and
+  \code{\link{capscale}} results.
+
+  The main plotting functions are \code{\link{plot.cca}} for all
+  methods, and \code{\link{biplot.rda}} for RDA and dbRDA.  However,
+  generic \pkg{vegan} plotting functions can also handle the results.
+  The scores can be accessed and scaled with \code{\link{scores.cca}},
+  and summarized with \code{\link{summary.cca}}. The eigenvalues can
+  be accessed with \code{\link{eigenvals.cca}} and the regression
+  coefficients for constraints with \code{\link{coef.cca}}.  The
+  eigenvalues can be plotted with \code{\link{screeplot.cca}}, and the
+  (adjusted) \eqn{R^2}{R-squared} can be found with
+  \code{\link{RsquareAdj.rda}}. The scores can be also calculated for
+  new data sets with \code{\link{predict.cca}} which allows adding
+  points to ordinations.  The values of constraints can be inferred
+  from ordination and community composition with
+  \code{\link{calibrate.cca}}.
+
+  Diagnostic statistics can be found with \code{\link{goodness.cca}},
+  \code{\link{inertcomp}}, \code{\link{spenvcor}},
+  \code{\link{intersetcor}} and \code{\link{vif.cca}}.  Function
+  \code{\link{as.mlm.cca}} refits the result object as a multiple
+  \code{\link{lm}} object, and this allows finding influence
+  statistics (\code{\link{lm.influence}}, \code{\link{cooks.distance}}
+  etc.).
+  
+  Permutation based signficance for the overall model, single
+  constraining variables or axes can be found with
+  \code{\link{anova.cca}}.  Automatic model building with \R{}
+  \code{\link{step}} function is possible with
+  \code{\link{deviance.cca}}, \code{\link{add1.cca}} and
+  \code{\link{drop1.cca}}.  Functions \code{\link{ordistep}} and
+  \code{\link{ordiR2step}} (for RDA) are special functions for
+  constrained ordination. Randomized data sets can be generated with
+  \code{\link{simulate.cca}}.
+
+  Separate methods based on constrained ordination model are principal
+  response curves (\code{\link{prc}}) and variance partioning between
+  several components (\code{\link{varpart}}).
+
+  Design decisions are explained in \code{\link{vignette}}
+  \file{decision-vegan} which also can be accessed with
+  \code{\link{vegandocs}}.
+
+  Package \pkg{ade4} provides alternative constrained ordination
+  functions \code{\link[ade4]{cca}} and \code{\link[ade4]{pcaiv}}.
+
 }
 
 \examples{

Modified: pkg/vegan/man/cca.object.Rd
===================================================================
--- pkg/vegan/man/cca.object.Rd	2013-02-07 16:20:38 UTC (rev 2419)
+++ pkg/vegan/man/cca.object.Rd	2013-02-07 17:39:54 UTC (rev 2420)
@@ -190,6 +190,10 @@
   linear model (\code{\link{lm}}) in order to more easily find some
   statistics (which in principle could be directly found from the
   \code{cca.object} as well). 
+
+  This section in \code{\link{cca}} gives a more complete list of
+  methods to handle the constrained ordination result object.
+
 }
 \references{
   Legendre, P. and Legendre, L. (2012) \emph{Numerical Ecology}. 3rd English