[Vegan-commits] r2106 - pkg/vegan/man

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

Author: jarioksa
Date: 2012-02-26 13:31:21 +0100 (Sun, 26 Feb 2012)
New Revision: 2106

Modified:
   pkg/vegan/man/scores.Rd
   pkg/vegan/man/vegdist.Rd
Log:
doc updates for scores and vegdist from github.com

Modified: pkg/vegan/man/scores.Rd
===================================================================
--- pkg/vegan/man/scores.Rd	2012-02-23 15:13:34 UTC (rev 2105)
+++ pkg/vegan/man/scores.Rd	2012-02-26 12:31:21 UTC (rev 2106)
@@ -4,10 +4,18 @@
 \alias{scores.lda}
 
 \title{ Get Species or Site Scores from an Ordination }
+
 \description{
-  Function to access either species or site scores for specified axes in
-  some ordination methods.
+  Function to access either species or site scores for specified axes
+  in some ordination methods. The \code{scores} function is generic in
+  \pkg{vegan}, and \pkg{vegan} ordination functions have their own
+  \code{scores} functions that are documented separately with the
+  method (see e.g. \code{\link{scores.cca}},
+  \code{\link{scores.metaMDS}}, \code{\link{scores.decorana}}). This
+  help file documents the default \code{scores} method that is only
+  used for non-\pkg{vegan} ordination objects.
 }
+
 \usage{
 \method{scores}{default}(x, choices, display=c("sites", "species"), ...)
 }
@@ -37,12 +45,11 @@
   analysis.
   
   The \code{scores.default} function is used to extract scores from
-  non-\pkg{vegan} ordination results.  Most standard ordination
-  methods of libraries \pkg{mva}, \pkg{multiv} and \pkg{MASS} do not
-  have a specific \code{class}, and no specific method can be written
-  for them.  However, \code{scores.default} guesses where some
-  commonly used functions keep their site scores and possible species
-  scores.
+  non-\pkg{vegan} ordination results.  Many standard ordination
+  methods of libraries do not have a specific \code{class}, and no
+  specific method can be written for them.  However,
+  \code{scores.default} guesses where some commonly used functions
+  keep their site scores and possible species scores.
 
   If \code{x} is a matrix, \code{scores.default} returns the chosen
   columns of that matrix, ignoring whether species or sites were
@@ -57,12 +64,15 @@
 \author{Jari Oksanen }
 
 \seealso{
-  \code{\link{scores.cca}}, \code{\link{scores.decorana}}.  These have
-  somewhat different interface -- \code{\link{scores.cca}} in
-  particular -- but all work with keywords \code{display="sites"} and
-  return a matrix. However, they may also return a list of matrices,
-  and some other \code{scores} methods will have quite different
-  arguments.  
+  Specific \code{scores} functions include (but are not limited to)
+  \code{\link{scores.cca}}, \code{\link{scores.rda}},
+  \code{\link{scores.decorana}}, \code{\link{scores.envfit}},
+  \code{\link{scores.metaMDS}}, \code{\link{scores.monoMDS}} and
+  \code{\link{scores.pcnm}}.  These have somewhat different interface
+  -- \code{\link{scores.cca}} in particular -- but all work with
+  keywords \code{display="sites"} and return a matrix. However, they
+  may also return a list of matrices, and some other \code{scores}
+  methods will have quite different arguments.
 }
 
 \examples{

Modified: pkg/vegan/man/vegdist.Rd
===================================================================
--- pkg/vegan/man/vegdist.Rd	2012-02-23 15:13:34 UTC (rev 2105)
+++ pkg/vegan/man/vegdist.Rd	2012-02-26 12:31:21 UTC (rev 2106)
@@ -28,7 +28,7 @@
     \code{"euclidean"}, \code{"canberra"}, \code{"bray"}, \code{"kulczynski"},
      \code{"jaccard"}, \code{"gower"}, \code{"altGower"}, \code{"morisita"}, 
      \code{"horn"}, \code{"mountford"}, \code{"raup"} , \code{"binomial"}, 
-     \code{"chao"} of \code{"cao"}.}
+     \code{"chao"} or \code{"cao"}.}
   \item{binary}{Perform presence/absence standardization before analysis
     using \code{\link{decostand}}.}
   \item{diag}{Compute diagonals. }