[Vegan-commits] r2445 - in branches/2.0: R inst man

Sun Feb 17 15:05:43 CET 2013

Author: jarioksa
Date: 2013-02-17 15:05:43 +0100 (Sun, 17 Feb 2013)
New Revision: 2445

Modified:
   branches/2.0/R/wcmdscale.R
   branches/2.0/inst/ChangeLog
   branches/2.0/man/cca.Rd
   branches/2.0/man/cca.object.Rd
   branches/2.0/man/wcmdscale.Rd
Log:
merge r2432, 2443 (edit Rd) & 2434 (wcmdscale object)

Modified: branches/2.0/R/wcmdscale.R
===================================================================

--- branches/2.0/R/wcmdscale.R	2013-02-17 07:28:04 UTC (rev 2444)
+++ branches/2.0/R/wcmdscale.R	2013-02-17 14:05:43 UTC (rev 2445)
@@ -8,6 +8,9 @@
     }
     if (add)
         .NotYetUsed("add")
+    ## Force eig=TRUE if add, x.ret or !missing(w)
+    if(add || x.ret || !missing(w))
+        eig <- TRUE
     ZERO <- sqrt(.Machine$double.eps)
     if (!inherits(d, "dist")) {
         op <- options(warn = 2)

Modified: branches/2.0/inst/ChangeLog
===================================================================
--- branches/2.0/inst/ChangeLog	2013-02-17 07:28:04 UTC (rev 2444)
+++ branches/2.0/inst/ChangeLog	2013-02-17 14:05:43 UTC (rev 2445)
@@ -2,6 +2,13 @@
 
 VEGAN RELEASE VERSIONS at http://cran.r-project.org/
 
+Version 2.0-7 (opened February 17, 2013)
+
+	* merge r2443: edit cca.object.Rd.
+	* merge r2434: return wcmdscale object always with non-default
+	arguments.
+	* merge r2432: edit cca.Rd.
+
 Version 2.0-6 (released February 11, 2013)
 
 	* merge 2420, 2425: cca cross references.

Modified: branches/2.0/man/cca.Rd
===================================================================
--- branches/2.0/man/cca.Rd	2013-02-17 07:28:04 UTC (rev 2444)
+++ branches/2.0/man/cca.Rd	2013-02-17 14:05:43 UTC (rev 2445)
@@ -105,9 +105,9 @@
   frames).
   The formula can include a special term \code{Condition}
   for conditioning variables (``covariables'') ``partialled out'' before
-  analysis.  So the following commands are equivalent: \code{cca(X, Y,
-    Z)}, \code{cca(X ~ Y + Condition(Z))}, where \code{Y} and \code{Z}
-  refer to constraints and conditions matrices respectively.
+  analysis.  So the following commands are equivalent:
+  \code{cca(X, Y, Z)},  \code{cca(X ~ Y + Condition(Z))}, where \code{Y}
+  and \code{Z} refer to constraints and conditions matrices respectively.
 
   Constrained correspondence analysis is indeed a constrained method:
   CCA does not try to display all variation in the
@@ -198,12 +198,12 @@
   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
+  (\code{\link{capscale}}). All these functions 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.
+  functions that can be used to access the result object. In the list
+  below, functions of type \code{cca} will handle all three constrained
+  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,

Modified: branches/2.0/man/cca.object.Rd
===================================================================
--- branches/2.0/man/cca.object.Rd	2013-02-17 07:28:04 UTC (rev 2444)
+++ branches/2.0/man/cca.object.Rd	2013-02-17 14:05:43 UTC (rev 2445)
@@ -177,19 +177,25 @@
   }
 }
   
-\seealso{The description here provides a hacker's interface.  For more
-  user friendly access to the \code{cca} object see
+\seealso{The description here provides a hacker's interface.  User
+  level functions for further analysis and handling of \code{cca}
+  objects are described in this section in \code{\link{cca}}. Also for
+  a hacker interface, it may be better to use following low level
+  functions to access the results:
+  \code{\link{scores.cca}} (which also scales results), 
+  \code{\link{predict.cca}} (which can also use \code{newdata}), 
+  \code{\link{fitted.cca}}, \code{\link{residuals.cca}},
   \code{\link{alias.cca}}, \code{\link{coef.cca}},
-  \code{\link{deviance.cca}}, \code{\link{predict.cca}},
-  \code{\link{scores.cca}}, 
-  \code{\link{summary.cca}},  \code{\link{vif.cca}},
-  \code{\link{weights.cca}}, \code{\link{spenvcor}} or \code{rda}
+  \code{\link{model.frame.cca}}, \code{\link{model.matrix.cca}},
+  \code{\link{deviance.cca}}, \code{\link{eigenvals.cca}},
+  \code{\link{RsquareAdj.cca}}, 
+  \code{\link{weights.cca}}, \code{\link{nobs.cca}}, or \code{rda}
   variants of these functions.
   You can use \code{\link{as.mlm}} to cast a \code{cca.object} into
   result of multiple response
   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). 
+  \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.

Modified: branches/2.0/man/wcmdscale.Rd
===================================================================
--- branches/2.0/man/wcmdscale.Rd	2013-02-17 07:28:04 UTC (rev 2444)
+++ branches/2.0/man/wcmdscale.Rd	2013-02-17 14:05:43 UTC (rev 2445)
@@ -49,10 +49,11 @@
 
   With default options, the function returns only a matrix of scores
   scaled by eigenvalues for all real axes. If the function is called
-  with \code{eig = TRUE} or \code{x.ret = TRUE}, the function returns an
-  object of class \code{"wcmdscale"} with \code{print}, \code{plot},
-  \code{scores}, \code{\link{eigenvals}} and \code{\link{stressplot}}
-  methods, and described in section Value.  }
+  with \code{eig = TRUE} or \code{x.ret = TRUE} or with weights
+  \code{w}, the function returns an object of class \code{"wcmdscale"}
+  with \code{print}, \code{plot}, \code{scores}, \code{\link{eigenvals}}
+  and \code{\link{stressplot}} methods, and described in section Value.
+  }
 
 \value{ If \code{eig = FALSE} and \code{x.ret = FALSE} (default), a
   matrix with \code{k} columns whose rows give the coordinates of the

