[Phylobase-commits] r472 - pkg/man

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

Author: bbolker
Date: 2009-08-18 20:16:12 +0200 (Tue, 18 Aug 2009)
New Revision: 472

Modified:
   pkg/man/check.phylo4.Rd
   pkg/man/check.phylo4d.Rd
   pkg/man/nNodes-methods.Rd
   pkg/man/phylo4.Rd
   pkg/man/phylo4d-class.Rd
   pkg/man/phylo4d.Rd
Log:

  more documentation cleanup



Modified: pkg/man/check.phylo4.Rd
===================================================================
--- pkg/man/check.phylo4.Rd	2009-08-18 18:08:03 UTC (rev 471)
+++ pkg/man/check.phylo4.Rd	2009-08-18 18:16:12 UTC (rev 472)
@@ -36,9 +36,8 @@
 }
 \seealso{
   the \code{\link{phylo4}} constructor and \linkS4class{phylo4} class;
-  \code{\link{checkData}}, the \code{\link{phylo4d}} constructor and
-  the \linkS4class{phylo4d}
-  class do checks for the data associated with trees.
+  \code{\link{formatData}},  the \code{\link{phylo4d}} constructor and
+  the \linkS4class{phylo4d} class do checks for the data associated with trees.
   See \code{\link{coerce-methods}} for translation functions.
 }
 \author{Ben Bolker}

Modified: pkg/man/check.phylo4d.Rd
===================================================================
--- pkg/man/check.phylo4d.Rd	2009-08-18 18:08:03 UTC (rev 471)
+++ pkg/man/check.phylo4d.Rd	2009-08-18 18:16:12 UTC (rev 472)
@@ -1,5 +1,6 @@
 \name{checkPhylo4d}
 \alias{formatData}
+\alias{addData}
 \alias{addData,phylo4d-method}
 \title{Data addition and validity checking for phylo4d objects}
 \description{

Modified: pkg/man/nNodes-methods.Rd
===================================================================
--- pkg/man/nNodes-methods.Rd	2009-08-18 18:08:03 UTC (rev 471)
+++ pkg/man/nNodes-methods.Rd	2009-08-18 18:16:12 UTC (rev 472)
@@ -25,6 +25,9 @@
 \alias{edgeLength}
 \alias{edgeLength-methods}
 \alias{edgeLength,phylo4-method}
+\alias{edgeLength<-}
+\alias{edgeLength<-,phylo4-method}
+\alias{edgeLength<-,phylo4,ANY-method}
 \alias{nodeType}
 \alias{nodeType,phylo4-method}
 \alias{isRooted}

Modified: pkg/man/phylo4.Rd
===================================================================
--- pkg/man/phylo4.Rd	2009-08-18 18:08:03 UTC (rev 471)
+++ pkg/man/phylo4.Rd	2009-08-18 18:16:12 UTC (rev 472)
@@ -45,7 +45,7 @@
 \author{phylobase team}
 \note{Translation functions are available from many valid tree formats. See \link{coerce-methods}.  
 }
-\seealso{\code{\link{coerce-methods}} for translation functions. The \linkS4class{phylo4} class, the \code{\link{checkData}}
+\seealso{\code{\link{coerce-methods}} for translation functions. The \linkS4class{phylo4} class, the \code{\link{formatData}}
   function to check the validity of \code{phylo4} objects. See also the \code{\link{phylo4d}} constructor, and \linkS4class{phylo4d} class.}
 \examples{
 # a three species tree:

Modified: pkg/man/phylo4d-class.Rd
===================================================================
--- pkg/man/phylo4d-class.Rd	2009-08-18 18:08:03 UTC (rev 471)
+++ pkg/man/phylo4d-class.Rd	2009-08-18 18:16:12 UTC (rev 472)
@@ -61,7 +61,7 @@
    The \code{names} method returns a vector of characters corresponding
    to the names of the slots.
   }
-\seealso{\code{\link{coerce-methods}} for translation functions. The \code{\link{phylo4d}} constructor and the \code{\link{checkData}} function to check the validity of trees and data. See also the \code{\link{phylo4}} constructor, the \linkS4class{phylo4} class, and the \code{\link{checkPhylo4}} function to check the validity of \code{phylo4} trees. }
+\seealso{\code{\link{coerce-methods}} for translation functions. The \code{\link{phylo4d}} constructor and the \code{\link{formatData}} function to check the validity of trees and data. See also the \code{\link{phylo4}} constructor, the \linkS4class{phylo4} class, and the \code{\link{checkPhylo4}} function to check the validity of \code{phylo4} trees. }
 \author{Ben Bolker, Thibaut Jombart}   
 \examples{
   library(ape)

Modified: pkg/man/phylo4d.Rd
===================================================================
--- pkg/man/phylo4d.Rd	2009-08-18 18:08:03 UTC (rev 471)
+++ pkg/man/phylo4d.Rd	2009-08-18 18:16:12 UTC (rev 472)
@@ -51,7 +51,7 @@
     labels or node labels with informative data (e.g., posterior
     probabilities).}
   \item{\dots}{further arguments to be passed to other methods. Used to
-    control the validity checking of the created object (see \code{\link{checkData}}).}
+    control the validity checking of the created object (see \code{\link{formatData}}).}
 }
 
 \details{
@@ -75,7 +75,7 @@
 
 \seealso{
 \code{\link{coerce-methods}} for translation functions. The
-  \linkS4class{phylo4d} class, the \code{\link{checkData}}
+  \linkS4class{phylo4d} class, the \code{\link{formatData}}
   function to check the validity of \code{phylo4d} objects;
   \linkS4class{phylo4} class and \link{phylo4} constructor.}