[Phylobase-commits] r914 - pkg/R

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

Author: francois
Date: 2014-04-08 20:06:20 +0200 (Tue, 08 Apr 2014)
New Revision: 914

Modified:
   pkg/R/edgeLength-methods.R
   pkg/R/formatData.R
   pkg/R/labels-methods.R
   pkg/R/phylo4-accessors.R
   pkg/R/root-methods.R
Log:
fixed a few things to make dev_tools::document() work

Modified: pkg/R/edgeLength-methods.R
===================================================================
--- pkg/R/edgeLength-methods.R	2014-04-08 17:55:55 UTC (rev 913)
+++ pkg/R/edgeLength-methods.R	2014-04-08 18:06:20 UTC (rev 914)
@@ -47,6 +47,7 @@
 ##' more information about tolerance.
 ##' @export
 ##' @docType methods
+##' @aliases hasEdgeLength
 ##' @rdname edgeLength-methods
 ##' @include phylo4-class.R phylo4-methods.R phylo4-accessors.R nodeId-methods.R
 ##' @examples
@@ -105,6 +106,7 @@
     return(elen)
 })
 
+##' @name edgeLength<-
 ##' @rdname edgeLength-methods
 ##' @aliases edgeLength<-,phylo4-method
 setReplaceMethod("edgeLength", signature(x="phylo4"),

Modified: pkg/R/formatData.R
===================================================================
--- pkg/R/formatData.R	2014-04-08 17:55:55 UTC (rev 913)
+++ pkg/R/formatData.R	2014-04-08 18:06:20 UTC (rev 914)
@@ -59,7 +59,6 @@
 ##' \linkS4class{phylo4d} class. See \code{\link{coerce-methods}} for
 ##' translation functions.
 ##' @keywords misc
-##' @include 
 formatData <- function(phy, dt, type=c("tip", "internal", "all"),
                        match.data=TRUE, rownamesAsLabels=FALSE,
                        label.type=c("rownames", "column"),

Modified: pkg/R/labels-methods.R
===================================================================
--- pkg/R/labels-methods.R	2014-04-08 17:55:55 UTC (rev 913)
+++ pkg/R/labels-methods.R	2014-04-08 18:06:20 UTC (rev 914)
@@ -121,6 +121,7 @@
                standardGeneric("labels<-")
            })
 
+##' @name labels<-
 ##' @rdname labels-methods
 ##' @aliases labels<-,phylo4,ANY,ANY,character-method
 setReplaceMethod("labels",
@@ -215,6 +216,7 @@
                standardGeneric("nodeLabels<-")
            })
 
+##' @name nodeLabels<-
 ##' @rdname labels-methods
 ##' @aliases nodeLabels<-,phylo4,character-method
 setReplaceMethod("nodeLabels", signature(x="phylo4", value="character"),
@@ -246,6 +248,7 @@
        standardGeneric("tipLabels<-")
 })
 
+##' @name tipLabels<-
 ##' @rdname labels-methods
 ##' @aliases tipLabels<-,phylo4,character-method
 setReplaceMethod("tipLabels", signature(x="phylo4", value="character"),
@@ -298,6 +301,7 @@
                standardGeneric("edgeLabels<-")
            })
 
+##' @name edgeLabels<-
 ##' @rdname labels-methods
 ##' @aliases edgeLabels<-,phylo4,character-method
 setReplaceMethod("edgeLabels", signature(x="phylo4", value="character"),

Modified: pkg/R/phylo4-accessors.R
===================================================================
--- pkg/R/phylo4-accessors.R	2014-04-08 17:55:55 UTC (rev 913)
+++ pkg/R/phylo4-accessors.R	2014-04-08 18:06:20 UTC (rev 914)
@@ -4,6 +4,7 @@
 ##' Function to return the number of tips, nodes and edges found in a
 ##' tree in the \code{phylo4} or \code{phylo4d} format.
 ##' @title nTips, nNodes, nEdges
+##' @aliases nTips
 ##' @param x a \code{phylo4} or \code{phylo4d} object
 ##' @return a numeric vector indicating the number of tips, nodes or
 ##' edge respectively.

Modified: pkg/R/root-methods.R
===================================================================
--- pkg/R/root-methods.R	2014-04-08 17:55:55 UTC (rev 913)
+++ pkg/R/root-methods.R	2014-04-08 18:06:20 UTC (rev 914)
@@ -52,6 +52,7 @@
     standardGeneric("rootNode<-")
 })
 
+##' @name rootNode<-
 ##' @rdname root-methods
 ##' @aliases rootNode<-,phylo4-method
 setReplaceMethod("rootNode", signature(x="phylo4"),