edits

NAMESPACE

@@ -42,6 +42,7 @@ export(nData)
 export(nEdges)
 export(nNodes)
 export(nTips)
+export(names)
 export(nodeData)
 export(nodeDepth)
 export(nodeHeight)

R/addData-methods.R

@@ -1,4 +1,3 @@
-
 ##' Adding data to a phylo4 or a phylo4d object
 ##'
 ##' \code{addData} adds data to a \code{phylo4} (converting it in a
@@ -14,41 +13,41 @@
 ##' The option \code{pos} is ignored (silently) if \code{x} is a
 ##' \code{phylo4} object. It is provided for compatibility reasons.
 ##'
-##' @param x a phylo4 or a phylo4d object
-##' @param tip.data a data frame (or object to be coerced to one)
-##' containing only tip data
-##' @param node.data a data frame (or object to be coerced to one)
-##' containing only node data
-##' @param all.data a data frame (or object to be coerced to one)
-##' containing both tip and node data
-##' @param merge.data if both \code{tip.data} and \code{node.data} are
-##' provided, it determines whether columns with common names will be
-##' merged together (default TRUE). If FALSE, columns with common
-##' names will be preserved separately, with ".tip" and ".node"
-##' appended to the names. This argument has no effect if
-##' \code{tip.data} and \code{node.data} have no column names in
-##' common.
-##' @param pos should the new data provided be bound \code{before} or
-##' \code{after} the pre-existing data?
-##' @param \dots additional arguments to control how matching between
-##' data and tree (see Details section of
-##' \code{\link{phylo4d-methods}} for more details).
-##' @return \code{addData} returns a \code{phylo4d} object.
-##' @author Francois Michonneau
-##' @seealso \code{\link{tdata}} for extracting or updating data and
-##' \code{\link{phylo4d-methods}} constructor.
-##' @keywords methods
-##' @rdname addData-methods
-##' @include phylo4d-class.R
-##' @export
-##' @examples
-##'   data(geospiza)
-##'   nDt <- data.frame(a=rnorm(nNodes(geospiza)), b=1:nNodes(geospiza),
-##'                     row.names=nodeId(geospiza, "internal"))
-##'   t1 <- addData(geospiza, node.data=nDt)
-setGeneric("addData", function(x, ...) {
+  ##' @param x a phylo4 or a phylo4d object
+  ##' @param tip.data a data frame (or object to be coerced to one)
+  ##' containing only tip data
+  ##' @param node.data a data frame (or object to be coerced to one)
+  ##' containing only node data
+  ##' @param all.data a data frame (or object to be coerced to one)
+  ##' containing both tip and node data
+  ##' @param merge.data if both \code{tip.data} and \code{node.data} are
+  ##' provided, it determines whether columns with common names will be
+  ##' merged together (default TRUE). If FALSE, columns with common
+  ##' names will be preserved separately, with ".tip" and ".node"
+  ##' appended to the names. This argument has no effect if
+  ##' \code{tip.data} and \code{node.data} have no column names in
+  ##' common.
+  ##' @param pos should the new data provided be bound \code{before} or
+  ##' \code{after} the pre-existing data?
+  ##' @param \dots additional arguments to control how matching between
+  ##' data and tree (see Details section of
+  ##' \code{\link{phylo4d-methods}} for more details).
+  ##' @return \code{addData} returns a \code{phylo4d} object.
+  ##' @author Francois Michonneau
+  ##' @seealso \code{\link{tdata}} for extracting or updating data and
+  ##' \code{\link{phylo4d-methods}} constructor.
+  ##' @keywords methods
+  ##' @rdname addData-methods
+  ##' @include phylo4d-class.R
+  ##' @export
+  ##' @examples
+  ##'   data(geospiza)
+  ##'   nDt <- data.frame(a=rnorm(nNodes(geospiza)), b=1:nNodes(geospiza),
+  ##'                     row.names=nodeId(geospiza, "internal"))
+  ##'   t1 <- addData(geospiza, node.data=nDt)
+  setGeneric("addData", function(x, ...) {
     standardGeneric("addData")
-})
+  })
 
 ##' @rdname addData-methods
 ##' @aliases addData-methods addData,phylo4-method

R/phylo4d-methods.R

@@ -88,7 +88,7 @@
 ##' @details This is the list of additional arguments that can be used
 ##' to control matching between the tree and the data:
 ##'
-##' \itemize{
+##' \describe{
 ##'
 ##' \item{match.data}{(logical) should the rownames of the data frame
 ##' be used to be matched against tip and internal node identifiers?}

R/print-methods.R

@@ -90,6 +90,7 @@ setMethod("show", signature(object="phylo4"),
 ##' @rdname print-methods
 ##' @aliases names
 ##' @exportMethod names
+##' @export
 setGeneric("names")
 
 ##' @rdname print-methods