[Phylobase-commits] r901 - pkg/R

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

Author: francois
Date: 2014-04-08 17:18:06 +0200 (Tue, 08 Apr 2014)
New Revision: 901

Modified:
   pkg/R/formatData.R
Log:
updated roxygen formatting

Modified: pkg/R/formatData.R
===================================================================
--- pkg/R/formatData.R	2014-04-08 15:07:30 UTC (rev 900)
+++ pkg/R/formatData.R	2014-04-08 15:18:06 UTC (rev 901)
@@ -1,58 +1,65 @@
-#' Format data for use in phylo4d objects
-#' 
-#' Associates data with tree nodes and applies consistent formatting rules.
-#' 
-#' 
-#' \code{formatData} is an internal function that should not be called directly
-#' by the user. It is used to format data provided by the user before
-#' associating it with a tree, and is called internally by the \code{phylo4d},
-#' \code{tdata}, and \code{addData} methods. However, users may pass additional
-#' arguments to these methods in order to control how the data are matched to
-#' nodes.
-#' 
-#' Rules for matching rows of data to tree nodes are determined jointly by the
-#' \code{match.data} and \code{rownamesAsLabels} arguments. If
-#' \code{match.data} is TRUE, data frame rows will be matched exclusively
-#' against tip and node labels if \code{rownamesAsLabels} is also TRUE, whereas
-#' any all-digit row names will be matched against tip and node numbers if
-#' \code{rownamesAsLabels} is FALSE (the default). If \code{match.data} is
-#' FALSE, \code{rownamesAsLabels} has no effect, and row matching is purely
-#' positional with respect to the order returned by \code{nodeId(phy, type)}.
-#' 
-#' \code{formatData} (1) converts labels provided in the data into node
-#' numbers, (2) makes sure that the data are appropriately matched against tip
-#' and/or internal nodes, (3) checks for differences between data and tree, (4)
-#' creates a data frame with the correct dimensions given a tree.
-#' 
-#' @param phy a valid \code{phylo4} object
-#' @param dt a data frame, matrix, vector, or factor
-#' @param type type of data to attach
-#' @param match.data (logical) should the rownames of the data frame be used to
-#' be matched against tip and internal node identifiers? See details.
-#' @param rownamesAsLabels (logical), should the row names of the data provided
-#' be matched only to labels (TRUE), or should any number-like row names be
-#' matched to node numbers (FALSE and default)
-#' @param label.type character, \code{rownames} or \code{column}: should the
-#' labels be taken from the row names of \code{dt} or from the
-#' \code{label.column} column of \code{dt}?
-#' @param label.column if \code{label.type=="column"}, column specifier (number
-#' or name) of the column containing tip labels
-#' @param missing.data action to take if there are missing data or if there are
-#' data labels that don't match
-#' @param extra.data action to take if there are extra data or if there are
-#' labels that don't match
-#' @param keep.all (logical), should the returned data have rows for all nodes
-#' (with NA values for internal rows when type='tip', and vice versa) (TRUE and
-#' default) or only rows corresponding to the type argument
-#' @return \code{formatData} returns a data frame having node numbers as row
-#' names. The data frame is also formatted to have the correct dimension given
-#' the \code{phylo4} object provided.
-#' @author Francois Michonneau
-#' @seealso the \code{\link{phylo4d}} constructor, the \linkS4class{phylo4d}
-#' class. See also the \code{\link{checkPhylo4}}, the \code{\link{phylo4}}
-#' constructor and the \linkS4class{phylo4} class. See
-#' \code{\link{coerce-methods}} for translation functions.
-#' @keywords misc
+##' Format data for use in phylo4d objects
+##' 
+##' Associates data with tree nodes and applies consistent formatting
+##' rules.
+##' 
+##' 
+##' \code{formatData} is an internal function that should not be
+##' called directly by the user. It is used to format data provided by
+##' the user before associating it with a tree, and is called
+##' internally by the \code{phylo4d}, \code{tdata}, and \code{addData}
+##' methods. However, users may pass additional arguments to these
+##' methods in order to control how the data are matched to nodes.
+##' 
+##' Rules for matching rows of data to tree nodes are determined
+##' jointly by the \code{match.data} and \code{rownamesAsLabels}
+##' arguments. If \code{match.data} is TRUE, data frame rows will be
+##' matched exclusively against tip and node labels if
+##' \code{rownamesAsLabels} is also TRUE, whereas any all-digit row
+##' names will be matched against tip and node numbers if
+##' \code{rownamesAsLabels} is FALSE (the default). If
+##' \code{match.data} is FALSE, \code{rownamesAsLabels} has no effect,
+##' and row matching is purely positional with respect to the order
+##' returned by \code{nodeId(phy, type)}.
+##' 
+##' \code{formatData} (1) converts labels provided in the data into
+##' node numbers, (2) makes sure that the data are appropriately
+##' matched against tip and/or internal nodes, (3) checks for
+##' differences between data and tree, (4) creates a data frame with
+##' the correct dimensions given a tree.
+##' 
+##' @param phy a valid \code{phylo4} object
+##' @param dt a data frame, matrix, vector, or factor
+##' @param type type of data to attach
+##' @param match.data (logical) should the rownames of the data frame
+##' be used to be matched against tip and internal node identifiers?
+##' See details.
+##' @param rownamesAsLabels (logical), should the row names of the
+##' data provided be matched only to labels (TRUE), or should any
+##' number-like row names be matched to node numbers (FALSE and
+##' default)
+##' @param label.type character, \code{rownames} or \code{column}:
+##' should the labels be taken from the row names of \code{dt} or from
+##' the \code{label.column} column of \code{dt}?
+##' @param label.column if \code{label.type=="column"}, column
+##' specifier (number or name) of the column containing tip labels
+##' @param missing.data action to take if there are missing data or if
+##' there are data labels that don't match
+##' @param extra.data action to take if there are extra data or if
+##' there are labels that don't match
+##' @param keep.all (logical), should the returned data have rows for
+##' all nodes (with NA values for internal rows when type='tip', and
+##' vice versa) (TRUE and default) or only rows corresponding to the
+##' type argument
+##' @return \code{formatData} returns a data frame having node numbers
+##' as row names. The data frame is also formatted to have the correct
+##' dimension given the \code{phylo4} object provided.
+##' @author Francois Michonneau
+##' @seealso the \code{\link{phylo4d}} constructor, the
+##' \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"),