[Phylobase-commits] r934 - pkg/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue May 6 22:26:51 CEST 2014
Author: francois
Date: 2014-05-06 22:26:51 +0200 (Tue, 06 May 2014)
New Revision: 934
Modified:
pkg/man/MRCA.Rd
pkg/man/addData-methods.Rd
pkg/man/ancestors.Rd
pkg/man/checkPhylo4.Rd
pkg/man/edgeLength-methods.Rd
pkg/man/edges-accessors.Rd
pkg/man/extractTree.Rd
pkg/man/formatData.Rd
pkg/man/geospiza.Rd
pkg/man/getNode-methods.Rd
pkg/man/labels-methods.Rd
pkg/man/multiPhylo-class.Rd
pkg/man/nTips-methods.Rd
pkg/man/nodeId-methods.Rd
pkg/man/owls4.Rd
pkg/man/pdata-class.Rd
pkg/man/pdata.Rd
pkg/man/phylo4-class.Rd
pkg/man/phylo4-methods.Rd
pkg/man/phylo4d-accessors.Rd
pkg/man/phylo4d-class.Rd
pkg/man/phylo4d-methods.Rd
pkg/man/phyloXXYY.Rd
pkg/man/phylobase-package.Rd
pkg/man/phylobase.options.Rd
pkg/man/phylobubbles.Rd
pkg/man/phylomat-class.Rd
pkg/man/plotOneTree.Rd
pkg/man/print-methods.Rd
pkg/man/readNexus.Rd
pkg/man/reorder-methods.Rd
pkg/man/root-methods.Rd
pkg/man/setAs-methods.Rd
pkg/man/shortestPath-methods.Rd
pkg/man/subset-methods.Rd
pkg/man/summary-methods.Rd
pkg/man/tdata-methods.Rd
pkg/man/tip.data.plot.Rd
pkg/man/treePlot-methods.Rd
pkg/man/treeStructure-methods.Rd
Log:
update docs
Modified: pkg/man/MRCA.Rd
===================================================================
--- pkg/man/MRCA.Rd 2014-05-06 20:26:32 UTC (rev 933)
+++ pkg/man/MRCA.Rd 2014-05-06 20:26:51 UTC (rev 934)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
\docType{methods}
\name{MRCA}
\alias{MRCA}
@@ -12,10 +13,9 @@
\S4method{MRCA}{phylo}(phy, ...)
}
\arguments{
- \item{phy}{a phylogenetic tree in phylo4, phylo4d or
- phylo format.}
+\item{phy}{a phylogenetic tree in phylo4, phylo4d or phylo format.}
- \item{...}{a vector of nodes}
+\item{...}{a vector of nodes}
}
\value{
the node corresponding to the most recent common ancestor
@@ -24,18 +24,17 @@
Most Recent Common Ancestor (MRCA) of 2 or more nodes.
}
\details{
-Given some nodes (i.e., tips and/or internal), this
-function returns the node corresponding to the most recent
-common ancestor.
+Given some nodes (i.e., tips and/or internal), this function
+returns the node corresponding to the most recent common ancestor.
-If \code{phy} is a \code{phylo4} or \code{phylo4d} object,
-the nodes can contain both numeric or character values that
-will be used by \code{getNode} to retrieve the correct
-node. However, if \code{phy} is a \code{phylo} object, the
-nodes must be a numeric vector.
+If \code{phy} is a \code{phylo4} or \code{phylo4d} object, the
+nodes can contain both numeric or character values that will be
+used by \code{getNode} to retrieve the correct node. However, if
+\code{phy} is a \code{phylo} object, the nodes must be a numeric
+vector.
-With \code{phylo4} and \code{phylo4d} objects, if a single
-node is provided, it will be returned.
+With \code{phylo4} and \code{phylo4d} objects, if a single node is
+provided, it will be returned.
}
\examples{
data(geospiza)
Modified: pkg/man/addData-methods.Rd
===================================================================
--- pkg/man/addData-methods.Rd 2014-05-06 20:26:32 UTC (rev 933)
+++ pkg/man/addData-methods.Rd 2014-05-06 20:26:51 UTC (rev 934)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
\docType{methods}
\name{addData}
\alias{addData}
@@ -15,51 +16,46 @@
all.data = NULL, merge.data = TRUE, pos = c("after", "before"), ...)
}
\arguments{
- \item{x}{a phylo4 or a phylo4d object}
+\item{x}{a phylo4 or a phylo4d object}
- \item{tip.data}{a data frame (or object to be coerced to
- one) containing only tip data}
+\item{tip.data}{a data frame (or object to be coerced to one) containing
+only tip data}
- \item{node.data}{a data frame (or object to be coerced to
- one) containing only node data}
+\item{node.data}{a data frame (or object to be coerced to one) containing
+only node data}
- \item{all.data}{a data frame (or object to be coerced to
- one) containing both tip and node data}
+\item{all.data}{a data frame (or object to be coerced to one) containing
+both tip and node data}
- \item{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.}
+\item{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.}
- \item{pos}{should the new data provided be bound
- \code{before} or \code{after} the pre-existing data?}
+\item{pos}{should the new data provided be bound \code{before} or
+\code{after} the pre-existing data?}
- \item{\dots}{additional arguments to be passed to
- \link{formatData}}
+\item{\dots}{additional arguments to be passed to \link{formatData}}
}
\value{
\code{addData} returns a \code{phylo4d} object.
}
\description{
-\code{addData} adds data to a \code{phylo4} (converting it
-in a \code{phylo4d} object) or to a \code{phylo4d} object
+\code{addData} adds data to a \code{phylo4} (converting it in a
+\code{phylo4d} object) or to a \code{phylo4d} object
}
\details{
-Rules for matching data to tree nodes are identical to
-those used by the \code{\link{phylo4d}} constructor.
+Rules for matching data to tree nodes are identical to those used by the
+\code{\link{phylo4d}} constructor.
-If any column names in the original data are the same as
-columns in the new data, ".old" is appended to the former
-column names and ".new" is appended to the new column
-names.
+If any column names in the original data are the same as columns in the new
+data, ".old" is appended to the former column names and ".new" is appended
+to the new column names.
-The option \code{pos} is ignored (silently) if \code{x} is
-a \code{phylo4} object. It is provided for compatibility
-reasons.
+The option \code{pos} is ignored (silently) if \code{x} is a \code{phylo4}
+object. It is provided for compatibility reasons.
}
\examples{
data(geospiza)
Modified: pkg/man/ancestors.Rd
===================================================================
--- pkg/man/ancestors.Rd 2014-05-06 20:26:32 UTC (rev 933)
+++ pkg/man/ancestors.Rd 2014-05-06 20:26:51 UTC (rev 934)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
\name{ancestor}
\alias{ancestor}
\alias{ancestors}
@@ -17,72 +18,70 @@
ancestors(phy, node, type = c("all", "parent", "ALL"))
}
\arguments{
- \item{phy}{a \linkS4class{phylo4} object (or one
- inheriting from \linkS4class{phylo4}, e.g. a
- \linkS4class{phylo4d} object)}
+\item{phy}{a \linkS4class{phylo4} object (or one inheriting from
+\linkS4class{phylo4}, e.g. a \linkS4class{phylo4d} object)}
- \item{node}{either an integer corresponding to a node ID
- number, or a character corresponding to a node label; for
- \code{ancestors} and \code{descendants}, this may be a
- vector of multiple node numbers or names}
+\item{node}{either an integer corresponding to a node ID number, or a
+character corresponding to a node label; for \code{ancestors} and
+\code{descendants}, this may be a vector of multiple node numbers or names}
- \item{type}{(\code{ancestors}) specify whether to return
- just direct ancestor ("parent"), all ancestor nodes
- ("all"), or all ancestor nodes including self ("ALL");
- (\code{descendants}) specify whether to return just
- direct descendants ("children"), all extant descendants
- ("tips"), or all descendant nodes ("all")}
+\item{type}{(\code{ancestors}) specify whether to return just direct
+ancestor ("parent"), all ancestor nodes ("all"), or all ancestor nodes
+including self ("ALL"); (\code{descendants}) specify whether to return just
+direct descendants ("children"), all extant descendants ("tips"), or all
+descendant nodes ("all")}
- \item{include.self}{whether to include self in list of
- siblings}
+\item{include.self}{whether to include self in list of siblings}
- \item{\dots}{a list of node numbers or names, or a vector
- of node numbers or names}
+\item{\dots}{a list of node numbers or names, or a vector of node numbers or
+names}
}
\value{
-\describe{ \item{\code{ancestors}}{ return a named vector
-(or a list of such vectors in the case of multiple input
-nodes) of the ancestors and descendants of a node}
-
-\item{\code{descendants}}{ return a named vector (or a list
+\describe{
+\item{\code{ancestors}}{ return a named vector (or a list
of such vectors in the case of multiple input nodes) of the
ancestors and descendants of a node}
+\item{\code{descendants}}{ return a named vector (or a list of
+such vectors in the case of multiple input nodes) of the ancestors
+and descendants of a node}
+
\item{\code{ancestor}}{ \code{ancestor} is analogous to
-\code{ancestors(\dots{}, type="parent")} (i.e. direct
-ancestor only), but returns a single concatenated vector in
-the case of multiple input nodes}
+\code{ancestors(\dots{}, type="parent")} (i.e. direct ancestor
+only), but returns a single concatenated vector in the case of
+multiple input nodes}
-\item{\code{children}}{is analogous to
-\code{descendants(\dots{}, type="children")} (i.e. direct
-descendants only), but is not currently intended to be used
-with multiple input nodes }
+\item{\code{children}}{is analogous to \code{descendants(\dots{},
+type="children")} (i.e. direct descendants only), but is not
+currently intended to be used with multiple input nodes }
-\item{\code{siblings}}{ returns sibling nodes (children of
-the same parent)} }
+\item{\code{siblings}}{ returns sibling nodes (children of the same
+parent)}
}
+}
\description{
-Functions for describing relationships among phylogenetic
-nodes (i.e. internal nodes or tips).
+Functions for describing relationships among phylogenetic nodes (i.e.
+internal nodes or tips).
}
\details{
-\code{ancestors} and \code{descendants} can take
-\code{node} vectors of arbitrary length, returning a list
-of output vectors if the number of valid input nodes is
-greater than one. List element names are taken directly
-from the input node vector.
+\code{ancestors} and \code{descendants} can take \code{node} vectors of
+arbitrary length, returning a list of output vectors if the number of valid
+input nodes is greater than one. List element names are taken directly from
+the input node vector.
-If any supplied nodes are not found in the tree, the
-behavior currently varies across functions. \itemize{ \item
-Invalid nodes are automatically omitted by \code{ancestors}
+If any supplied nodes are not found in the tree, the behavior currently
+varies across functions.
+\itemize{
+\item Invalid nodes are automatically omitted by \code{ancestors}
and \code{descendants}, with a warning.
-\item \code{ancestor} will return \code{NA} for any invalid
-nodes, with a warning.
+\item \code{ancestor}
+will return \code{NA} for any invalid nodes, with a warning.
-\item Both \code{children} and \code{siblings} will return
-an empty vector, again with a warning. }
+\item Both \code{children} and \code{siblings} will return an empty
+vector, again with a warning.
}
+}
\examples{
data(geospiza)
nodeLabels(geospiza) <- LETTERS[1:nNodes(geospiza)]
@@ -103,7 +102,7 @@
sumEdgeLength(geospiza, ancestors(geospiza, "fortis", type="ALL"))
}
\seealso{
-\code{\link[ape]{mrca}}, in the ape package, gives a list
-of all subtrees
+\code{\link[ape]{mrca}}, in the ape package, gives a list of all
+subtrees
}
Modified: pkg/man/checkPhylo4.Rd
===================================================================
--- pkg/man/checkPhylo4.Rd 2014-05-06 20:26:32 UTC (rev 933)
+++ pkg/man/checkPhylo4.Rd 2014-05-06 20:26:51 UTC (rev 934)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
\name{checkPhylo4}
\alias{checkPhylo4}
\alias{checkPhylo4Data}
@@ -7,59 +8,50 @@
checkPhylo4(object)
}
\arguments{
- \item{object}{A prospective phylo4 or phylo4d object}
+\item{object}{A prospective phylo4 or phylo4d object}
}
\value{
-As required by \code{\link[methods]{validObject}}, returns
-an error string (describing problems) or TRUE if everything
-is OK.
+As required by \code{\link[methods]{validObject}}, returns an error
+string (describing problems) or TRUE if everything is OK.
}
\description{
Basic checks on the validity of S4 phylogenetic objects
}
\note{
-These functions are only intended to be called by other
-phylobase functions.
+These functions are only intended to be called by other phylobase functions.
-\code{checkPhylo4} is an (inflexible) wrapper for
-\code{checkTree}. The rules for \code{phylo4} objects
-essentially follow those for \code{phylo} objects from the
-\code{ape} package, which are in turn defined in
-\url{http://ape.mpl.ird.fr/misc/FormatTreeR_28July2008.pdf}.
-These are essentially that: \itemize{ \item if the tree has
-edge lengths defined, the number of edge lengths must match
-the number of edges; \item the number of tip labels must
-match the number of tips; \item in a tree with \code{ntips}
-tips and \code{nnodes} (total) nodes, nodes 1 to
-\code{ntips} must be tips \item if the tree is rooted, the
-root must be node number \code{ntips+1} and the root node
-must be the first row of the edge matrix \item tip labels,
-node labels, edge labels, edge lengths must have proper
-internal names (i.e. internal names that match the node
-numbers they document) \item tip and node labels must be
-unique }
+\code{checkPhylo4} is an (inflexible) wrapper for \code{checkTree}. The
+rules for \code{phylo4} objects essentially follow those for \code{phylo}
+objects from the \code{ape} package, which are in turn defined in
+\url{http://ape.mpl.ird.fr/misc/FormatTreeR_28July2008.pdf}. These are
+essentially that: \itemize{ \item if the tree has edge lengths defined, the
+number of edge lengths must match the number of edges; \item the number of
+tip labels must match the number of tips; \item in a tree with \code{ntips}
+tips and \code{nnodes} (total) nodes, nodes 1 to \code{ntips} must be tips
+\item if the tree is rooted, the root must be node number \code{ntips+1} and
+the root node must be the first row of the edge matrix \item tip labels,
+node labels, edge labels, edge lengths must have proper internal names (i.e.
+internal names that match the node numbers they document) \item tip and node
+labels must be unique }
-You can alter some of the default options by using the
-function \code{phylobase.options}.
+You can alter some of the default options by using the function
+\code{phylobase.options}.
For \code{phylo4d} objects, \code{checkTree} also calls
-\code{checkPhylo4Data} to check the validity of the data
-associated with the tree. It ensures that (1) the data
-associated with the tree have the correct dimensions, (2)
-that the row names for the data are correct.
+\code{checkPhylo4Data} to check the validity of the data associated with the
+tree. It ensures that (1) the data associated with the tree have the correct
+dimensions, (2) that the row names for the data are correct.
}
\author{
Ben Bolker, Steven Kembel, Francois Michonneau
}
\seealso{
-the \code{\link{phylo4}} constructor and
-\linkS4class{phylo4} class; \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 and
-\code{\link{phylobase.options} to change some of the
-default options of the validator.}
+the \code{\link{phylo4}} constructor and \linkS4class{phylo4}
+class; \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 and
+\code{\link{phylobase.options} to change some of the default options of the
+validator.}
}
\keyword{misc}
Modified: pkg/man/edgeLength-methods.Rd
===================================================================
--- pkg/man/edgeLength-methods.Rd 2014-05-06 20:26:32 UTC (rev 933)
+++ pkg/man/edgeLength-methods.Rd 2014-05-06 20:26:51 UTC (rev 934)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
\docType{methods}
\name{hasEdgeLength}
\alias{depthTips}
@@ -45,52 +46,47 @@
\S4method{isUltrametric}{phylo4}(x, tol = .Machine$double.eps^0.5)
}
\arguments{
- \item{x}{a \code{phylo4} or \code{phylo4d} object.}
+\item{x}{a \code{phylo4} or \code{phylo4d} object.}
- \item{value}{a numeric vector indicating the new values
- for the edge lengths}
+\item{value}{a numeric vector indicating the new values for the edge lengths}
- \item{node}{optional numeric or character vector
- indicating the nodes for which edge}
+\item{node}{optional numeric or character vector indicating the
+nodes for which edge}
- \item{use.names}{should the the name attributes of
- \code{value} be used to match the length to a given
- edge.}
+\item{use.names}{should the the name attributes of \code{value} be
+used to match the length to a given edge.}
- \item{tol}{the tolerance to decide whether all the tips
- have the same depth to test if the tree is ultrametric.
- Default is \code{.Machine$double.eps^0.5}.}
+\item{tol}{the tolerance to decide whether all the tips have the
+same depth to test if the tree is ultrametric. Default is
+\code{.Machine$double.eps^0.5}.}
- \item{\dots}{optional arguments (none used at present).}
+\item{\dots}{optional arguments (none used at present).}
}
\value{
\describe{
-\item{hasEdgeLength}{whether or not the object has edge
-lengths (logical)}
+\item{hasEdgeLength}{whether or not the object has edge lengths
+(logical)}
\item{edgeLength}{a named vector of the edge length for the
object}
-\item{nodeDepth}{a named vector indicating the
-\dQuote{depth} (the distance between the root and the tip)
-of each tip.}
+\item{nodeDepth}{a named vector indicating the \dQuote{depth} (the
+distance between the root and the tip) of each tip.}
-\item{isUltrametric}{whether or not the tree is ultrametric
-(all the tips are have the same depth (distance from the
-root) (logical)}
+\item{isUltrametric}{whether or not the tree is ultrametric (all
+the tips are have the same depth (distance from the root) (logical)}
-\item{sumEdgeLength}{the sum of the edge lengths for a set
-of nodes (intended to be used with \code{ancestors} or
-\code{descendants})} }
+\item{sumEdgeLength}{the sum of the edge lengths for a set of
+nodes (intended to be used with \code{ancestors} or \code{descendants})}
}
+}
\description{
-These functions give information about and allow
-replacement of edge lengths.
+These functions give information about and allow replacement of edge lengths.
}
\details{
-The \code{edgeLength} function returns the edge length in
-the same order as the edges in the matrix.
+The \code{edgeLength} function returns the edge length in the same
+order as the edges in the matrix.
}
\examples{
data(geospiza)
Modified: pkg/man/edges-accessors.Rd
===================================================================
--- pkg/man/edges-accessors.Rd 2014-05-06 20:26:32 UTC (rev 933)
+++ pkg/man/edges-accessors.Rd 2014-05-06 20:26:51 UTC (rev 934)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
\docType{methods}
\name{edges}
\alias{edgeOrder}
@@ -27,31 +28,29 @@
\S4method{terminalEdges}{phylo4}(x)
}
\arguments{
- \item{x}{a \code{phylo4} or \code{phylo4d} object.}
+\item{x}{a \code{phylo4} or \code{phylo4d} object.}
- \item{drop.root}{logical (default FALSE), should the edge
- connecting the root be included in the edge matrix?}
+\item{drop.root}{logical (default FALSE), should the edge
+connecting the root be included in the edge matrix?}
- \item{\dots}{Optional arguments used by specific methods.
- (None used at present).}
+\item{\dots}{Optional arguments used by specific methods. (None
+used at present).}
}
\value{
-\describe{ \item{\code{edges}}{returns the edge matrix that
-represent the ancestor-descendant relationships among the
-nodes of the tree.}
+\describe{
+\item{\code{edges}}{returns the edge matrix that represent the
+ancestor-descendant relationships among the nodes of the tree.}
-\item{\code{edgeOrder}}{returns the order in which the edge
-matrix is in.}
+\item{\code{edgeOrder}}{returns the order in which the edge matrix
+is in.}
-\item{\code{internalEdges}}{returns a logical vector
-indicating internal edges (edges that connect an internal
-node to another). This vector is named with the
-\code{edgeId}}.
+\item{\code{internalEdges}}{returns a logical vector indicating
+internal edges (edges that connect an internal node to
+another). This vector is named with the \code{edgeId}}.
-\item{\code{terminalEdges}}{returns a logical vector
-indicating terminal edges (edges that connect an internal
-node to a tip). This vector is named with the \code{edgeId}
-}}
+\item{\code{terminalEdges}}{returns a logical vector indicating
+terminal edges (edges that connect an internal node to a
+tip). This vector is named with the \code{edgeId} }}
}
\description{
Access or modify information about the edges.
Modified: pkg/man/extractTree.Rd
===================================================================
--- pkg/man/extractTree.Rd 2014-05-06 20:26:32 UTC (rev 933)
+++ pkg/man/extractTree.Rd 2014-05-06 20:26:51 UTC (rev 934)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
\name{extractTree}
\alias{extractTree}
\title{Get tree from tree+data object}
@@ -5,22 +6,21 @@
extractTree(from)
}
\arguments{
- \item{from}{a \code{phylo4d} object, containing a
- phylogenetic tree plus associated phenotypic data.
- Created by the \code{phylo4d()} function.}
+\item{from}{a \code{phylo4d} object, containing a phylogenetic
+tree plus associated phenotypic data. Created by the
+\code{phylo4d()} function.}
}
\description{
Extracts a \code{phylo4} tree object from a \code{phylo4d}
tree+data object.
}
\details{
-\code{extractTree} extracts just the phylogeny from a
-tree+data object. The phylogeny contains the topology (how
-the nodes are linked together), the branch lengths (if
-any), and any tip and/or node labels. This may be useful
-for extracting a tree from a \code{phylo4d} object, and
-associating with another phenotypic dataset, or to convert
-the tree to another format.
+\code{extractTree} extracts just the phylogeny from a tree+data
+object. The phylogeny contains the topology (how the nodes are
+linked together), the branch lengths (if any), and any tip and/or
+node labels. This may be useful for extracting a tree from a
+\code{phylo4d} object, and associating with another phenotypic
+dataset, or to convert the tree to another format.
}
\examples{
tree.phylo <- ape::read.tree(text = "((a,b),c);")
Modified: pkg/man/formatData.Rd
===================================================================
--- pkg/man/formatData.Rd 2014-05-06 20:26:32 UTC (rev 933)
+++ pkg/man/formatData.Rd 2014-05-06 20:26:51 UTC (rev 934)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
\name{formatData}
\alias{formatData}
\title{Format data for use in phylo4d objects}
@@ -8,85 +9,80 @@
extra.data = c("warn", "OK", "fail"), keep.all = TRUE)
}
\arguments{
- \item{phy}{a valid \code{phylo4} object}
+\item{phy}{a valid \code{phylo4} object}
- \item{dt}{a data frame, matrix, vector, or factor}
+\item{dt}{a data frame, matrix, vector, or factor}
- \item{type}{type of data to attach}
+\item{type}{type of data to attach}
- \item{match.data}{(logical) should the rownames of the
- data frame be used to be matched against tip and internal
- node identifiers? See details.}
+\item{match.data}{(logical) should the rownames of the data frame
+be used to be matched against tip and internal node identifiers?
+See details.}
- \item{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)}
+\item{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)}
- \item{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}?}
+\item{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}?}
- \item{label.column}{if \code{label.type=="column"},
- column specifier (number or name) of the column
- containing tip labels}
+\item{label.column}{if \code{label.type=="column"}, column
+specifier (number or name) of the column containing tip labels}
- \item{missing.data}{action to take if there are missing
- data or if there are data labels that don't match}
+\item{missing.data}{action to take if there are missing data or if
+there are data labels that don't match}
- \item{extra.data}{action to take if there are extra data
- or if there are labels that don't match}
+\item{extra.data}{action to take if there are extra data or if
+there are labels that don't match}
- \item{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}
+\item{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}
}
\value{
\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.
+as row names. The data frame is also formatted to have the correct
+dimension given the \code{phylo4} object provided.
}
\description{
-Associates data with tree nodes and applies consistent
-formatting rules.
+Associates data with tree nodes and applies consistent formatting
+rules.
}
\details{
-\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.
+\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)}.
+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.
+\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.
}
\author{
Francois Michonneau
}
\seealso{
the \code{\link{phylo4d}} constructor, the
-\linkS4class{phylo4d} class. See
-\code{\link{coerce-methods}} for translation functions.
+\linkS4class{phylo4d} class. See \code{\link{coerce-methods}} for
+translation functions.
}
\keyword{misc}
Modified: pkg/man/geospiza.Rd
===================================================================
--- pkg/man/geospiza.Rd 2014-05-06 20:26:32 UTC (rev 933)
+++ pkg/man/geospiza.Rd 2014-05-06 20:26:51 UTC (rev 934)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
\docType{data}
\name{geospiza}
\alias{geospiza}
@@ -11,12 +12,12 @@
Dolph Schluter via Luke Harmon
}
\description{
-Phylogenetic tree and morphological data for Darwin's
-finches, in different formats
+Phylogenetic tree and morphological data for Darwin's finches, in different
+formats
}
\note{
-Stolen from Luke Harmon's Geiger package, to avoid
-unnecessary dependencies
+Stolen from Luke Harmon's Geiger package, to avoid unnecessary
+dependencies
}
\examples{
data(geospiza)
Modified: pkg/man/getNode-methods.Rd
===================================================================
--- pkg/man/getNode-methods.Rd 2014-05-06 20:26:32 UTC (rev 933)
+++ pkg/man/getNode-methods.Rd 2014-05-06 20:26:51 UTC (rev 934)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.0): do not edit by hand
\docType{methods}
\name{getNode}
\alias{getEdge}
@@ -20,70 +21,57 @@
missing = c("warn", "OK", "fail"))
}
\arguments{
- \item{x}{a \linkS4class{phylo4} object (or one inheriting
- from \linkS4class{phylo4}, e.g. a \linkS4class{phylo4d}
- object)}
+\item{x}{a \linkS4class{phylo4} object (or one inheriting from
+\linkS4class{phylo4}, e.g. a \linkS4class{phylo4d} object)}
- \item{node}{either an integer vector corresponding to
- node ID numbers, or a character vector corresponding to
- node labels; if missing, all nodes appropriate to the
- specified type will be returned by \code{getNode}, and
- all edges appropriate to the specified type will be
- returned by \code{getEdge}.}
+\item{node}{either an integer vector corresponding to node ID numbers, or a
+character vector corresponding to node labels; if missing, all nodes
+appropriate to the specified type will be returned by \code{getNode}, and
+all edges appropriate to the specified type will be returned by
+\code{getEdge}.}
- \item{type}{(\code{getNode}) specify whether to return
- nodes matching "all" tree nodes (default), only "tip"
- nodes, or only "internal" nodes; (\code{nodeId, edgeId})
- specify whether to return "all" tree nodes, or only those
- corresponding to "tip", "internal", or "root" nodes;
- (\code{getEdge}) specify whether to look up edges based
- on their descendant node ("descendant") or ancestral node
- ("ancestor")}
+\item{type}{(\code{getNode}) specify whether to return nodes matching "all"
+tree nodes (default), only "tip" nodes, or only "internal" nodes;
+(\code{nodeId, edgeId}) specify whether to return "all" tree nodes, or only
+those corresponding to "tip", "internal", or "root" nodes; (\code{getEdge})
+specify whether to look up edges based on their descendant node
+("descendant") or ancestral node ("ancestor")}
- \item{missing}{what to do if some requested node IDs or
- names are not in the tree: warn, do nothing, or stop with
- an error}
+\item{missing}{what to do if some requested node IDs or names are not in the
+tree: warn, do nothing, or stop with an error}
}
\value{
-\item{list("getNode")}{returns a named integer vector of
-node IDs, in the order of input nodes if provided,
-otherwise in nodeId order} \item{list("getEdge")}{returns a
-named character vector of edge IDs, in the order of input
-nodes if provide, otherwise in nodeId order}
-\item{list("nodeId")}{returns an unnamed integer vector of
-node IDs, in ascending order}
-\item{list("getEdge")}{returns an unnamed character vector
+\item{list("getNode")}{returns a named integer vector of node IDs,
+in the order of input nodes if provided, otherwise in nodeId order}
+\item{list("getEdge")}{returns a named character vector of edge IDs, in the
+order of input nodes if provide, otherwise in nodeId order}
+\item{list("nodeId")}{returns an unnamed integer vector of node IDs, in
+ascending order} \item{list("getEdge")}{returns an unnamed character vector
of edge IDs, in edge matrix order}
}
\description{
-Functions for retrieving node and edge IDs (possibly with
-corresponding labels) from a phylogenetic tree.
+Functions for retrieving node and edge IDs (possibly with corresponding
+labels) from a phylogenetic tree.
}
\details{
-\code{getNode} and \code{getEdge} are primarily intended
-for looking up the IDs either of nodes themselves or of
-edges associated with those nodes. Note that they behave
-quite differently. With \code{getNode}, any input nodes are
-looked up against tree nodes of the specified type, and
-those that match are returned as numeric node IDs with node
-labels (if they exist) as element names. With
-\code{getEdge}, any input nodes are looked up against edge
-ends of the specified type, and those that match are
-returned as character edge IDs with the corresponding node
-ID as element names.
+\code{getNode} and \code{getEdge} are primarily intended for looking up the
+IDs either of nodes themselves or of edges associated with those nodes. Note
+that they behave quite differently. With \code{getNode}, any input nodes are
+looked up against tree nodes of the specified type, and those that match are
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/phylobase -r 934
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