added untracked files

inst/example.R

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+# Load libraries
+library(ape)
+
+# An example of how to produce a zero-constraint tree based on the Agalmatidae 
+# sensu stricto + Bargmannia constraint of Dunn et al. 2005 
+# (http://dx.doi.org/10.1080/10635150500354837)
+
+data( siphonophore_ml )
+data( siphonophore_constraint )
+
+zc <- zero_constrained( siphonophore_ml, siphonophore_constraint )
+plot( zc )

man/are_bipartitions_incompatible.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/utility_functions.R
+\name{are_bipartitions_incompatible}
+\alias{are_bipartitions_incompatible}
+\title{Check if two bipartitions drawn from trees with the same tips are incompatible with eachother.
+Each bipartition is defined as a vector of the names of the tips on one side of the
+bipartition.}
+\usage{
+are_bipartitions_incompatible(bi1, bi2, phy)
+}
+\arguments{
+\item{bi1}{The first bipartition.}
+
+\item{bi2}{The second bipartition.}
+
+\item{phy}{A phylo object describing a tree that includes all tips under investigation.
+This is used to infer the other half of each bipartition.}
+}
+\value{
+TRUE if bi1 is incompatible with bi2, otherwise FALSE.
+}
+\description{
+Check if two bipartitions drawn from trees with the same tips are incompatible with eachother.
+Each bipartition is defined as a vector of the names of the tips on one side of the
+bipartition.
+}
+

man/bipartition_for_edge.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/utility_functions.R
+\name{bipartition_for_edge}
+\alias{bipartition_for_edge}
+\title{Get a bipartition, described as a vector of tip numbers, from a specified tree and
+edge number.}
+\usage{
+bipartition_for_edge(phy, edge)
+}
+\arguments{
+\item{phy}{A phylo object that specifies the tree.}
+
+\item{edge}{The number of the edge that defines the bipartition.}
+}
+\value{
+A vector of tip nodes (specified by numbers) that define one half of the
+bipartition (the other half is the set of tip nodes that are not in this vector).
+}
+\description{
+Get a bipartition, described as a vector of tip numbers, from a specified tree and
+edge number.
+}
+

man/bipartition_for_edge_by_label.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/utility_functions.R
+\name{bipartition_for_edge_by_label}
+\alias{bipartition_for_edge_by_label}
+\title{Get a bipartition, described as a vector of tip labels, from a specified tree and
+edge number.}
+\usage{
+bipartition_for_edge_by_label(edge, phy)
+}
+\arguments{
+\item{edge}{The number of the edge that defines the bipartition.}
+
+\item{phy}{A phylo object that specifies the tree.}
+}
+\value{
+A vector of tip nodes (specified by labels) that define one half of the
+bipartition (the other half is the set of tip nodes that are not in this vector).
+}
+\description{
+Get a bipartition, described as a vector of tip labels, from a specified tree and
+edge number.
+}
+

man/descendants.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/utility_functions.R
+\name{descendants}
+\alias{descendants}
+\title{Get all the descendants of a given node in a tree.}
+\usage{
+descendants(phy, a, keep_node = FALSE)
+}
+\arguments{
+\item{phy}{A phylo object that specifies the tree.}
+
+\item{a}{The number of a node in phy.}
+
+\item{keep_node}{If FALSE, do not include a in the result.}
+}
+\value{
+A vector of nodes (specified by number) that are descendants of a. Includes
+internal and tip nodes.
+}
+\description{
+Get all the descendants of a given node in a tree.
+}
+

man/get_bipartitions.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/utility_functions.R
+\name{get_bipartitions}
+\alias{get_bipartitions}
+\title{Get a list of all the bipartitions in a tree.}
+\usage{
+get_bipartitions(phy)
+}
+\arguments{
+\item{phy}{A phylo object that specifies the tree.}
+}
+\value{
+A list of bipartitions for the tree. The order of the list corresponds to the
+edges in phy$edge. Bipartitions are specified as a vector of the tip labels that make
+up one half of the bipartition.
+}
+\description{
+Get a list of all the bipartitions in a tree.
+}
+

man/hutan.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/hutan.R
+\docType{package}
+\name{hutan}
+\alias{hutan}
+\alias{hutan-package}
+\title{hutan: A collection of tools for phylogenetic tree manipulation.}
+\description{
+The hutan package provides functions for common phylogenetic tree
+manipulation tasks, and uses these fascilitate some more specialized
+tasks. It is named after the Indonesian word for forest.
+}
+

man/incompatible_edges.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/utility_functions.R
+\name{incompatible_edges}
+\alias{incompatible_edges}
+\title{Identify the edges in one phylo object that are incompatible with the edges in another
+phylo object. Requires the same tip labels for each tree.}
+\usage{
+incompatible_edges(phy1, phy2)
+}
+\arguments{
+\item{phy1}{The tree under consideration}
+
+\item{phy2}{The tree to be compared to}
+}
+\value{
+A boolean vector corresponding to the edges in phy1. Each element is FALSE if
+the edge is compatible with phy2, or TRUE if incompatible.
+}
+\description{
+Identify the edges in one phylo object that are incompatible with the edges in another
+phylo object. Requires the same tip labels for each tree.
+}
+

man/is_incompatible_with_set.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/utility_functions.R
+\name{is_incompatible_with_set}
+\alias{is_incompatible_with_set}
+\title{Check if bipartition bi is incompatible with the bipartitions in bi_list.
+Each bipartition is defined as a vector of the names of the tips on one side of the
+bipartition.}
+\usage{
+is_incompatible_with_set(bi, bi_list, phy)
+}
+\arguments{
+\item{bi}{The query bipartition.}
+
+\item{bi_list}{A list of the bipartitions to be compared against.}
+
+\item{phy}{A phylo object describing a tree that includes all tips under investigation.
+This is used to infer the other half of each bipartition.}
+}
+\value{
+TRUE if bi is incompatible with any bipartition in bi_list, otherwise FALSE.
+}
+\description{
+Check if bipartition bi is incompatible with the bipartitions in bi_list.
+Each bipartition is defined as a vector of the names of the tips on one side of the
+bipartition.
+}
+

man/tip_descendants.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/utility_functions.R
+\name{tip_descendants}
+\alias{tip_descendants}
+\title{Get all the tips that are descendants of a given node in a tree.}
+\usage{
+tip_descendants(phy, a)
+}
+\arguments{
+\item{phy}{A phylo object that specifies the tree.}
+
+\item{a}{The number of a node in phy.}
+}
+\value{
+A vector of tip nodes (specified by number) that are descendants of a. If a is
+a tip, it is the sole element of this vector.
+}
+\description{
+Get all the tips that are descendants of a given node in a tree.
+}
+

man/tips.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/utility_functions.R
+\name{tips}
+\alias{tips}
+\title{Get tips and labels of a phylo object.}
+\usage{
+tips(phy)
+}
+\arguments{
+\item{phy}{A phylo object.}
+}
+\value{
+A vector of all the tips, annotated with their names
+}
+\description{
+Get tips and labels of a phylo object.
+}
+

man/zero_constrained.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/utility_functions.R
+\name{zero_constrained}
+\alias{zero_constrained}
+\title{Generates the "zero-constrained" tree described by Susko 2014
+(http://dx.doi.org/10.1093/molbev/msu039)}
+\usage{
+zero_constrained(phy_resolved, phy_constraint, epsilon = 1e-06)
+}
+\arguments{
+\item{phy_resolved}{A fully resolved phylogeny stored as a phylo object, e.g. an ML
+tree.}
+
+\item{phy_constraint}{A partially resolved constraint tree.}
+
+\item{epsilon}{}
+}
+\value{
+A phylo object containing a tree that is the same as phy_resolved, except that
+the length of edges that are incompatible with phy_constraint are replaced with epsilon.
+}
+\description{
+Generates the "zero-constrained" tree described by Susko 2014
+(http://dx.doi.org/10.1093/molbev/msu039)
+}
+\examples{
+zc <- zero_constrained( ml, constraint )
+}
+