Man pages for caseywdunn/hutan
A Collection of Tools for Phylogenetic Tree Manipulation

ancestral_edgesFor a node in a tree, get a vector of the edges between the...
are_bipartitions_compatibleCheck if two bipartitions drawn from trees with the same tips...
bipartition_for_edgeGet a bipartition, described as a vector of tip numbers, from...
bipartition_for_edge_by_labelGet a bipartition, described as a vector of tip labels, from...
calc_diffsFor each internal node, calculate the difference in state...
compatible_edgesIdentify the edges in one phylo object that are compatible...
connecting_edgesFor two nodes in a tree, get a vector of the edges that...
cut_treeCuts a single tree on the branch subtending a specified node
decompose_treeDecomposes a single tree into a series of subtrees designated...
descendantsGet all the descendants of a given node in a tree.
difference_from_calibratedAssesses how much phy deviates from an ultrametric tree
distance_from_tipFor each node in the tree (including internal nodes and tips)...
extend_terminal_branchesExtends each terminal branch by specified length
flip_bipartitionGiven a tree and a bipartition, described as a vector of tip...
get_bipartitionsGet a list of all the bipartitions in a tree.
get_corresponding_nodesGiven two trees phy1 and phy2 with the same topology and tip...
hutanhutan: A collection of tools for phylogenetic tree...
is_compatible_with_setCheck if bipartition bi is compatible with the bipartitions...
is_monophyleticTest if a set of tips, specified as a vector of tip labels,...
picxEstimate the extended phylogenetic independent contrast....
safe.drop.tipDrops specified tips from a phylogeny. Like ape's drop.tip(),...
sim_diffsFor each internal node, simulate the difference between state...
siphonophore_constraintSiphonophores constraint phylogeny.
siphonophore_mlSiphonophores phylogeny.
slide_root_edgesRepartitions lengths along edges that descend from root node...
tip_descendantsGet all the tips that are descendants of a given node in a...
tipsGet tips and labels of a phylo object.
zero_constrainedGenerates the "zero-constrained" tree described by Susko 2014...
caseywdunn/hutan documentation built on Nov. 21, 2017, 5:02 a.m.