MetaPhylo
Documentation for MetaPhylo.
AbstractTrees.treebreadthAbstractTrees.treeheightAbstractTrees.treesizeMetaPhylo.add_child!MetaPhylo.ancestorsMetaPhylo.common_ancestorMetaPhylo.distanceMetaPhylo.distance_matrixMetaPhylo.findbranchesMetaPhylo.findnodesMetaPhylo.freezeMetaPhylo.isinternalMetaPhylo.isinternalMetaPhylo.isleafMetaPhylo.isleafMetaPhylo.isrerootableMetaPhylo.isrootedMetaPhylo.ladderize!MetaPhylo.leafedgesMetaPhylo.leavesMetaPhylo.parent_branchMetaPhylo.reindex!MetaPhylo.rem_descendants!MetaPhylo.reroot!MetaPhylo.swap!MetaPhylo.swapchildren!MetaPhylo.treelength
AbstractTrees.treebreadth — MethodAbstractTrees.treebreadth(tree::AbstractPhyloTree)Return the number of leaves in the tree.
AbstractTrees.treeheight — MethodAbstractTrees.treeheight(tree::AbstractPhyloTree)Return the maximum depth from the root to the leaves in the tree. See also treelength.
AbstractTrees.treesize — MethodAbstractTrees.treesize(tree::AbstractPhyloTree)Return the size og the tree.
MetaPhylo.add_child! — Methodadd_child!(tree::Tree, idx::Integer, branch_data::Dict{Symbol, Any}, node_data::Dict{Symbol, Any})Add a child node to the specified node with branch and node data. Return true on success.
MetaPhylo.ancestors — Methodancestors(tree::AbstractPhyloTree, idx::Integer)Return the indices of all ancestor nodes of the specified idx node.
MetaPhylo.common_ancestor — Methodcommon_ancestor(tree::AbstractPhyloTree, idx::Integer...)Return the lowest common ancestor index among specified nodes.
MetaPhylo.distance — Methoddistance(tree::AbstractPhyloTree, idx1::Integer, idx2::Integer)Return distance between two nodes on a tree.
MetaPhylo.distance_matrix — Methoddistance_matrix(tree::AbstractPhyloTree, [indices::Vector{<:Integer}])Return pairwise distances between all indices on the tree as an AxisArray. If not indices are specified, all leaves are used as input.
MetaPhylo.findbranches — Methodfindbranches(tree::AbstractPhyloTree, args...; ifnot_haskey::Bool=false)Return indices of tree branch which all values proceed by transformation(s) args for a given attribute are true.
MetaPhylo.findnodes — Methodfindnodes(tree::AbstractPhyloTree, args...; ifnot_haskey::Bool=false)Return indices of tree node which all values proceed by transformation(s) args for a given attribute are true.
MetaPhylo.freeze — Methodfreeze(tree::MetaPhylo.Tree)Generate a StaticTree from a tree. NamedTuple stores only the keys that are common to all data among the node and branch data of previous tree.
MetaPhylo.isinternal — Methodisinternal(tree::AbstractPhyloTree, idx::Integer)Return true if the edge is both connected to internal nodes of the tree.
MetaPhylo.isinternal — Methodisinternal(tree::AbstractPhyloTree, idx::Integer)Return true if the idx is contained in an internal node of the tree.
MetaPhylo.isleaf — Methodisleaf(tree::AbstractPhyloTree, edge::Edge)Return true if the edge is connected to a leaf node of the tree.
MetaPhylo.isleaf — Methodisleaf(tree::AbstractPhyloTree, idx::Integer)Return true if the idx is contained in a leaf node of the tree.
MetaPhylo.isrerootable — Methodisrerootable(tree::AbstractPhyloTree)Return true if tree is rerootable.
MetaPhylo.isrooted — Methodisrooted(tree::AbstractPhyloTree)Return true if tree is rooted.
MetaPhylo.ladderize! — Methodladderize!(tree::Tree; left=false)Ladderize the tree structure. By default, the smallest clade is on the right side; if left=true, on the left side.
MetaPhylo.leafedges — Methodleafedges(tree::AbstractPhyloTree, [idx::Integer])Return the edges of all edges connected to the leaves in the tree. If the index is specified, this returns the edges connected to its leaves in the tree.
MetaPhylo.leaves — Methodleaves(tree::AbstractPhyloTree, [idx::Integer])Return the indices of all leaves in the tree. If the index is specified, this returns the indices of leaves in its subtree.
MetaPhylo.parent_branch — Methodparent_branch(tree::AbstractPhyloTree, idx::Integer)Return the baranch (edge) between the specified idx node and its parent node. If the node is root, this returns nothing
MetaPhylo.reindex! — Methodreindex!(tree::Tree)Reindex the tree in PreOderDFS order from the root.
MetaPhylo.rem_descendants! — Methodrem_descendants(tree::Tree, idx::Integer)Remove all descendants of the specified node. Return true on success.
MetaPhylo.reroot! — Methodreroot!(tree::Tree, idx::Integer)Reroot the tree at the specified node. Return true if rerooting success.
MetaPhylo.swap! — Methodswap!(tree::Tree, idx::Integer, old_new::Pair{<:Integer, <:Integer})Swap the two child elements of the specified idx node. The old and new in old_new must be child of idx node. Return ture if swapping fails; true otherwise.
MetaPhylo.swapchildren! — Methodswapchildren!(tree::Tree, idx::Integer, newchildren)Swap the child indices of the specified idx node to the given newchildren. The elements of children and newchildren must be match. Return false if swapping fails; true otherwise.
MetaPhylo.treelength — Methodtreelength(tree::AbstractPhyloTree, [idx::Integer])Return maximum distance from the root to the leaves in the tree. If the index is specified, this returns maximum distance from the specified idx to its leaves in the tree.