Class Tree

constructor

• new Tree(root: Node): Tree

  The constructor of the Tree class.

  Parameters

  • root: Node

    Root node

  Returns Tree

labelNodeMap

nodeIDMap

recombEdgeMap

root

ultrametric

leafList

• get leafList(): Node[]

  A getter that returns an array of nodes (Node[]) from private _nodeList property in order determined by a pre-order search

  Returns Node[]

nodeList

• get nodeList(): Node[]

  A getter that returns an array of nodes (Node[]) from private _nodeList property in order determined by a pre-order search

  Returns Node[]

applyPostOrder

• applyPostOrder(func: (node: Node) => void): void

  Convenience function applied function post-order to all nodes in the tree. Is a wrapper for Node.applyPostOrder()

  Parameters

  • func: (node: Node) => void

    Function to apply to each node

  Returns void

applyPreOrder

• applyPreOrder(func: (node: Node) => void): void

  Convenience function applied function pre-order to all nodes in the tree. Is a wrapper for Node.applyPreOrder()

  Parameters

  • func: (node: Node) => void

    Function to apply to each node

  Returns void

clearCaches

• clearCaches(): void

  Clear various node caches

  Returns void

collessIndex

• collessIndex(method?: "standard" | "corrected" | "quadratic"): number

  Returns the Colless Imbalance (CI) index, with an option to normalise or use the standard method. The CI is defined for binary trees, so NaN is returned if the tree is not binary. In essence, the CI adds the difference between the number of tips descending from each internal node. The square of each difference is taking if the method selected is quadratic. If the method is set to "corrected", then the overall sum is scaled by the number of tips. If method is "standard", then sum is returned. The value should be smaller for more balanced trees (less ladder-like). As for the Sacking Index, see "Tree balance indices: a comprehensive survey (https://doi.org/10.1007/978-3-031-39800-1_12, https://doi.org/10.1007/978-3-031-39800-1_13, https://doi.org/10.1007/978-3-031-39800-1_15) for further details.

  Parameters

  • method: "standard" | "corrected" | "quadratic" = 'standard'

  Returns number

computeNodeHeights

• computeNodeHeights(): void

  Computes height of each node above the root. Automatically done if rerooting. NaN if any undefined branch lengths ancestral to a particular node. Contrasts Tree.getRTTD() in not converting undefined branch lengths to 0.0.

  Returns void

gammaStatistic

• gammaStatistic(tol?: number): number

  Calculates Gamma statistic from Pybus and Harvey 2000 (10.1098/rspb.2000.1278 ). The Gamma statistic measures deviation from a constant rate pure-birth process in the underlying population (also known as a Yule process). Values above 0 indicate longer external branches, while values corresond to internal branches. Calculating the Gamma statistic involves manipulations that mean the statistic should follow a standard normal distribution, such that one can perform a frequentist test to measure consistency with the pure birth process.

  Since the Gamma statistic applies to a pure birth process, the tree is expected to be ultrametric and the method throws an error if it is not. It also returns NaN if any node node heights are undefined, due to undefined branch lengths.

  Parameters

  • tol: number = 1e-6

    Tolerance for ultrametricity passed to .isUltrametric()

  Returns number

getBranchLengths

• getBranchLengths(): (undefined | number)[]

  Return branch lengths in order matching .nodeList

  Returns (undefined | number)[]

getClade

• getClade(node: Node): Tree

  Return sub-stree descending from a given node

  Parameters

  • node: Node

  Returns Tree

  Parm

  root node root of desired subtree

getInternalNodeHeights

• getInternalNodeHeights(): number[]

  Returns height above the root for each internal node. Root height is assumed to be 0 and undefined branch lengths are assumed to be zero.

  Returns number[]

getMRCA

• getMRCA(nodes: Node[]): null | Node

  Get the most recent common ancestor of a set of nodes

  Parameters

  • nodes: Node[]

    Nodes for which the MRCA is sought

  Returns null | Node

getNode

• getNode(nodeID: number): null | Node

  Get node given its numerical id

  Parameters

  • nodeID: number

    Numerical id of node

  Returns null | Node

getNodeByLabel

• getNodeByLabel(label: string): null | Node

  Retrieve node having given label

  Parameters

  • label: string

    Node's label

  Returns null | Node

getRecombEdgeMap

• getRecombEdgeMap(): { [key: string]: Node[] }

  Retrieve map from recomb edge IDs to src/dest node pairs

  Returns { [key: string]: Node[] }

getRTTDist

• getRTTDist(): number[]

  Returns root to tip distances. Counts undefined branch lengths as zero

  Returns number[]

getTipLabels

• getTipLabels(node?: Node): string[]

  Get all tip names from tree or descending from a node

  Parameters

  • Optionalnode: Node

    Optional node whose descending tips are returned. Defaults to root

  Returns string[]

getTotalBranchLength

• getTotalBranchLength(): number

  Sum of all defined branch lengths. Elsewhere referred to tree "length" if all baranch lengths are defined

  Returns number

isBinary

• isBinary(): boolean

  Check whether the tree is binary (each internal node has <= 2 descendents)

  Returns boolean

isNetwork

• isNetwork(): boolean

  Check if the tree is a phylogenetic network.

  Returns boolean

isRecombDestNode

• isRecombDestNode(node: Node): boolean

  Check if node is a destination node for a hybrid edge in the tree.

  Parameters

  • node: Node

  Returns boolean

isRecombSrcNode

• isRecombSrcNode(node: Node): boolean

  Check if node is a source node for a hybrid edge in the tree.

  Parameters

  • node: Node

  Returns boolean

isUltrametric

• isUltrametric(tol?: number): boolean

  Reflects whether all tips are the same age (0), equivalently if they are all the same height about the root. Only makes sense for time trees. Sets property on tree object and returns boolean. The tolerance for differences in tip heights is 1e-6 as a default, but can be adjusted.

  Parameters

  • tol: number = 1e-6

  Returns boolean

ladderise

• ladderise(): void

  Ladderises the tree. Applies a pre-order search. For each node, child nodes are ordered by increasing number of descending tips

  Returns void

reassignNodeIDs

• reassignNodeIDs(): void

  Assign new node IDs (use with care!)

  Returns void

reroot

• reroot(edgeBaseNode: Node, prop?: number): void

  Reroot a tree at a given node.

  Parameters

  • edgeBaseNode: Node

    Node to reroot at
  • prop: number = 0.5

    Proportion of the branch descending from edgeBaseNode at which to cut and place the root. Defaults ot 0.5

  Returns void

sackinIndex

• sackinIndex(): number

  Returns the Sackin Index, which measures imbalance as the sum of the number of tips descending from each internal node. The sum increases for more imbalances (ladder-like) trees. See Chapter 5 in "Tree balance indices: a comprehensive survey" (https://doi.org/10.1007/978-3-031-39800-1_5) for further details, a reference we point to from the treebalance R package

  Returns number