majorlineage: Major lineage

In alexwailan/maria: Defines sub-lineages of a clonal expansion via an phylogenetic tree.

Description

Function to identify major lineages composed of identified lineages Singletons which may not have a lineage can also be inlcuded in major lineage

Usage

majorlineage(slnum, tree, assign, rthreshold)

Arguments

slnum	Number of Sub-lineage identified.
tree	The rooted phylogenetic tree.
assign	Vector of lineage numbers corresponding to tips on a tree.
rthreshold	Number of internal nodes to the root each lineage must have intersecting to be declared as a major sub-lineage.
ntips	Number of tips on the phylogenetic tree.
treeNnodes	Number of internal nodes on phylogenetic tree. majorlineage()

alexwailan/maria documentation built on Sept. 29, 2020, 9:37 a.m.