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Pin tips to a tree

Source: R/a.R
pinTips.Rd

Returns a tree with new tips added based on given lineages and time points

Usage

pinTips(tree, tids, lngs, end_ages, tree_age)

Arguments

tree

TreeMan object

tids

new tip ids

lngs

list of vectors of the lineages of each tid (ordered high to low rank)

end_ages

end time points for each tid

tree_age

age of tree

Details

User must provide a vector of new tip IDs, a list of the ranked lineages for these IDs (in ascending order) and a vector of end time points for each new ID (0s for extant tips). The function expects the given tree to be taxonomically informed; the txnym slot for every node should have a taxonomic label. The function takes the lineage and tries to randomly add the new tip at the lowest point in the taxonomic rank before the end time point. Note, returned tree will not have a node matrix.

See also

addTip, rmTips, https://github.com/DomBennett/treeman/wiki/manip-methods

Examples

# see https://github.com/DomBennett/treeman/wiki/Pinning-tips for a detailed example