GetSimilarity: Get similarity Uses ape's cophenetic.phylo to get patristic...
In bomeara/closesamples: Gets feasible taxon samples on a tree
Description
Usage
Arguments
Value
Description
Get similarity
Uses ape's cophenetic.phylo to get patristic distances between pairs of taxa, then makes the diagonals Inf. If the tree has no branch lengths, makes every edge length 1.
Usage
1
GetSimilarity(phy_full, taxa_feasible, truncate_full_to_mrca = FALSE)
Arguments
phy_full
A phylo object with all feasible taxa to sammple from
taxa_feasible
A vector of taxon names that are feasible to study (often on another tree)
truncate_full_to_mrca
If TRUE, prune the full tree to the node that is the MRCA of the
Value
A matrix with tips on the rows and columns and patristic distances in the cells. Rows are tips on the phy_full tree, columns are taxa in the taxa_feasible vector
bomeara/closesamples documentation built on Nov. 14, 2021, 9:48 a.m.
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Description Usage Arguments Value
Description
Get similarity Uses ape's cophenetic.phylo to get patristic distances between pairs of taxa, then makes the diagonals Inf. If the tree has no branch lengths, makes every edge length 1.
Usage
1 | GetSimilarity(phy_full, taxa_feasible, truncate_full_to_mrca = FALSE)
|
Arguments
phy_full |
A phylo object with all feasible taxa to sammple from |
taxa_feasible |
A vector of taxon names that are feasible to study (often on another tree) |
truncate_full_to_mrca |
If TRUE, prune the full tree to the node that is the MRCA of the |
Value
A matrix with tips on the rows and columns and patristic distances in the cells. Rows are tips on the phy_full tree, columns are taxa in the taxa_feasible vector
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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