tci: Calculate the Consistency Index and the Retention Index for...

In eberlejonas/TaxCI: Calculate the Consistency Index and the Retention Index for taxonomic data

Description

Main function for calculating the Taxonomic Consistency Index.

Usage

tci(tree, x, level)

Arguments

tree	A fully bifurcating tree (phylo-object).
x	A table with taxonomic information (e.g. genus and species in columns). rownames(x) must exactly match the tip labels of tree.
level	Column-name or number (integer) of x , i.e. the level for which the Taxonomic CI should be calculated.

Details

Functions for calculating the Consistency Index (Kluge and Farris 1969) along phylogenetic trees. Especially intended for use with taxonomic data on different levels. Uses phangorn (Schliep 2011).

Value

A list with the following entries:

tax.ci	A vector of taxonomic consistency indices with taxa as names.
level	the level, i.e. column that was used in the inference

Author(s)

Jonas Eberle

References

Kluge, A.G, Farris, J.S. (1969). Quantitative phyletics and the evolution of anurans. Syst. Zool. 18: 1-32.

Schliep K.P. (2011). phangorn: phylogenetic analysis in R. Bioinformatics, 27(4) 592-593.

See Also

See TaxCI for example.

Related: CI

eberlejonas/TaxCI documentation built on July 20, 2021, 9:46 a.m.