Description Usage Arguments Details Value Author(s) References See Also
Main function for calculating the Taxonomic Consistency Index.
1 | tci(tree, x, level)
|
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. |
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).
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 |
Jonas Eberle
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 TaxCI
for example.
Related: CI
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