plotParamTCI: Get indices for tci plotting.

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

Description

Get indices for plotting the results of tci-analyses on the phylogeny.

Usage

plotParamTCI(tree, x, tci.result)

Arguments

tree	A fully bifurcating tree (phylo-object). Must be the same one that was used in the previous tci-analysis.
x	A table with taxonomic information (e.g. genus and species in columns). Must be the same one that was used in the previous tci-analysis.
tci.result	Results-List of the tci-analysis.

Details

Finds the species with Taxonomic Consistency Index < 1 and the specimens belonging to these species in the results of an tci-analysis. The specimens indices in tree$tip.label are saved for plotting the results with plot.phylo.

Value

A list with the following elements:

species	species with CI < 1
specimen	specimens belonging to species with CI < 1
i	index of these specimens in tree$tip.label
tips	a vector 1:number_of_tips_in_tree. Usefull for plottig something on all tips except the indexed (tips[-i])

Author(s)

Jonas Eberle

See Also

See TaxCI for example.

Related: tci

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