TaxCIsummary: Statistics of a TaxCI-analysis

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

Description

Get numbers of species in different kinds of clusters.

Usage

TaxCIsummary(tree, x, sp.col = "binomial", BCCluster.result, plotParamTCI.result, plotParamBCC.result, analysis = "TaxCI.analysis", file=NA)

Arguments

tree	The tree that was used for the previous analyses.
x	The table with taxonomic information (must contain a column with species names which is specified with sp.col). Must be the same one that was used in the previous analyses.
sp.col	The column of the metadata that contains the species names.
BCCluster.result	The list that resulted from a BCCluster-analysis.
plotParamTCI.result	The output of plotParamTCI.
plotParamBCC.result	The output of plotParamBCC.
analysis	Optional. A name for the summarized analysis provided as character string.
file	Optional. If a filename is given the table will be printed to it. Defaults to NA (table is returned as data.frame).

Value

A data frame with the following entries:

noMorphospecies	Number of a priori identified species.
no.tci.positive.sp	Number of species with TCI < 1.
no.cluster	Number of barcode clusters.
no.homogen	Number of homogeneous clusters (Containing only one species).
no.heterogen	Number of heterogeneous clusters (Containing multiple species.
no.species.in.multiple.clusters	Number of species that appear in more than one cluster.
no.species.in.multiple.hom.clusters	Number of species that appear in more than one homogeneous cluster.
threshold	The barcode-threshold that was used for clustering. "external" if clustering was done with an external method.
Q-measure	A quality measure...

Author(s)

Jonas Eberle

See Also

See TaxCI for example.

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