TaxCIsummary: Statistics of a TaxCI-analysis

Description Usage Arguments Value Author(s) See Also

Description

Get numbers of species in different kinds of clusters.

Usage

1
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.