findInClusters: Search for clusters matching a given pattern

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

Description

Functions to search occurances of a genus / species / RegEx in the clusters of a BCCluster-analysis.

Usage

findInClusters(pattern="vulgaris", BCCluster.result, verbose = TRUE)
findSpeciesInClusters(pattern="vulgaris", BCCluster.result, md, verbose = TRUE)

Arguments

pattern	A RegEx - pattern that is passed to grep in order to match against the clusters. See details section.
BCCluster.result	The result object of a BCCluster analysis.
md	Metadata table that was used for the BCCluster analysis.
verbose	Set to 'FALSE' to suppress printing to console.

Details

findInClusters directly matches against the specimen ids in BCCluster.result$clusters. findSpeciesInClusters matches the pattern against BCCluster.result$sp.in.clusters which should equal the species column entry in the metadata. Specimen indices are searched in the respective species column entries in the metadata of the ids in BCCluster.result$clusters. This is useful if the actual specimens are labelled by their IDs only.

Value

Prints indices of matching clusters and the indices of matching specimens within the cluster on the console and returns a vector of cluster indices invisibly.

Author(s)

Jonas Eberle

See Also

BCCluster

Examples

### Sorry, still no examples.

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