dataQC.TaxonListFromData: extract the finest resolution taxonomy from a dataset

In biodiversity-aq/OmicsMetaData: OmicsMetaData: an R-package for interoperable and re-usable biodiversity 'omics (meta)data

Description

tries to find taxonomic names for samples (rows) in a dataset (data.frame),

Usage

dataQC.TaxonListFromData(dataset)

Arguments

dataset

a data.frame. The dataset with samples as rows, and taxonomy information in the columns. using the MIxS or DarwinCore taxonomy terms, the taxonomy information will be extracted

Value

a vector with the highest level taxonomic name found, with genus and species epithet separated by a space.

Author(s)

Maxime Sweetlove CC-0 2020

See Also

Other quality control functions: dataQC.LatitudeLongitudeCheck(), dataQC.TermsCheck(), dataQC.completeTaxaNamesFromRegistery(), dataQC.dateCheck(), dataQC.eventStructure(), dataQC.findNames(), dataQC.generate.footprintWKT(), dataQC.guess.env_package.from.data(), dataQC.taxaNames()

Examples

test_metadata <- data.frame(sample_name=paste("sample", 1:5, sep="_"),
                           genus=c("Aulacoseira", "Calothrix confervicola", 
                           "unknown species", "Micrasterias cf. denticulata", 
                           "Calothrix sp."),
                           row.names=paste("sample", 1:5, sep="_"))
dataQC.TaxonListFromData(test_metadata)

biodiversity-aq/OmicsMetaData documentation built on Dec. 19, 2021, 9:44 a.m.