dataQC.guess.env_package.from.data: make an educated guess to the MIxS environmental package of a...

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

Description

looks in the columns of a dataset for clues to what the most appropriate MIxS environmental could be for each sample.

Usage

dataQC.guess.env_package.from.data(dataset, 
  pckge.colnames=c("env_package", "ScientificName"))

Arguments

dataset	dataframe. The dataset for which the MIxS environmental package should be found or guessed
pckge.colnames	a character vector. A vector with the potential names for the column where the environmental package can be found. Place the terms in order of decreasing likeliness.

Details

The "Minimum Information on any (x) Sequence" (MIxS) standard requires an appropriate environmental package with MIxS terms to be selected to document the data. Some data and nucleotide archives enforce their users to select such a package. This function is made to automatically either find the package in a dataset, of guess it based on the data that is present.

Value

a list of length 2, with "$values" a vector of same length as the number of rows in the dataset argument, and "$warningmessages" a vector with potential warning messages as character strings.

Author(s)

Maxime Sweetlove CC-0 2019

See Also

Other quality control functions: dataQC.LatitudeLongitudeCheck(), dataQC.TaxonListFromData(), dataQC.TermsCheck(), dataQC.completeTaxaNamesFromRegistery(), dataQC.dateCheck(), dataQC.eventStructure(), dataQC.findNames(), dataQC.generate.footprintWKT(), dataQC.taxaNames()

Examples

test_metadata <- data.frame(sample_name=paste("sample", 1:5, sep="_"),
                           collection_date=c("2020-09-23", 
                                             "2020", 
                                             "16 Jan. 2020", 
                                             "November 1998", 
                                             "12/01/1999"),
                           env_package=rep("water", 5),
                           row.names=paste("sample", 1:5, sep="_"))
dataQC.guess.env_package.from.data(test_metadata, 
                                   pckge.colnames=c("env_package"))

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