dataQC.DwC: format dataframes into a DarwinCore object

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

Description

Takes one or more dataframes or a DarwinCore Archive and performs a basic Quality Controll. (see details)

Usage

dataQC.DwC(Event=NA, Occurrence=NA, eMoF=NA, EML.url=NA, out.type="event", ask.input=TRUE)

Arguments

Event	data.frame. A dataframe with the event data, structured with DarwinCore terms
Occurrence	data.frame. A dataframe with the occurrence data, structured with DarwinCore terms
eMoF	data.frame. A dataframe with the extended MeasurementOrFact (eMoF) data, structured with DarwinCore terms
EML.url	character. A URL to the Ecological Metadata Language (EML) file.
out.type	character. The type of DarwinCore of the output, either event or occurrence. If event, the output will have an event core with possible occurrence and eMoF extensions. If occurrence, the output will have an occurrence core with possibly an eMoF extension. Default event, if the parameter Event is not NA, out.type will be fixed as event.
ask.input	logical. If TRUE, console input will be requested to the user when a problem occurs. Default TRUE

Details

DarwinCore is the biodiversity data standard develloped by TDWG, and is used by the Global Biodiversity Information Facility (GBIF). This function performs a basic and user-supervised quality control. This includes cheking all variables terms adhere to the DarwinCore vocabulary, listing other variables in an eMoF file or in the dynamicProperties field, and checking for obvious errors in the content of the data (typos, different NA values,...). All dataframes are combined into a DwC.event or DwC.occurrence object

Value

a DwC.event (event core with occurrence and/or eMoF extensions) or DwC.occurence (occurrence core with eMoF extension) object

Author(s)

Maxime Sweetlove CC-0 2020

See Also

Other standardization functions: coordinate.to.decimal(), dataQC.DwC_general(), dataQC.MIxS()

Examples

## Not run: 
dataQC.DwC(Event=event_data.frame, out.type="event")
dataQC.DwC(Occurrence=occurrence_data.frame, out.type="occurrence")
dataQC.DwC(Event=event_data.frame, eMoF=emof_data.frame, out.type="event")
dataQC.DwC(Event=event_data.frame, occurrence=occurrence_data.frame, out.type="event")

## End(Not run)

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