read.genesys
Convert 'Darwin Core - Germplasm' zip archive to a flat file
read.genesys reads PGR data in a Darwin Core - germplasm zip
archive downloaded from genesys database and creates a flat file
data.frame from it.
Usage
read.genesys(zip.genesys, scrub.names.space = TRUE, readme = TRUE)Arguments
- zip.genesys
A character vector giving the file path to the downloaded zip file from Genesys.
- scrub.names.space
logical. If
TRUE, all space characters are removed from name field in names extension (see Details).- readme
logical. If
TRUE, the genesys zip file readme is printed to console.
Details
This function helps to import to R environment, the PGR data
downloaded from genesys database https://www.genesys-pgr.org/ as a
Darwin Core - germplasm (DwC-germplasm) zip archive. The different csv files
in the archive are merged as a flat file into a single data.frame.
All the space characters can be removed from the fields corresponding to
accession names such as acceNumb, collNumb, ACCENAME, COLLNUMB, DONORNUMB and
OTHERNUMB using the argument scrub.names.space to facilitate creation
of KWIC index with KWIC function and subsequent
matching operations to identify probable duplicates with
ProbDup function.
The argument readme can be used to print the readme file in the
archive to console, if required.
Value
A data.frame with the flat file form of the genesys data.
See Also
Examples
# NOT RUN {
# Import the DwC-Germplasm zip archive "genesys-accessions-filtered.zip"
PGRgenesys <- read.genesys("genesys-accessions-filtered.zip",
scrub.names.space = TRUE, readme = TRUE)
# }