PGRdup (version 0.2.3.9)

KWIC: Create a KWIC index

Description

KWIC creates a Keyword in Context index from PGR passport database fields.

Usage

KWIC(x, fields, min.freq = 10)

Value

A list of class KWIC containing the following components:

KWIC	The KWIC index in the form of a data frame.
KeywordFreq	A data frame of the keywords detected with frequency greater than min.freq.
Fields	A character vector with the names of the PGR database fields from which the keywords were extracted.

Arguments

x

A data frame from which KWIC index is to be generated.

fields

A character vector with the names of fields(columns) of the data frame from which KWIC index is to be generated. The first field is considered as the primary key or identifier (see Details).

min.freq

Frequency of keywords are not computed if below min.freq. Default is 10.

Details

The function generates a Keyword in Context index from a data frame of a PGR passport database based on the fields(columns) stated in the arguments, using data.table package.

The first element of vector fields is considered as the primary key or identifier which uniquely identifies all rows in the data frame.

Cleaning of the data the input fields(columns) using the DataClean function with appropriate arguments is suggested before running this function.

References

Knüpffer, H. 1988. "The European Barley Database of the ECP/GR: An Introduction." Die Kulturpflanze 36 (1): 135-62. tools:::Rd_expr_doi("10.1007/BF01986957").

Knüpffer, H., L. Frese, and M. W. M. Jongen. 1997. "Using Central Crop Databases: Searching for Duplicates and Gaps." In Central Crop Databases: Tools for Plant Genetic Resources Management. Report of a Workshop, Budapest, Hungary, 13-16 October 1996, edited by E. Lipman, M. W. M. Jongen, T. J. L. van Hintum, T. Gass, and L. Maggioni, 67-77. Rome, Italy and Wageningen, The Netherlands: International Plant Genetic Resources Institute and Centre for Genetic Resources.

See Also

data.table, print.KWIC

Examples

# \dontshow{
threads_dt <- data.table::getDTthreads()
threads_OMP <- Sys.getenv("OMP_THREAD_LIMIT")
data.table::setDTthreads(2)

data.table::setDTthreads(2)
Sys.setenv(`OMP_THREAD_LIMIT` = 2)
# }

# Load PGR passport database
GN <- GN1000

# Specify as a vector the database fields to be used
GNfields <- c("NationalID", "CollNo", "DonorID", "OtherID1", "OtherID2")

# Clean the data
GN[GNfields] <- lapply(GN[GNfields], function(x) DataClean(x))

if (FALSE) {

# Generate KWIC index
GNKWIC <- KWIC(GN, GNfields)
GNKWIC

# Retrieve the KWIC index from the KWIC object
KWIC <- GNKWIC[[1]]

# Retrieve the keyword frequencies from the KWIC object
KeywordFreq <- GNKWIC[[2]]

# Show error in case of duplicates and NULL values
# in the primary key/ID field "NationalID"
GN[1001:1005,] <- GN[1:5,]
GN[1001,3] <- ""
GNKWIC <- KWIC(GN, GNfields)
}

# \dontshow{
data.table::setDTthreads(threads_dt)
Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP)
# }