DataClean: Clean PGR passport data
In PGRdup: Discover Probable Duplicates in Plant Genetic Resources Collections

DataClean

R Documentation

Clean PGR passport data

Description

DataClean cleans the data in a character vector according to the conditions in the arguments.

Usage

DataClean(
  x,
  fix.comma = TRUE,
  fix.semcol = TRUE,
  fix.col = TRUE,
  fix.bracket = TRUE,
  fix.punct = TRUE,
  fix.space = TRUE,
  fix.sep = TRUE,
  fix.leadzero = TRUE
)

Arguments

`x`	A character vector. If not, coerced to character by `as.character`.
`fix.comma`	logical. If `TRUE`, all the commas are replaced by space (see Details).
`fix.semcol`	logical. If `TRUE`, all the semicolons are replaced by space (see Details).
`fix.col`	logical. If `TRUE`, all the colons are replaced by space (see Details).
`fix.bracket`	logical. If `TRUE`, all the brackets are replaced by space (see Details).
`fix.punct`	logical. If `TRUE`, all punctuation characters are removed (see Details).
`fix.space`	logical. If `TRUE`, all space characters are replaced by space and multiple spaces are converted to single space (see Details).
`fix.sep`	logical. If `TRUE`, space between alphabetic characters followed by digits is removed (see Details).
`fix.leadzero`	logical. If `TRUE`, leading zeros are removed (see Details).

Details

This function aids in standardization and preparation of the PGR passport data for creation of a KWIC index with KWIC function and the identification of probable duplicate accessions by the ProbDup function. It cleans the character strings in passport data fields(columns) specified as the input character vector x according to the conditions in the arguments in the same order. If the input vector x is not of type character, it is coerced to a character vector.

This function is designed particularly for use with fields corresponding to accession names such as accession ids, collection numbers, accession names etc. It is essentially a wrapper around the gsub base function with regex arguments. It also converts all strings to upper case and removes leading and trailing spaces.

Commas, semicolons and colons which are sometimes used to separate multiple strings or names within the same field can be replaced with a single space using the logical arguments fix.comma, fix.semcol and fix.col respectively.

Similarly the logical argument fix.bracket can be used to replace all brackets including parenthesis, square brackets and curly brackets with space.

The logical argument fix.punct can be used to remove all punctuation from the data.

fix.space can be used to convert all space characters such as tab, newline, vertical tab, form feed and carriage return to spaces and finally convert multiple spaces to single space.

fix.sep can be used to merge together accession identifiers composed of alphabetic characters separated from as series of digits by a space character. For example IR 64, PUSA 256 etc.

fix.leadzero can be used to remove leading zeros from accession name fields to facilitate matching to identify probable duplicates. e.g. IR0064 -> IR64

Value

A character vector with the cleaned data converted to upper case. NAs if any are converted to blank strings.

Examples

names <- c("S7-12-6", "ICG-3505", "U 4-47-18;EC 21127", "AH 6481", "RS   1",
           "AK 12-24", "2-5 (NRCG-4053)", "T78, Mwitunde", "ICG 3410",
           "#648-4 (Gwalior)", "TG4;U/4/47/13", "EC0021003")
DataClean(names)

PGRdup documentation built on Sept. 1, 2023, 1:05 a.m.