Clean PGR passport data

Source: R/DataClean.R

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

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).

Value

A character vector with the cleaned data converted to upper case.

NAs if any are converted to blank strings.

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

See also

gsub, regex, MergeKW, KWIC, ProbDup

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)
#>  [1] "S7126"          "ICG3505"        "U44718 EC21127" "AH6481"        
#>  [5] "RS1"            "AK1224"         "25 NRCG4053"    "T78 MWITUNDE"  
#>  [9] "ICG3410"        "6484 GWALIOR"   "TG4 U44713"     "EC21003"