export: Export the codelists to the definitive .csv format or .dta...

In CALIBERcodelists: Generate ICD10, Read and OPCS codelists

Description

The function export exports a single codelist, and exportall exports codelists from each of the master dictionaries (Read, OPCD, ICD-10) that are in use. export exports to a specific file; exportall exports to a given directory and automatically names the files varname_gprd.codelist.1.csv (where 1 is the version number and gprd can be replaced by hes or opcs) etc.

Terms with category 0 or negative categories are not exported.

Usage

export(x, ...)
## S3 method for class 'codelist'
export(x, filename = NULL, categories = 'all',
    contractIfICD10 = TRUE, contractIfICD9 = TRUE)
exportall(directory = getwd(), varname = NULL, saveMessage = TRUE)

Arguments

x	A codelist object created by as.codelist.
filename	Filename to export to. The file type (comma separated or Stata file) is chosen by the file extension. With an ICD-10 codelist, if the filename contains _ons or _hes, the Source attribute of the codelist is automatically updated.
categories	Which categories to export, either the character string 'all' or a numeric vector
contractIfICD10	Whether to represent 4-character ICD-10 codes which have the same 3-character prefix using the prefix only. This is recommended because it means that codelists are shorter and easier to understand.
contractIfICD9	Whether to represent 4-character ICD-9 codes which have the same 3-character prefix using the prefix only. This is recommended because it means that codelists are shorter and easier to understand.
directory	Directory to export to. Uses the current working directory if no directory stated.
varname	Filename and codename (CALIBER variable name) for the exported codelist. If it is not supplied as an argument, it is obtained from the 'Name' field of the META table. If the codelist selection process is done by calling process on a R Markdown file, the variable name is drawn from a line such as "Name|angina" for the angina codelist.
saveMessage	If there already exists a file of the same name as the codelist being exported, exportall compares the code selection in this previous file with the new version being exported. If saveMessage is TRUE, this comparison is saved in the 'message' field of the META table rather than being printed on screen immediately. When processing a R Markdown file using process, this feature is used to prevent the comparison message from being printed in the HTML document, and it is shown on the screen instead after the file has been processed.
...	Arguments for generic export function.

Details

The function exportall extracts the selected terms from the master dictionary as up to four codelists (one per dictionary), and calls export to export each of them as a CSV file.

Value

export invisibly returns the codelist as a data.table in the format it was exported to .CSV (i.e. no longer a codelist object). exportall does not return anything.

See Also

as.codelist, assigncat, codematch, CALIBER_DICT, dictis, explode, getdictionary, setdictionary, termhas

Examples

# Generate and export a codelist
setdictionary('read', 'icd10', 'opcs')
# Ensure that category labels containing . are exported and
# re-imported correctly
assigncat(3, 'P.C.O.S.', 'polycystic ov|drill.*ovar')
assigncat(2, 'FH: PCOS', 'fh|family', cats_to_convert=3)

setMetadata(Date = '13 Feb 2013')
setMetadata(Author = 'An epidemiologist')
setMetadata(Name = 'pcos')
setMetadata(Version = 0)
setMetadata(Source = 'GPRD, HES, OPCS')
# Another way of setting the Source metadata
setMetadata(Source = c('GPRD', 'HES', 'OPCS'))
# Only one source per dictionary

pcos_gprd <- as.codelist('read')
pcos_opcs <- as.codelist('opcs')
pcos_hes <- as.codelist('icd10')

# Export codelists in Stata and CSV format
export(pcos_gprd, paste(tempdir(), '/pcos_gprd.codelist.0.csv', sep=''))
export(pcos_opcs, paste(tempdir(), '/pcos_opcs.codelist.0.csv', sep=''))
export(pcos_hes, paste(tempdir(), '/pcos_ons.codelist.0.csv', sep=''))
export(pcos_hes, paste(tempdir(), '/pcos_hes.codelist.0.csv', sep=''))
export(pcos_gprd, paste(tempdir(), '/pcos_gprd.codelist.0.dta', sep=''))
export(pcos_opcs, paste(tempdir(), '/pcos_opcs.codelist.0.dta', sep=''))
export(pcos_hes, paste(tempdir(), '/pcos_ons.codelist.0.dta', sep=''))
export(pcos_hes, paste(tempdir(), '/pcos_hes.codelist.0.dta', sep=''))

# Re-import codelists and check against the originals
csv_gprd <- as.codelist(paste(tempdir(), '/pcos_gprd.codelist.0.csv', sep=''))
csv_opcs <- as.codelist(paste(tempdir(), '/pcos_opcs.codelist.0.csv', sep=''))
csv_hes <- as.codelist(paste(tempdir(), '/pcos_hes.codelist.0.csv', sep=''))
csv_ons <- as.codelist(paste(tempdir(), '/pcos_ons.codelist.0.csv', sep=''))
dta_gprd <- as.codelist(paste(tempdir(), '/pcos_gprd.codelist.0.dta', sep=''))
dta_opcs <- as.codelist(paste(tempdir(), '/pcos_opcs.codelist.0.dta', sep=''))
dta_hes <- as.codelist(paste(tempdir(), '/pcos_hes.codelist.0.dta', sep=''))
dta_ons <- as.codelist(paste(tempdir(), '/pcos_ons.codelist.0.dta', sep=''))

# Check that ONS and HES codelists are identical apart from Source
# attribute
setMetadata(dta_ons, Source='HES')
setMetadata(csv_ons, Source='HES')
setMetadata(dta_ons, Name='pcos_hes')
setMetadata(csv_ons, Name='pcos_hes')
stopifnot(compare(dta_ons, dta_hes)$identical)
stopifnot(compare(csv_ons, csv_hes)$identical)

# Export and re-import
export(dta_gprd, paste(tempdir(), '/dta_gprd.codelist.0.csv', sep=''))
export(dta_opcs, paste(tempdir(), '/dta_opcs.codelist.0.csv', sep=''))
export(dta_hes, paste(tempdir(), '/dta_hes.codelist.0.csv', sep=''))
dta_csv_gprd <- as.codelist(paste(tempdir(), '/dta_gprd.codelist.0.csv', sep=''))
dta_csv_opcs <- as.codelist(paste(tempdir(), '/dta_opcs.codelist.0.csv', sep=''))
dta_csv_hes <- as.codelist(paste(tempdir(), '/dta_hes.codelist.0.csv', sep=''))

# Check if roundtrip export / import produces an identical codelist
stopifnot(compare(csv_gprd, pcos_gprd)$identical)
stopifnot(compare(csv_opcs, pcos_opcs)$identical)
stopifnot(compare(csv_hes, pcos_hes)$identical)
stopifnot(compare(dta_csv_gprd, pcos_gprd)$identical)
stopifnot(compare(dta_csv_opcs,
	removeUnusedCategories(pcos_opcs))$identical)
stopifnot(compare(dta_csv_hes,
	removeUnusedCategories(pcos_hes))$identical)

# Check if codelist can be exported with NULL name
setattr(pcos_gprd, 'Name', NULL)
export(pcos_gprd, paste(tempdir(), '/pcos_gprd.codelist.0.csv', sep=''))

# Clean up temporary directory
unlink(paste(tempdir(), '/pcos_gprd.codelist.0.csv', sep=''))
unlink(paste(tempdir(), '/pcos_opcs.codelist.0.csv', sep=''))
unlink(paste(tempdir(), '/pcos_hes.codelist.0.csv', sep=''))
unlink(paste(tempdir(), '/pcos_gprd.codelist.0.dta', sep=''))
unlink(paste(tempdir(), '/pcos_opcs.codelist.0.dta', sep=''))
unlink(paste(tempdir(), '/pcos_hes.codelist.0.dta', sep=''))
unlink(paste(tempdir(), '/dta_gprd.codelist.0.dta', sep=''))
unlink(paste(tempdir(), '/dta_opcs.codelist.0.dta', sep=''))
unlink(paste(tempdir(), '/dta_hes.codelist.0.dta', sep=''))

CALIBERcodelists documentation built on Feb. 28, 2020, 3:01 a.m.