CALIBERcodelists-package: Generate ICD, Read and OPCS codelists

In CALIBERcodelists: Generate ICD10, Read and OPCS codelists

Description

Facilitate the generation, documentation and comparision of codelists for identifying diagnoses, procedures, investigations and other events recorded for patients in CALIBER electronic health record data. The CALIBER programme is funded by the Wellcome Trust [086091/Z/08/Z] and the National Institute for Health Research (NIHR) under its Programme Grants for Applied Research programme (RP-PG-0407-10314). The author is supported by a Wellcome Trust Clinical Research Training Fellowship [0938/30/Z/10/Z].

If using this package for the first time, please read the user guide.

To explore the dictionaries in an interactive way, or convert codelists in another format to the standard CALIBER format, type demo(explore) and press ENTER.

To create a Markdown document for defining a new codelist interactively, type demo(makecodelist) and press ENTER.

If you are not a CALIBER user, you will need to create your own lookup tables using demo(loadnewdicts) (see loadDicts for documentation).

The CALIBERlookups package contains the International Classification of Diseases sub-licensed to the Department of Health from the World Health Organization, and is valid only for NHS and academic use in the United Kingdom, hence it cannot not be distributed outside the UK academic community. The Read Terms are licensed under the UK Open Government Licence. The program code is licensed under GPL-3.

Details

Package:	CALIBERcodelists
Type:	Package
Version:	0.2-11
Date:	2020-02-27
License:	GPL-3

This code list generation package aims to simplify the process of creating codelists and enable existing codelists to be converted to a standard format with metadata included.

The file format of the definitive codelist is a comma-separated values file with the following columns:

• metadata - quoted text, containing Name: value pairs and the category table. The text is padded with spaces to ensure that the categories line up. The width of the column is determined by the length of the variable names and category levels.

• category - the category, right justified by adjusting the amount of right padding of the metadata column

• icd_code, opcs_code or readcode - the relevant code, quoted text

• medcode - only for Read code lists, integer

• readterm, icd_term or opcs_term - the relevant term, quoted text

These codelists are created by the export function.

The rationale for choosing comma as the delimiter is that .csv files are opened in a spreadsheet by default, making them easy to view and to add extra columns. They can also be loaded directly into a statistical package or database, the metadata column can be discarded.

The codelist generation process can be documented in R Markdown, which can be processed by process to produce a HTML document. The function exportall in the Markdown document will cause the new codelists to be exported to the working directory and produce HTML documentation.

Code lists can be generated via a number of sources:

• Using the interactive mode (exploreCodes)

• Existing code lists (as.codelist)

• Search for specific Read, ICD10 or OPCS4 codes (codematch)

• Text search of terms (termhas)

Author(s)

Anoop Shah

Maintainer: Anoop Shah <[e-mail]>

See Also

Interactive mode: exploreCodes

Browsing a selection or codelist as a spreadsheet: browseSelection, browseCodelist

Creating a selection of terms: termhas, codematch

Assigning categories to a codelist under development: assigncat

Assigning metadata: setMetadata

Creating a codelist object: as.codelist

Manipulating codelists: compare, merge.codelist, convert

Exporting a codelist: export

Processing an R Markdown file containing a codelist definition: process

Master dictionary: CALIBER_DICT, CALIBER_DICTMAPS

Storage of metadata for codelist under development: META

Examples

library(CALIBERcodelists)
setdictionary('read', 'icd10')
assigncat(2, 'SA|Stable angina', termhas('angina') %AND% 
    NOT(termhas('vincent|herpangina|abdominal|ludwig')))
assigncat(3, 'USA|Unstable angina', termhas('unstable|crescendo'),
    cats_to_convert = 2)
assigncat(1, 'Hx|History of angina', termhas('history|h/o'),
    cats_to_convert = 2:3)
assigncat(0, 'Excluded', termhas('^fh|no fh'), cats_to_convert = 1:3)
print(as.codelist('read'))
print(as.codelist('icd10'))

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