Package: codeditr 0.0.0.9000

Ernest Guevarra

codeditr: Implementing Cause-of-Death Data Checks Based on the WHO CoDEdit Tool

The World Health Organization's CoDEdit electronic tool is intended to help producers of cause-of-death statistics in strengthening their capacity to perform routine checks on their data. This package ports the original tool built using Microsoft Access into R so as to leverage the utility and function of the original tool into a usable application program interface that can be used for building more universal tools or for creating programmatic scientific workflows aimed at routine, automated, and large-scale monitoring of cause-of-death data.

Authors:Anita Makori [aut, cph], Ernest Guevarra [aut, cre, cph], Sanjeev Pugazhendhi [ths, rev], Williams Udoh Ituen-Umanah [rev], Proochista Ariana [rev, cph]

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codeditr.pdf |codeditr.html✨
codeditr/json (API)
NEWS

# Install 'codeditr' in R:
install.packages('codeditr', repos = c('https://oxfordihtm.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/oxfordihtm/codeditr/issues

Pkgdown/docs site:https://oxford-ihtm.io

Datasets:

On CRAN:

Conda:

codicd

3.65 score 3 stars 6 scripts 28 exports 27 dependencies

Last updated from:71bd8a061b. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK147
source / vignettesOK207
linux-release-x86_64OK153
macos-release-arm64OK117
macos-oldrel-arm64OK80
windows-develOK98
windows-releaseOK115
windows-oldrelOK125
wasm-releaseOK116

Exports:cod_calculate_agecod_calculate_agescod_check_agecod_check_codecod_check_code_age_icd10cod_check_code_age_icd10_cod_check_code_age_icd11cod_check_code_age_icd11_cod_check_code_ill_defined_icd10cod_check_code_ill_defined_icd11cod_check_code_sex_icd10cod_check_code_sex_icd10_cod_check_code_sex_icd11cod_check_code_sex_icd11_cod_check_code_structure_icd10cod_check_code_structure_icd11cod_check_code_summarycod_check_code_unlikely_icd10cod_check_code_unlikely_icd11cod_check_codedit_inputcod_check_dodcod_check_sexcod_recode_age_typecod_recode_sexcod_structure_inputexpand_icd10_code_rangeget_age_valueslist_ill_defined_icd11

Dependencies:askpassclicodigocpp11curldplyrgenericsgluehttr2lifecyclemagrittropensslpillarpkgconfigpurrrR6rappdirsrlangstringistringrsystibbletidyrtidyselectutf8vctrswithr

Cause-of-death code checks

Anita Makori and Ernest Guevarra

Rendered fromcause_of_death_code_checks.Rmdusingknitr::rmarkdownon Apr 12 2026.

Last update: 2024-07-04
Started: 2024-07-03

Implementing Cause-of-Death Data Checks with codeditr

Rendered fromcodeditr.Rmdusingknitr::rmarkdownon Apr 12 2026.

Last update: 2024-07-04
Started: 2024-07-03

Introduction to ICD and cause-of-death reporting

Ernest Guevarra

Rendered fromintroduction_to_icd.Rmdusingknitr::rmarkdownon Apr 12 2026.

Last update: 2024-07-04
Started: 2024-07-04

Readme and manuals

Help Manual

Help pageTopics
Calculate age at death based on date of birth and date of deathcod_calculate_age cod_calculate_ages
Check age values in cause-of-death data based on CoDEdit rulescod_check_age
Check cause-of-death code for code entry mistakes and/or code completenesscod_check_code cod_check_code_age_icd10 cod_check_code_age_icd10_ cod_check_code_age_icd11 cod_check_code_age_icd11_ cod_check_code_ill_defined_icd10 cod_check_code_ill_defined_icd11 cod_check_code_sex_icd10 cod_check_code_sex_icd10_ cod_check_code_sex_icd11 cod_check_code_sex_icd11_ cod_check_code_structure_icd10 cod_check_code_structure_icd11 cod_check_code_unlikely_icd10 cod_check_code_unlikely_icd11
Summarise cause-of-death check resultscod_check_code_summary
Check structure and values of input data to CoDEdit toolcod_check_codedit_input
Check date of death value in cause-of-death data based on CoDEdit rulescod_check_dod
Check sex values in cause-of-death data based on CoDEdit rulescod_check_sex
Example raw cause-of-death datasetcod_data_raw_example
Recode age type of cause-of-death data based on CoDEdit rulescod_recode_age_type
Recode sex value of cause-of-death data based on CoDEdit rulescod_recode_sex
Structure cause-of-death data into CoDEdit tool input datacod_structure_input
Enumerate ICD 10 codes given a code rangeexpand_icd10_code_range
Get various age values for all three age typesget_age_values
Sex-specific causes of death for ICD 10icd10_cod_by_sex
Child-specific cause-of-death for ICD 10icd10_cod_child
Neonate-specific cause-of-death for ICD 10icd10_cod_neonate
Example death records dataset with ICD10 cause-of-death codingicd10_example
Unlikely causes of death for ICD 10icd10_unlikely_cod
Sex-specific causes of death for ICD 11icd11_cod_by_sex
Child-specific cause-of-death for ICD 11icd11_cod_child
Neonate-specific cause-of-death for ICD 11icd11_cod_neonate
Example death records dataset with ICD11 cause-of-death codingicd11_example
Unlikely causes of death for ICD 11icd11_unlikely_cod
List ill-defined ICD 11 codeslist_ill_defined_icd11