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 site:https://oxford-ihtm.io

Datasets:

cod_data_raw_example - Example raw cause-of-death dataset
icd10_cod_by_sex - Sex-specific causes of death for ICD 10
icd10_cod_child - Child-specific cause-of-death for ICD 10
icd10_cod_neonate - Neonate-specific cause-of-death for ICD 10
icd10_example - Example death records dataset with ICD10 cause-of-death coding
icd10_unlikely_cod - Unlikely causes of death for ICD 10
icd11_cod_by_sex - Sex-specific causes of death for ICD 11
icd11_cod_child - Child-specific cause-of-death for ICD 11
icd11_cod_neonate - Neonate-specific cause-of-death for ICD 11
icd11_example - Example death records dataset with ICD11 cause-of-death coding
icd11_unlikely_cod - Unlikely causes of death for ICD 11

On CRAN:

cod icd

4.22 score 1 stars 6 scripts 28 exports 28 dependencies

Last updated 2 months agofrom:71bd8a061b. Checks:3 OK, 4 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 01 2025
R-4.5-win	OK	Jan 01 2025
R-4.5-linux	OK	Jan 01 2025
R-4.4-win	NOTE	Jan 01 2025
R-4.4-mac	NOTE	Jan 01 2025
R-4.3-win	NOTE	Jan 01 2025
R-4.3-mac	NOTE	Jan 01 2025

Exports:cod_calculate_age cod_calculate_ages cod_check_age cod_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_summary cod_check_code_unlikely_icd10 cod_check_code_unlikely_icd11 cod_check_codedit_input cod_check_dod cod_check_sex cod_recode_age_type cod_recode_sex cod_structure_input expand_icd10_code_range get_age_values list_ill_defined_icd11

Dependencies:askpass cli codigo cpp11 curl dplyr fansi generics glue httr2 lifecycle magrittr openssl pillar pkgconfig purrr R6 rappdirs rlang stringi stringr sys tibble tidyr tidyselect utf8 vctrs withr

Cause-of-death code checks

Anita Makori and Ernest Guevarra

Rendered fromcause_of_death_code_checks.Rmdusingknitr::rmarkdownon Jan 01 2025.

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

Implementing Cause-of-Death Data Checks with codeditr

Rendered fromcodeditr.Rmdusingknitr::rmarkdownon Jan 01 2025.

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 Jan 01 2025.

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

Help page	Topics
Calculate age at death based on date of birth and date of death	cod_calculate_age cod_calculate_ages
Check age values in cause-of-death data based on CoDEdit rules	cod_check_age
Check cause-of-death code for code entry mistakes and/or code completeness	cod_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 results	cod_check_code_summary
Check structure and values of input data to CoDEdit tool	cod_check_codedit_input
Check date of death value in cause-of-death data based on CoDEdit rules	cod_check_dod
Check sex values in cause-of-death data based on CoDEdit rules	cod_check_sex
Example raw cause-of-death dataset	cod_data_raw_example
Recode age type of cause-of-death data based on CoDEdit rules	cod_recode_age_type
Recode sex value of cause-of-death data based on CoDEdit rules	cod_recode_sex
Structure cause-of-death data into CoDEdit tool input data	cod_structure_input
Enumerate ICD 10 codes given a code range	expand_icd10_code_range
Get various age values for all three age types	get_age_values
Sex-specific causes of death for ICD 10	icd10_cod_by_sex
Child-specific cause-of-death for ICD 10	icd10_cod_child
Neonate-specific cause-of-death for ICD 10	icd10_cod_neonate
Example death records dataset with ICD10 cause-of-death coding	icd10_example
Unlikely causes of death for ICD 10	icd10_unlikely_cod
Sex-specific causes of death for ICD 11	icd11_cod_by_sex
Child-specific cause-of-death for ICD 11	icd11_cod_child
Neonate-specific cause-of-death for ICD 11	icd11_cod_neonate
Example death records dataset with ICD11 cause-of-death coding	icd11_example
Unlikely causes of death for ICD 11	icd11_unlikely_cod
List ill-defined ICD 11 codes	list_ill_defined_icd11

Package: codeditr 0.0.0.9000

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

Cause-of-death code checks

Implementing Cause-of-Death Data Checks with codeditr

Introduction to ICD and cause-of-death reporting

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)