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]

codeditr_0.0.0.9000.tar.gz
codeditr_0.0.0.9000.zip(r-4.7)codeditr_0.0.0.9000.zip(r-4.6)codeditr_0.0.0.9000.zip(r-4.5)
codeditr_0.0.0.9000.tgz(r-4.6-any)codeditr_0.0.0.9000.tgz(r-4.5-any)
codeditr_0.0.0.9000.tar.gz(r-4.7-any)codeditr_0.0.0.9000.tar.gz(r-4.6-any)
codeditr_0.0.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
codeditr/json (API)

# 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_64OK145
source / vignettesOK193
linux-release-x86_64OK151
macos-release-arm64OK127
macos-oldrel-arm64OK89
windows-develOK109
windows-releaseOK87
windows-oldrelOK95
wasm-releaseOK109

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

Introduction to ICD and cause-of-death reporting
Key Features of the ICD | ICD and Cause-of-Death reporting | Standardisation | Comparability | Data Aggregation and Analysis | Quality of Healthcare | Legal and Administrative Use | Example of ICD in Cause-of-Death Reporting
Rendered fromintroduction_to_icd.Rmdusingknitr::rmarkdown

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

Cause-of-death code checks
Code structure | Cause-of-death code structure checks for ICD-10 version | Cause-of-death code structure checks for ICD-11 version | Ill-defined cause-of-death codes | Ill-defined codes for ICD_10 and ICD-11 | Checks for ill-defined cause-of-death codes | Unlikely cause-of-death codes | Unlikely cause-of-death codes for ICD-10 and ICD-11 | Checks for unlikely cause-of-death codes | Cause-of-death code not appropriate for sex | Male-specific cause-of-death codes | Female-specific cause-of-death codes | Checks for sex-specific cause-of-death codes | Cause-of-death codes not appropriate for age | Neonate-specific cause-of-death codes | Child-specific cause-of-death codes | Checks for age-specific cause-of-death codes
Rendered fromcause_of_death_code_checks.Rmdusingknitr::rmarkdown

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

Implementing Cause-of-Death Data Checks with codeditr
Workflows for cause-of-death data processing and data quality checks using codeditr | Perform checks on existing input data for CoDEdit tool | Structure raw cause-of-death data for input into CoDEdit tool | Perform all checks on cause-of-death data | Perform specific check types on cause-of-death data
Rendered fromcodeditr.Rmdusingknitr::rmarkdown

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

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