cghr-toronto / icd Goto Github PK

data/icd10towbd10.csv

Road trafic accidents -> Road traffic accidents

We are using it to create standardized mortality maps for SL, please let me know when fixed!

Create ICD datasets to get code labels for RAPID as VA data does not include labels.

Check if the CGHR 2019 codes correspond to the COD categories in the appendix of the Automated vs Physician Study.

Also check if the WBD codes correspond to the CGHR 2019 codes and the AVP appendix COD codes.

There seems to be confusion with the CGHR, AVP study, and WBD codes.

Data

• CGHR 2019 codes: https://github.com/cghr-toronto/icd/blob/main/data/cghr2019.csv
• AVP Appendix COD codes: https://static-content.springer.com/esm/art%3A10.1186%2Fs12916-019-1353-2/MediaObjects/12916_2019_1353_MOESM5_ESM.docx
• WBD List from Wilson (updated Jan 2023): https://github.com/cghr-toronto/icd/files/10862275/Version.10.-.Final.CGHR-GBD.list.18.April.2013_Updated.12Jan2023.xls

Compile CGHR's ICD data for the open mortality portal.

Noted by Leslie from Sam's InterVA5 and InSilicoVA results for child deaths.

Files below contain mappings for the WHO VA 2016 categories to ICD 10.

01_Manual and guidelines for application and use of simplified WHO VA tool_2016v1-5.pdf
map1.pdf
map2.pdf
map3.pdf
map4.pdf
map5.pdf

There are set of WHO VA codes used to code verbal autopsy records and produce standardized outputs for VA models.

Bryan will compile a list of these and add it to the icd repo.

The cghrCodes package might be helpful in expanding and collapsing ICD-10 codes.

Compile ICD to WBD mappings for ICD-10 from Wilson's table (already provided from Peter).

Include ICD code agreement/equivalence list from Rajeev.

Notes

• This is the Central Medical Evaluation Agreement (CMEA) list used to check agreement between two ICD codes assigned for verbal autopsy records
• Prabhat is more concerned with the groupings so the most recently assigned code can be used when two codes agree
• Catherine uses physician 1's code when two codes agree
• Wilson mentioned a trumping algorithm, but no response since then

Some ICD codes were found in Version 10 - Final CGHR-GBD list 18 April 2013 RW (original Wilson).xls, but not found in icd10towbd10.csv.

For example, Child-G03 code is found in Wilson's, but only Neo-G03 and Adult-G03 were found in icd10towbd10.csv. Furthermore, there are 2 duplicates of Neo-G03.

The list of ICD codes missing from icd10towbd10.csv are here:
missing_icd_2023-02-28.csv

@git-cheryl Cheryl compiled a mapping of WHO VA (WVA) codes to ICD-10 codes from Sam's InterVA and InSilicoVA neonate and child outputs provided by Leslie @lanewcombe.

Files

• Mappings: WVAtoICD_map1-5.csv
• WHO VA 2016 v1.5 Manual: 01_Manual and guidelines for application and use of simplified WHO VA tool_2016v1-5.pdf

Note: There is an updated version 1.5.3 of the manual, but it does not have ICD-10 mappings as opposed to v1.5 of the manual

Mappings were compiled by Cheryl with the following files from Leslie:

map1.pdf
map2.pdf
map3.pdf
map4.pdf
map5.pdf

Process WHO VA codes from Bryan in #8 into complete datasets and document them.