Add support for latest AHRQ Elixhauser comorbidity calculation #29
Conversation
ensure fork is up to date
|
Hi! |
|
I think implementing #35 will greatly simplify implementing scores with DRG codes. What do you think @salmasian and @fiksdala? |
|
Thanks @ellessenne for this update! I think that would make sense both from an end-user perspective and in light of recent AHRQ updates to Elixhauser. The SAS program provided by AHRQ only returns the domains (plus some generic summary stats in a separate procedure), and my most recent work (i.e. the 2021 update, not yet finalized) also only returns the comorbidity domains anyway. That decision was made both to more closely replicate the SAS output and because the 2021 AHRQ update includes new comorbidity categories that are incompatible with the scoring schemes used previously. |
|
Sounds good, thanks. I will work on the API on a separate branch, I'll let you know once ready to test! |
add icd10cm_2020_1 ahrq maintenance files add icd10cm_2021_1 ahrq maintenance files add 2021 ahrq function delete duplicate files update directory references in for 2020 convert-sas.R update directory references in make-data.R streamline ahrq 2020 lofregex and add 2021 formats add formats directory for ahrq versions add directory for sas parsing scripts add parameters for 2021 ahrq remove extaneous options ahrq 2021 remove maintenance dir, replace with sas-parse/sas-formats update mapping reference to list produced in get_mappings rename elixhauser_ahrq option to elixhauser_ahrq_2020 update internal data fix ahrq labels in .check_output fix drg_id class = factor error fix ahrq_2020 assertions, add assertions for ahrq_2021, add ahrq_2021 to .check_output add total score column isolate internal/external score calculations and add ahrq2021 support roxygen2 upgrade calculate ahrq using discrete functions fixes POA required with not present logic fix class assertions for tibbles w/spec_tbl_df subclass add assertion for ic10cm_vers values fix exempt matching fixes missing columns error when poa=F fix icd10cm_vers assertion remove missing columns references when poa=F fix cbvd exemptions update documentation update documentation remove testing scripts fix id name error add elixhauser 2021 examples to README
Kr branch
Bug fixes for elixhauser_ahrq_2022
bug fixes, confirms 2022 matches AHRQ SAS program
|
Thanks for the update! I've been doing some preliminary work to adapt my
code to your updated API as well, and will dive into that more once your
new release is ready. I'll be sure to reach out down the line when my fok
is close to being ready for a PR.
Thanks,
Alex
…On Mon, Jan 17, 2022 at 5:36 AM Alessandro Gasparini < ***@***.***> wrote:
Hi @fiksdala <https://github.com/fiksdala>, I am preparing a new release
of {comorbidity} for CRAN with the new API (see #43
<#43>). Once that is
done, it will be easier to work on the AHRQ version of the Elixhauser
score. Thank you again for your patience!
—
Reply to this email directly, view it on GitHub
<#29 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AGIXMBMT4WZMBPE5EMHDFV3UWPWMVANCNFSM4R6H6VLA>
.
Triage notifications on the go with GitHub Mobile for iOS
<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>
or Android
<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.
You are receiving this because you were mentioned.Message ID:
***@***.***>
|
Fixes Elixhauser .rds mapping files
|
I had forgotten that we had actually submitted this older PR. Yes, we can
close this one and focus on #52 instead. Thanks! -Alex
…On Tue, Mar 8, 2022 at 1:59 AM Alessandro Gasparini < ***@***.***> wrote:
Given the new PR in #52
<#52>, do you think it
would be okay to close this @fiksdala <https://github.com/fiksdala>?
—
Reply to this email directly, view it on GitHub
<#29 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AGIXMBIJS4JFQJPGU4LYT5DU633ETANCNFSM4R6H6VLA>
.
Triage notifications on the go with GitHub Mobile for iOS
<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>
or Android
<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.
You are receiving this because you were mentioned.Message ID:
***@***.***>
|
Hi @ellessenne ,
My colleague @salmasian has mentioned this work to you previously, but this PR aims to address Issue #28 and replicates the AHRQ SAS program (version 3.7) functionality. This required changes to comorbidity.R as well as some other supporting scripts. Of particular note, ICD-10 ranks and DRG codes must be passed to comorbidity() to replicate the AHRQ SAS program. While my fork is 100% functional, some changes to this PR may be required for better integration with the parent repo. Please let me know if there's anything I can do to facilitate those efforts or if you have any other questions.
Kind regards,
Alex Fiksdal