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jackwasey
adding procedure codes
Hi Jack. I need to use procedure codes in addition to diagnoses codes. I could not find it in current version of your package so for now I'm creating my own list similar to icd9cm_billable and, if I have enough time, another one similar to icd9cm_hierarchy (i.e. icd9cm_sg_billable and icd9cm_sg_hierarchy respectively). I wnat to make sure I'm not recreating somebody's effort. If nobody has done it, I'd be happy to share mine (I forked our project).
That would be great, David. I would love to include functions to extract procedure code data from online canonical sources, and the resulting data.
Did you see parse_leaf_descriptions_all and icd9_parse_leaf_desc_ver in parse.R? I'd think these would be a good base to get annual ICD-9-CM procedure code lists: you'd just have to add code to add the procedure codes to the download, then parse the text.
Thanks very much, Jack
Great, thank you Jack! I did not know about these function but I will use them now.
I've made a good bit of progress on this. If you're working in it, too, let me know.
I'm sorry, I did not get to it yet. I saw you added a whole lot of new codes including two related repos (icd.data & icd-file_generator) but I had no time to go over them yet. Can we continue this conversation off-line, please? I'm in RWJ Medical School (Rutgers), NJ. Our whole group wants to connect with you, if you don't mind. Also, please see the quick-and-dirty first version of a Shiny app I wrote using your package: https://github.com/CVIRU/shiny.icd You can see I added procedure codes but only for a single year.
icd-file_generator is just afork of someone else's repo. I'm going to try to move the increasingly big icd data to a new package, but keep all the code in icd, but it won't change the use of icd at all, just add a dependency on icd.data.
I posted ICD-9 procedure codes here: https://github.com/jackwasey/icd.data/issues/3 I kept the same logic you applied to ICD-9 procedure codes by separating chapters, sub-chapters and billable codes (all available versions). There are no major categories for procedures, if i'm not mistaken.
Hi, David. Thanks. Was great talking to you and your team. Sorry for break in contact: available again now.
Did you look at integrating the procedure codes into icd.data already? You've probably seen the standard way icd builds and stores the data. I then just dump the results into the icd.data package data directory.
Hi Jack. It was a pleasure speaking with you, thank you for accepting our invitation. Totally fine with the timing, we had enough to work on after our meeting :) I made the data objects manually but I think they are in the right format. I did not commit the files, they are attached as a zipped folder here: https://github.com/jackwasey/icd.data/issues/3 I think I got it all correctly, ready to be added to icd.data but if this is not good enough, please let me know - I'll go back and rerun it with your scripts. Thanks!
Hi Jack,
You are doing a great job! Let me know if you need any kind of data file to work on. We develop cross-ref, subcategories and a lot more in various formats.
Respectfully, Abbey
Abbey, can't believe I just came across your message. Thanks so much. ICD-9-CM procedure codes are still outstanding. There are numerous other coding schemes inside and outside the US which are related or descended from ICD. I am open to accepting anything ICD or comorbidity calculation related in this package. Happy to be in touch here or by email. Jack
FYI David and Abbey - the icd.data and icd separate packages turned out to require a huge amount of heavy lifting due to reverse dependencies and so on. I've got a trial icd package with all the data and code in one 'icd' package again, just as it was a couple of years ago, and this greatly simplifies everything. icd.data also pulls in data on demand, so it doesn't acutally need to be a big(tm) data package. I'll migrate the issues from icd.data over here.