incorporate annual changes to the ICD-9 specifications

[jackwasey]

This is a thorny issue. There have been small updates to ICD-9 each year, until recently.

Furthermore, AHRQ have updated their version of Elixhauser ICD-9 to co-morbidities annually.

A thorough implementation would optionally accept year or date with every ICD-9 code, and treat it appropriately.

[jackwasey]

This is mostly fixed in release 1.2, but it is not yet possible to specify which ICD-9 version to be used in all functions.

[jackwasey]

This document:
http://www.cdc.gov/nchs/data/icd/ICD-9-CM_FY14_CNVTBL_Final.pdf
contains a summary of when and what ICD-9 codes were changed over the years.

Need to read Quan papers carefully to see how they handled ICD specification changing over time. Did they set up a list of codes and apply it blindly to all past cases regardless of specification changes (most likely), or did they translate codes before updating? If they did it blindly, then it is probably reasonable to do the same, especially as there have been few changes in recent years.

[StephenSinger]

There are only 5 changes listed after 2011. I've been slowly working on
making this machine readable, but its not ready yet.

On Sat, May 16, 2015 at 6:33 AM Jack Wasey notifications@github.com wrote:

This document:
http://www.cdc.gov/nchs/data/icd/ICD-9-CM_FY14_CNVTBL_Final.pdf
contains a summary of when and what ICD-9 codes were changed over the
years.

Need to read Quan papers carefully to see how they handled ICD
specification changing over time. Did they set up a list of codes and apply
it blindly to all past cases regardless of specification changes (most
likely), or did they translate codes before updating? If they did it
blindly, then it is probably reasonable to do the same, especially as there
have been few changes in recent years.

—
Reply to this email directly or view it on GitHub
https://github.com/jackwasey/icd9/issues/6#issuecomment-102605297.

[jackwasey]

Good to know, thanks. Now I've included code that parses all the billable code lists, all the raw materials are there to compare and icd9Explain the differences from year to year. It would be great to also have the above PDF machine readable, and to see whether the results match up: perhaps this could be codified in the form of some testthat action, and a function to read in your hand-written data from the PDF.

[jackwasey]

This is partially implemented. Ideally, ICD coding data should reference the ICD-9 code table for the year it was entered. Assuming most or all changes involved adding code, using the last published ICD-9-CM codes will work well. Earlier versions are available in icd9. E.g.

> icd9cm_billable[["28"]] %>%  head
  code               short_desc                             long_desc
1 0010 Cholera d/t vib cholerae        Cholera due to vibrio cholerae
2 0011   Cholera d/t vib el tor Cholera due to vibrio cholerae el tor
3 0019              Cholera NOS                  Cholera, unspecified
4 0020            Typhoid fever                         Typhoid fever
5 0021      Paratyphoid fever a                   Paratyphoid fever A
6 0022      Paratyphoid fever b                   Paratyphoid fever B

icd9_sources has information about the ICD-9-CM source data:

icd9_sources[1:3]