NEWS.md

In jackwasey/icd9: Tools for Working with ICD-9 Codes, and Finding Comorbidities

Version 1.3

• With many thanks to @wmurphyrd, Quan's revised scoring system for Charlson comorbidities is now included.
• Re-enabled OpenMP, and also use GNU C++ standard library parallel extensions (which also use OpenMP) when available. Thoroughly tested with various docker compiler configurations and no memory or undefined behavior problems appear.
• Use fastmatch for fast factor generation, but with the tweak of not sorting the levels. This had been by far the slowest step in generating comorbidities.

Version 1.2.2

• Completed fix from version 1.2.1 by temporarily disabling OpenMP on all platforms. Still runs quickly due to other optimizations made in supporting the OpenMP. It'll be back, but only when I or someone else can create a docker or VM image which runs Clang 3.7 or greater, OpenMP, with/without LLVM C++ standard library. See #75

Version 1.2.1

• Partly fixed obscure memory access violation error seen only withwhen using OpenMP clang 3.7 on fedora, and maybe OS X.

Version 1.2

• Make annual revisions of ICD-9-CM available. The package includes data from each year which CMS has published (versions 23 to 32). The default is to use version 32. More work will be needed to make it straightforward to use an arbitrary version when running icd9 commands. These are avaiable in the package data icd9Billable. See vignette for examples.
• Inexplicably, the only canonical list which includes both ICD-9-CM codes and headings is an RTF file. icd9 can now parse this eclectically formatted document to extract all the headings, so it is not possible to do icd9Explain on a non-billable four-digit code, e.g. 643.0 (Mild hyperemesis of pregnancy). Previously on three-digit and billable (i.e. lead node) codes were used. In principle, the RTF parsing code could be run on previous versions going back to about year 2000. It seems that most years are the same or expand previous years, although there are a few deletions. Ideally, we would know what year/version a given ICD-9 code was coded under, and then validate or interpret accordingly. This can indeed be done for billable codes, but until the RTF is parsed for previous years, not for headings.
• Condense and range functions has been completely reworked now that all the intermediate heading codes are available. This means there will be slight differences in the results produced, and there are still very minor quirks, but the tests cover thoroughly all known ICD-9-CM codes in existence from any available version.
• The package data was refreshed with comorbidities derived from source ranges specified by the original authors. These deliberately produce valid but non-existent codes, and these are now slightly different with the range work. This should not have any impact on comorbidity assignmentments from real ICD-9 codes, but keeps the package consistent with itself.
• OpenMP and C++11 are now both enabled on platforms which allow this (i.e. everything except Solaris), which gives performance improvements.
• Van Walvaren comorbidity score (analagous to Charlson score, but based on Elixhauser comorbidities) added by @wmurhpyrd, with thanks.
• Dropped most included data from the package, as most can be retrieved from reliable web sites. The data is still in the github repo, but is downloaded automatically when needed (which is only working in the package source tree.)
• stopped exporting 'parts' functions, as these complicate the namespace and are unlikely to end-user, but still available with icd9:::icd9PartsToShort etc.
• code clean-up with excellent lintr package from @jimhester
• bug fixes
• more tests, with coverage at about 85% with the full test suite
• included first thousand patients from a public domain dataset from Vermont, available as vermont_dx.

Version 1.1

• C++ OpenMP parallel processing of comorbidities for further many-fold speed improvement, scaling to cores available in a machine, allocating about a million rows of comorbidities in a second or two, on a moderate workstation. Some speed is lost by (optionally) allowing disordered input visit IDs.
• C++ optimization using simpler, faster STL structures, working with R factors (converted automatically) so comorbidity assignment is done using integer logic only
• drop unwanted old vignette from the build. Fixes #42
• refinement of many functions to specifically accept factors or character vectors, but not integers in most cases. Fixes #38
• more natural use of matrix for comorbidities, with option to return data frames. Allow matrix or data.frame in fuctions which accept comorbidities
• bug fixes with thanks to @wmurhpyrd. Fixes #44, fixes #46
• fixes #41
• extensive use of the excellent and very efficient checkmate package for validating function arguments
• improved test coverage, demonstrated by the excellent covr package and coveralls.io . Fixes #4

Version 1.0

• Calculate Charlson scores
• Sum distinct comorbidities or diagnoses by patient
• Core rewrite in C++ for 50+ times speed improvement. 100,000 patients assigned comorbidities in ~2 seconds.
• Simplified handling validation of codes. No longer done in every function.
• Most functions now guess the ICD-9 code type automatically (e.g. 00321 vs 003.21)
• Reduced external dependencies down to Rcpp and checkmate (a very lightweight and fast function argument checker)
• Bug fixes (see github)
• API changes
  • no more validation except in the icd9IsValidXxx functions. Removed stopIfInvalidIcd9, icd9InvalidActions
  • internalized utility functions. They are also packaged and tested in jwutil
  • deprecated icd9ValidXxx in favour of icd9IsValidXxx
  • deprecated icd9ComorbditiesXxx replacing with briefer icd9ComorbidXxx
  • stopped exporting benchmarking and SAS code processing.

Version 0.5

• Filter icd9 data for validity or existence. Fixes issue #27
• Guess whether a code is short or decimal. Fixes #22
• Enable ranges for Exxx codes. Fixes #9
• Explain and condense long lists of ICD-9 codes using maximum number of higher-level descriptions without being overly broad. Fixes #3
• Include high level descriptions, chapters, majors, which do not have CMS descriptions because they are not themselves billable codes. Fixes #2
• E codes <800 can be valid in 2014. Fixes #1
• Bug fixes, vignette and other documentation updated.
• Test suite ever more comprehensive.
• Rename Elixhauser arguments and functions to "Elix" for clarity of code, and ease of typing.

Version 0.4

• Present-on-arrival field handled gracefully
• Revised co-morbidity handling, with functions specific to each mapping
• Standardized naming of fields across Elixhauser and Charlson based mappings for clarity, consistency and comparaibility
• Handle mild and severe co-morbidities without double-counting. Fixes issue #23
• Enable magrittr-style piping as option to clarify chains of operations. Issue #5
• many more test cases, including specific tests for individual values in each computed mapping, and also for the new comorbidity functions
• Vignette updated to demonstrate clearer new functions

Version 0.3

• Addition of several utility functions, mostly kept for internal use, but which clarify the code
• Consistent behavior with invalid codes, allowing ignore, silent conversion to NA, warn with conversion to NA, or stopping.
• Outline of code to read top level ICD-9 definitions from canonical CDC RTF file.
• Progress to
• Made functions magrittr friendly
• Bug fixes, refactoring, more tests
• Include parsing of hierarchy
• Internal function which reads a file from a zip at a URL
• The included pre-parsed data are slightly updated to include some missing top-level numbers when all the children were also present. ("043" %i9s% "04499" should equal "043" %i9s% "044")

Version 0.2.1

• trivial changes to appease CRAN

Version 0.2

• Added more co-morbidity mappings, Elixhauser original and Quan/Elixhauser.
• Exposed more functions to public API
• Better conversion of ICD-9 codes to textual representation
• Expanded vignette
• Bug fixes and test cases
• Improved documentation

Version 0.1.1

• Include missing import for memoise
• optionally process AHRQ comorbidity subcategories into parent categories
• include the processed binary data. Unlikely to change often, and not too big.

Version 0.1

• First release. Fully functional, no known bugs, but will benefit from addition of planned features described in README.

jackwasey/icd9 documentation built on May 18, 2019, 7:57 a.m.