NEWS.md

In jackwasey/icd: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes

icd NEWS

Version 4.0.9.9000

• bug-fix version for the latest CRAN release 4.0.9
• JSON handling bug for WHO downloads introduced by a code merge error

Version 4.0.9

• happy to add Alessandro Gasparini as collaborator, as we move comorbidity API from icd to the comorbidity package in subsequent releases, and separate out the fast comorbidity calculation engine into a new, tighter package. icd will continue to provide icd conversion, validation, translation, mapping, etc., and keep backward compatibility for a year during this migration.
• also adding the tireless @patrickmd as a contributor, with his significant pull requests, testing and patience.
• likewise for
• fixed CRAN submission broken links
• Updated French ICD code URL
• dropped r-lib/rappdirs in favor of copy of backports::R_app_dirs
• dropped extraneous files from source tarball sent to CRAN
• clean-up prebuilt pdf paths, both keeping package smaller, and fixing broken links, as noted by CRAN but missed by R CMD check somehow.
• anticipate next version including work from the NIH hackathon for general equivalence mapping of ICD-9-CM to ICD-10-CM codes, thanks to those women, and also the contributions from @dapritchard @dprtichlibre

Version 4.0.8

• Work-around rappdirs problem affecting some Windows users with default cache data directory.
• ICD-10 vignette link to efficiency vignette updated.
• CRAN: removed a deprecated compiler flag, and udpated documentation
• (pending updates for next release: fix for Windows JSON error for some ICD data downloads; ICD-9 to ICD-10 cross-walk)
• fix test failure due to new 4.0 R-devel policy for stringsAsFactors=FALSE by default, thanks to @patrickmdnet.

Version 4.0.6

• Major update. Highlights include: wide/long data both handled efficiently without conversion; WHO, France, Belgium ICD-10 codes; more comprehensive ICD-10 comorbidity maps to span historic ICD-10 versions
• The ICD-10 comorbidity maps have been expanded to include the union of all codes for each year in which ICD-10-CM and WHO ICD-10 are available. E.g., HIV in WHO scheme has more detail than the US version. (The ICD-9 code algorithm does not rely on exact ICD-10 codes in maps, so is unchanged). This will flag a few more comorbidities than before, especially when data doesn't correspond to the most recent map. CCS maps are only expanded over history ICD-10-CM since they are US-oriented. This is an important user-facing change which will improve capture of comorbidities in international and historic ICD-10 data. Again, ICD-9 computations are unaffected.
• Thanks to @vitallish for update to CCS maps see #163, #168
• Framework for using WHO ICD-10 codes, which icd will download as needed from the WHO web site. English and French are available, but currently only for the years 2016 and 2008 respectively. (Note from the future: the icd.data package is completely deprecated, never updated, and should be uninstalled, except in the case of reproducible research, when the CRAN Archive should be consulted, MRAN, etc..)
• Access to French and Dutch translations of ICD-10-CM, used in Belgium.
• Handle 'wide' format data much more efficiently, without having to convert to long format first.
• Add ICD-9 and ICD-10 WHO and US Clinical Modification procedure codes.
• New function plot_comorbid uses simple base R graphics to quickly summarise comorbidities in a bar plot.
• Newly exported functions: decimal_to_short and short_to_decimal.
• Dropped all deprecated function names, which have been giving warning messages for a long time.
• drop deprecated arguments to 'comorbid': visitId and icd9Field. Use 'visit_name' and 'icd_name' instead.
• default not to do (minimal) code cleaning before calculating comorbidities. To re-enable, use preclean = TRUE. Decimal-format codes are still converted to the short form used in the maps. For huge data with decimal format codes, converting the maps to decimal will be more efficient than converting the ICD data to decimal format.
• drop unique_ids argument to comorbid and categorize since it no longer provides any optimization opportunity.
• Let icd work better when not lodaded with library, so icd::comorbid_ahrq etc. should work with just requireNamespace or using icd::function()
• Prefer 'leaf' over 'billable' to indicate a leaf node. Most coding systems are not all about money, and 'icd' should reflect this. 'billable' as an argument to functions such as is_defined() and get_defined(). Functions named like is_billable() are left in place for ICD-9-CM and ICD-10-CM, but in general, is_leaf() and that family of functions is preferred.
• Drop dependency on magrittr, although it may still be used nicely with icd functions
• Increased test coverage with resulting fixes in corner cases
• Accept integer identifiers in patient data
• Default to not validating input factors: all factors generated by R are valid. This gives a significant performance increase for big data.
• sort_icd renamed to be a simple S3 method for base R sort. Sorting and ordering ICD-10-CM and ICD-10-BE codes is now supported. sort_icd is still available so that ICD-9 versus ICD-10 can be guessed, since base sort cannot do this.
• PCCC: renamed column names to be more consistent with the other comorbidity maps, with both abbreviated and full names; added short vignette; benchmarking improved (icd is about 10x faster than the pccc package, which also uses 'Rcpp')
• Better documentation, including more links between documentation, removed internal documentation from public view. Added "Table One" example demonstration to README.
• code cleaning, simplification and linting, e.g. replaced sapply with vapply throughout, and dropped custom wide-long-wide conversion C++ code in favour of base R.

Version 3.3

• Fixes #160, #161
• Includes replication code for benchmarking, showing enormous speed of 'icd' over alternatives.
• Improved referencing and documentation
• Functions to print vectors of ICD codes more cleanly when they have 'icd' classes or attributes.

Version 3.2.1

• Pediatric Complex Chronic Condition functions more consistent with the other comorbidity functions
• Minor bug fixes
• Fixes #157
• Eigen library is multi-threaded, so OpenMP dependencies now dropped from this package, simplifying and speeding up build, dropping configure script, etc..

Version 3.2.0

• added Pediatric Complex Chronic Condition comorbidity classification
• added ICD-10 procedure code data, and AHRQ procedure code classification -- see ICD-10 vignette
• added ICD-10-CM data from US CMS for 2015 to 2018
• fixed 588 instead of 588.0 in Quan Elixhauser ICD-9 comorbidity map
• fix regression where codes appearing in two comorbidities would only count once
• default best-effort ordering of identifiers (e.g. Visit ID, Encounter, Patient ID) is done. There are many cases where this is not possible (disordered input data), or obvious (the IDs are given as a factor, where the factor level order does not resemble the order of appearance in the vector). For performance, this can be turned off using restore_id_order = FALSE in comorbidity calculations.
• added icd9_comorbid_charlson and icd10_comorbid_charlson as synonyms for the Quan/Deyo comorbidity calculations. comorbid_charlson will infer the ICD type.
• depend on new package icd.data for large, rarely modified data files. (Note from the future: the icd.data package is completely deprecated, never updated, and should be uninstalled, except in the case of reproducible research, when the CRAN Archive should be consulted, MRAN, etc..)

Version 3.1.2

• Documentation improved
• https://jackwasey.github.io/icd/ now has pkgdown generated site in gh-pages branch.
• Allow more functions to work without having called library(icd) first

Version 3.1.1

• Includes article submitted to the Journal of Statistical Software, brings in minimal new dependencies with rticles and tinytex
• Drop RODBC dependency. Uranium sample data can still be reproduced offline.

Version 3.0

• major improvement in comorbidity calculation speed using matrix multiplication behind the scenes. ICD-10 codes were slower than ICD-9 code comorbidities before, and are now 1.5 - 2 orders of magnitude faster.
• Added AHRQ clinical condition software (CCS) classification for ICD-9 and ICD-10, thanks to Vitaly Druker, fixes #127
• added 'charlson' synonyms for 'Quan/Deyo', e.g. Charlson comorbidities can now be found using comorbid_charlson(patient_data)
• Added AHRQ clinical condition software (CCS) classification for ICD-9 and ICD-10, thanks to Vitaly Druker, fixes #127
• function names have lost the 'icd_' prefix, old names kept for compatibility, but easier now to write comorbid(patient_data), and icd::comorbid may also be used, and which many consider good practice. explain_icd synonym avoids name conflict with the popular dplyr package, but icd::explain also a nice option.
• Assume C++11, which is now four years old, enabling code simplification
• rename all functions to remove the icd_, people can use the concise icd:: if library(icd) was not called
• deprecated rarely or unused code, including %i9in%

Version 2.4.1

• updated HCC to include 2017 data, thanks to @anobel fixes #136
• fixed github #133 - segfault with empty ICD-10 string in icd10_comorbid
• add Suggested dependency on microbenchmark, now CRAN is sensibly not requiring Suggests to be installed even for testing
• re-enabled testthat C++ Catch tests and make examples tests run correctly
• drop Wercker continuous integration support
• fixed #108 - when no valid codes are given to icd_explain_table

Version 2.3

• Fixed nasty bug which failed to sort the names of a vector of ICD codes correctly, resulting in some incorrect icd_explain. Fixes github #123, #124, #126.
• update stale URLs for example data sources

Version 2.2

• Removed deprecated functions and data. icd9 still available in CRAN repo, but not being updated. This greatly speeds up and simplifies the test suite.
• Bug fixes #89 #99 #106 #109 #100 #111 #113 #115 #116 #117 with many thanks to bug reporters and users
• stopped changing an attribute by reference, thanks to Tomas Kalibera for highlighting.

Version 2.1

• Many thanks to @anobel for providing parsing and lookup of Hierarchical Condition Codes.
• Many thanks to @edlee123 for contributing explain_table which tabulates results of looking up various information about a list of ICD codes. This is a new feature which may be changed as it is used in the real world, and more tests are developed.
• removed stringr family of dependencies: it was often slower on benchmarking than built-ins, and no clear benefits other than internally consistent syntax, and stringr updates caused CRAN warnings due to a documentation change.
• Fixes #86, thanks to @anobel
• Fixes #91
• Fixes #93 thanks to @nancyorgan
• Fixes #97, thanks to @michaelgao8
• Speed improvements, mostly simply from using base R hashed Environments instead of lists

Version 2.0

• ICD-10 support, including ICD-10 comorbidity mappings, validation and explanations (code to description). ICD-10-CM 2016 is included.
• Extended the already comprehensive test suite to cover ICD-10 and fixed various bugs. Thanks to @wmurphyrd for providing some Elixhauser test data.
• Package icd9 should now be uninstalled.
• Simplify functions
• Automatic detection of ICD version when not specified
• Automatic detection of use of short or decimal format codes
• e.g. icd9ExplainShort becomes icd_explain
• Optional use of the S3 class system so data can be described as ICD-9 or ICD-10, so appropriate functions are used without guesswork. This means that you can optionally label your data with the appropriate class, e.g. as.icd10("A01") or as.icd9cm("0101"). This will help avoid mistakes when working with mixed data.
• ICD-9 and ICD-10 sub-versions, particularly for distinguishing of ICD-9 (WHO) from ICD-9-CM, and same for ICD-10. This can also be extended to other countries, e.g. ICD-10-CA, or other code types altogether.
• Soft deprecated all icd9 prefix functions, now this package equally covers ICD-10. New naming scheme follows Hadley Wickham's preferred coding style, using underscores. Most public functions begin with icd_. Package data, and version specific functions, are named with icd_, icd9_, icd10_, prefixes. E.g. icd10_chapters and icd9cm_hierarchy. All deprecated functions will still work, but they give warnings (sometimes many). The warnings can be turned off with an option. The original test suite from icd9 runs and passes on the icd package, with only minimal changes.
• Completely deprecated some previously soft deprecated functions, e.g. icd9ValidDecimal
• Works with very latest testthat which has backward-incompatible changes
• Minimized dependencies, but icd does import stringi via stringr to give cleaner string processing. Base string processing is still used as it is often faster. magrittr is now too useful not to import, has no dependencies of its own, and is imported by stringr anyway. CRAN now also seems to need base packages to be listed as imports.
• More automated testing with Travis and Wercker, Codecov and Coveralls.

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 when 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 available 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 assignments 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 Walraven comorbidity score (analogous 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 icd:::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 functions 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 comparability
• 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/icd documentation built on Nov. 23, 2021, 9:56 a.m.