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medicalcoder 0.10.0

New Features

  • Add FY2027 ICD-10-CM and ICD-10-PCS from CMS. The CDC-hosted FY2027 CM order file agrees with CMS; the package's cdc source label continues to refer to mortality codes.
  • Extend ICD-10-AM code coverage through Australian financial year 2027 using the current Thirteenth Edition.

Bug Fixes

  • Select CMS source archives explicitly so the original FY2026 PCS archive cannot mask the April 2026 update. Correct affected FY2026 code validity.
  • Repair recursive ICD build dependencies and track selected source files so importer and source updates propagate to generated package data.
  • Preserve the union of codes from supported annual AHRQ ICD-10 mappings in elixhauser_ahrq_icd10. This method has no encounter year or quarter input, so codes from earlier releases remain included even if a later release no longer lists them as assignable.
  • Add a data-build check that mapped, assignable ICD-10 codes retain the same POA-exemption status across supported AHRQ releases. This guards the assumption behind the combined elixhauser_ahrq_icd10 method (#47).

Other Changes

  • Add a CITATION file and cite the JAMIA Open manuscript in the README.
  • Organize tests into attached, unattached, and extended groups, with a runner that isolates each test script in its own environment. Routine checks now disable extended tests explicitly; use make check-extended to run them. Tests that require an unavailable optional dependency can use skip_test() so the runner records a skip and continues with the group.

Breaking Changes

  • Corrected the Elixhauser method name from elixhauser_elixhauser1988 to elixhauser_elixhauser1998. The get_elixhauser_codes() and get_elixhauser_index_scores() lookup tables now use the elixhauser_elixhauser1998 column and no longer include the old column name. Update code that selects the old column. Calls to comorbidities(method = "elixhauser_elixhauser1988") remain temporarily supported with a deprecation warning. (#50)

medicalcoder 0.9.0

New Features

  • comorbidities() gains a mapping argument. The default mapping = "precomputed" uses the precomputed ICD code-condition links included with medicalcoder. mapping = "regex" applies method regular expressions directly to input ICD codes. Regex mapping is currently available for Charlson methods except charlson_beyrer2021. (part of #45)

  • Clarify flag.method = "cumulative" documentation for longitudinal data. Users should validate encounter ordering and POA behavior carefully for their study design.

  • Add validation for the encounter-order column used by flag.method = "cumulative". Missing values and factor columns now error; character columns are allowed with a warning because they are sorted lexicographically.

  • Add charlson_sundararajan2004

  • Add charlson_ludvigsson2021, a Charlson-style Swedish register-based comorbidity method.

  • Add charlson_mimicivcode, a mapping between ICD-10 codes and Charlson comorbidities to be consistent with mimiciv-code

  • Add charlson_beyrer2021, a Charlson style comorbidity based on U.S. ICD-10-CM diagnostic and ICD-10-PCS (procedure) codes from Beyrer et al. (2021)

  • Add ICD-10-AM (Australian Modification) to the ICD database

  • Add ICD-10-SE (Swedish) to the ICD database. Source files from Socialstyrelsen.

Bug Fixes

  • summary() falls back to the next applicable method with a warning when a modified medicalcoder_comorbidities object no longer has the structure required by medicalcoder's methods.

  • Prevent unrelated input columns from colliding with internal lookup columns while mapping ICD codes to comorbidities in comorbidities().

  • ICD-10 Z49.1 has been added to elixhauser_quan2005; it was missing by error in the prior version of medicalcoder.

Improvements

  • comorbidities() now warns, without stopping, when column-backed icdv.var, dx.var, poa.var, or primarydx.var values fall outside the values used by the supported comorbidity mappings.

  • Clarify that AHRQ SAS present-on-admission indicators should be converted to numeric values before using poa.var: "Y" and "W" map to 1L, "N" and "U" map to 0L, and blank or missing values map to NA_integer_.

  • Clarify that rows with icdv.var values other than 9 or 10 are not used when mapping ICD codes to comorbidities.

  • Clarify that rows with dx.var values other than 0 or 1 are not used when mapping ICD codes to comorbidities.

  • WHO ICD-10 codes extend 2019 to 2020 and 2021. WHO last published ICD-10 in 2019 and transitioned to ICD-11 on January 1, 2022.

medicalcoder 0.8.1

Bug Fixes

  • Fix Charlson age.var handling when id.vars is missing or has multiple ages per ID. (#43)

  • Fix summary() for Charlson results when age.var is omitted and age_score is all missing.

  • Account for possible zero nrow sets in mdcr_set()

  • Harden sort order for the results from lookup_icd_codes()

medicalcoder 0.8.0

License Change

medicalcoder <= 0.7.0 was under GPL-2 for no other reason that that was the default in the template DESCRIPTION file. With this release we have transitioned from GPL-2 to BSD-3-Clause to reduce almost all barriers to use of the package in other environments.

New Features

  • If a tibble is passed to comorbidities() and the dplyr namespace is available, then dplyr methods will be used for data manipulation. This change will generally result in less computation time than base R data.frames (data.tables require even less time).

  • Add the elixhauser_ahrq2026 method for comorbidities() (#32)

Bug Fixes

  • summary.medicalcoder_comorbidites() no longer crashes when a zero row input is passed in. Consistently return NA instead of NaN when counts are zeros. (#26, #27)

  • Improve the conditional and multiple comorbidities mapped by a code under AHRQ ICD-10 codes for fiscal years 2023 through 2026. The bug was found and fixed as part of the extension #32.

  • Add ICD-9-PCS 35.7 to the PCCC codes. (#38) The v2 docs have 37.52, 37.53, 37.54, 37.55 as cvd (device) and 37.5, 37.51 as cvd (transplant). v3 docs have 3751 as cvd (transplant), all other four digit codes under 37.5 as cvd (device). One issue here is that 37.5 was an assignable code from CDC through 2003 and then was a header with the same four digit codes as CMS through 2012. CMS continued to use the four digit codes through 2015.

  • Improve Elixhauser (Quan 2005) ICD-10 codes

    • omitting F42.2 for depression
    • adding G36.x for neuro
    • adding 333.4 for neuro

  • Add checks for data structures (#41)

  • Handle zero length patterns in regex (#42)

Other Changes

  • Extend and improve the internal ICD-9 database to distinguish between CDC and CMS source.

  • Fix documentation of the mdcr and mdcr_longitudinal datasets.

  • Clarified internal data.frame/data.table helpers: documented that mdcr_select() deep-copies data.table subsets to avoid aliasing, noted the selfref fix in mdcr_set(), and added inline guidance in the longitudinal section of comorbidities() to explain the first-occurrence logic.

  • Improve cumulative flagging to apply first-occurrence logic more efficiently.

  • Extend documentation for the expected default behavior between the present-on-admission flags and flag.method argument in comorbidities() (re: #28)

  • Add mdcr_unique() to the data.frame utilities. This reduced the computational time required to apply comorbidities() to tibbles and data.tables. (#31)

medicalcoder 0.7.0

Bug Fixes

  • Elixhauser AHRQ 2022 - 2025

    • exclusions for less severe conditions when more severe conditions are flagged.
    • Improved POA, NPOA, and EXEMPTPOA. This came about from #20.

  • Make internal data.frame tool mdcr_duplicated() data.table aware.

  • Elixhauser (Quan 2005) - added missing ICD-10 codes to the mappings

New Features

  • comorbidities() will return a tibble when the input data is a tbl_df (#9). Assuming the data.table and/or tibble namespaces are available, then the initial release (v0.6.0) would return a data.table if a data.table was passed to a comorbidities() due to the S3 method dispatches. If a tibble (tbl_df) or a data.frame was passed to comorbidities() then the return would be a data.frame. In this release we have added logic to determine if the input is a tibble and if the tibble namespace is available, then the return from comorbidities() will be a tibble (or list of tibbles when subconditions = TRUE).

    The tests were extended to consider the cases of passing in a data.table or tibble to comorbidities when the associated namespaces are not available.

  • Added elixhauser_ahrq_icd10 to use all the ICD codes ever defined from 2022 to 2025. This will capture any future years as well.

Other Changes

  • Improve formatting of vignettes/articles.

medicalcoder 0.6.0

  • Initial CRAN submission, providing a dependency-free toolkit for ICD-9/10 code lookups
    • lookup_icd_codes(),
    • get_icd_codes(),
    • icd_compact_to_full(), and
    • is_icd().
  • Introduces a unified comorbidities() interface covering Charlson (Deyo, Quan 2005/2011, Glasheen), Elixhauser (original, Quan 2005, AHRQ 2017-2025), and Pediatric Complex Chronic Conditions (v2.0/2.1/3.0/3.1).
  • Adds support for present-on-admission indicators, longitudinal look-back, age scoring, and PCCC sub-condition flags within comorbidities().
  • Bundles curated ICD dictionaries alongside example datasets (mdcr, mdcr_longitudinal) for reproducible testing and demonstrations.
  • Includes vignettes and benchmarking summaries that document usage patterns and showcase performance without non-base dependencies.