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.

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.

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.