plot_comorbiduses simple base R graphics to quickly summarise comorbidities in a bar plot.
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.
categorizesince it no longer provides any optimization opportunity.
icdwork better when not lodaded with
icd::comorbid_ahrqetc. should work with just
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.
icdis about 10x faster than the
pcccpackage, which also uses ‘Rcpp’)
restore_id_order = FALSEin comorbidity calculations.
icd10_comorbid_charlsonas synonyms for the Quan/Deyo comorbidity calculations.
comorbid_charlsonwill infer the ICD type.
icd::comorbidmay also be used, and which many consider good practice.
explain_icdsynonym avoids name conflict with the popular
icd::explainalso a nice option.
icd9still available in CRAN repo, but not being updated. This greatly speeds up and simplifies the test suite.
explain_tablewhich 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.
stringrfamily 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.
icd9should now be uninstalled.
as.icd9cm("0101"). This will help avoid mistakes when working with mixed data.
icd9prefix 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
icd10_, prefixes. E.g.
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
icd9runs and passes on the
icdpackage, with only minimal changes.
testthatwhich has backward-incompatible changes
stringrto give cleaner string processing. Base string processing is still used as it is often faster.
magrittris now too useful not to import, has no dependencies of its own, and is imported by
stringranyway. CRAN now also seems to need base packages to be listed as imports.
fastmatchfor fast factor generation, but with the tweak of not sorting the levels. This had been by far the slowest step in generating comorbidities.
icd9commands. These are available in the package data
icd9Billable. See vignette for examples.
icd9can now parse this eclectically formatted document to extract all the headings, so it is not possible to do
icd9Explainon 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.
lintrpackage from @jimhester