Nothing
plot_comorbid
uses 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.unique_ids
argument to comorbid
and categorize
since it no longer provides any optimization opportunity.icd
work better when not lodaded with library
, so icd::comorbid_ahrq
etc. should work with just requireNamespace
or using icd::function()
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.icd
is about 10x faster than the pccc
package, which also uses 'Rcpp')restore_id_order = FALSE
in comorbidity calculations.icd9_comorbid_charlson
and icd10_comorbid_charlson
as synonyms for the Quan/Deyo comorbidity calculations. comorbid_charlson
will infer the ICD type.pkgdown
generated site in gh-pages
branch.library(icd)
firstrticles
and tinytex
comorbid_charlson(patient_data)
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.icd9
still available in CRAN repo, but not being updated. This greatly speeds up and simplifies the test suite.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.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.icd9
should now be uninstalled.icd9ExplainShort
becomes icd_explain
as.icd10("A01")
or as.icd9cm("0101")
. This will help avoid mistakes when working with mixed data.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.icd9ValidDecimal
testthat
which has backward-incompatible changesicd
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.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.icd9
commands. These are available in the package data icd9Billable
. See vignette for examples.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.icd:::icd9PartsToShort
etc.lintr
package from @jimhestervermont_dx
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