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comorbidity (development version)

comorbidity 1.1.0

  • Added a second version of the ICD10-AM score including U codes to "increases the capture of some chronic conditions up to 15-fold", according to the Australian Institute of Health and Welfare (#72, thanks to @DesiQuintans for contributing this);

  • Updated Swedish version of the Charlson comorbidity score according to the corrigendum published online at: https://doi.org/10.2147/CLEP.S425901;

  • Removed startup message highlighting changes in the package API introduced with {comorbidity} 1.0.0;

  • Updated hex sticker;

  • Minor improvements to {pkgdown} website accessibility;

  • Fixed invalid language field in DESCRIPTION file (#75).

comorbidity 1.0.7

  • Identified (and adjusted) some tests that could spuriously fail.

comorbidity 1.0.6

  • Adjusted name of weights (leftover from #53, thanks @sciatro for reporting this). This bug did not seem to affect any calculation.

  • Updated CITATION file to use the new interface.

  • Some internal housekeeping (removed old documentation, updated GitHub actions to new version, etc.).

comorbidity 1.0.5

  • Adjusted some tests that were spuriously failing on CRAN.

comorbidity 1.0.4

  • Updated maintainer e-mail.

  • Updated hex sticker.

  • Improved documentation for arguments of the comorbidity() and score() functions (#61, thanks @dsjoho).

  • Fixed broken references to the old vignettes' names (#61, thanks @dsjoho).

  • Overall, package documentation has been tidied up a bunch.

  • The startup message pointing out changes in the API now appears less often (10% probability).

comorbidity 1.0.3

  • Fixed a bug that did not allowed ID columns other than numeric (#55, thanks @norihikorihiko for reporting this).

comorbidity 1.0.2

  • The copd and ami comorbidities for the Charlson index have been renamed to cpd and mi, respectively (#53, thanks @DrYan1102). Please be aware that this might break some old code if you were selecting comorbidities by name.

  • New dataset: ICD10-CM, 2022 version, named icd10cm_2022.

comorbidity 1.0.1

  • The startup message pointing out changes in the API now appears less often (40% probability).

  • Fixed a bug that was causing all comorbidities to be assigned a value of one when there was missing data in the code column (#50), thanks @Chris-M-P for reporting this.

comorbidity 1.0.0

  • comorbidity version 1.0.0 is a release that substantially modifies and updates the package API. There are a lot of improvements in terms of performance, supported algorithms, and user-facing functions; see e.g. this thread on GitHub. Specific user-facing changes, including examples of the new API, are discussed in more detail here: https://ellessenne.github.io/comorbidity/articles/C-changes.html

  • If required, you can revert to the previous release by installing from GitHub: remotes::install_github("ellessenne/comorbidity@0.5.3").

  • A startup message pointing out the changes in the API is now displayed with a 50% probability when attaching the package and will be removed in future releases.

  • New contributors: Sing Yi Chia and Edmund Teo.

comorbidity 0.5.3

  • comorbidity now accepts data.table objects as input (#23);

  • comorbidity can deal with non-syntactically valid names (#25);

  • Fixed coding typo in vignette (#10, #26);

  • Reduced number of random tests, as R CMD check was taking too long on some platforms getting killed on CRAN (as reported by Kurt Hornik).

comorbidity 0.5.2

  • Fixed another bug introduced by the switch to data.table that only occurred when the input dataset had extra columns other than id and code.

comorbidity 0.5.1

  • The melt generic in data.table has been deprecated; the dependency on reshape2 has now been removed;

  • Fixed bugs introduced by switching to data.table in comorbidity 0.5.0: column names id and code were expecting these specific names, now fixed and behaves as expected.

comorbidity 0.5.0

  • comorbidity is now 10+ times faster, thanks to Jonathan Williman contributing code based on the data.table package;

  • Fixed typo in vignette regarding weighting algorithm for the AHRQ Elixhauser comorbidity score (#14, thanks to @cornflakegrl);

  • Added pkgdown website: https://ellessenne.github.io/comorbidity.

comorbidity 0.4.1

  • Fixed bug in regex patterns (#10, thanks to @francisco003 for reporting it and @salmasian for the pull request).

comorbidity 0.4.0

BREAKING CHANGES

Modified the behaviour of the assign0 argument after further discussion with Anders Alexandersson in Issue #9: now there is no default, forcing the user to decide whether to apply a hierarchy of comorbidity codes or not. This will make the algorithm more transparent to the end user, allowing an informed choice. See ?comorbidity::comorbidity and vignette("comorbidityscores", package = "comorbidity") for further details on the hierarchy being applied.

comorbidity 0.3.0

BREAKING CHANGES

comorbidity now returns two Elixhauser scores, one computed using the algorithm of van Walraven et al. (2009) and a second one computed using the AHRQ algorithm (Moore et al., 2017). Thanks to Yumiko Abe-Jones for feedback and the discussion regarding weighted Elixhauser scores.

More information can be found on the package vignette: vignette("comorbidityscores", package = "comorbidity").

comorbidity 0.2.1

  • Fixed bug in weighting algorithm of Elixhauser comorbidity score;
  • The assign0 argument of comorbidity now defaults to FALSE;
  • Improved documentation for the comorbidity function:
    • assign0 now explains in details what hierarchy of comorbidities is applied;
    • added reference to package vignette where comorbidity scores and weighting algorithms are explained in more detail.

comorbidity 0.2.0

  • comorbidity is faster, with a conservative estimated speed-up of >60%;
  • Lots of internal housekeeping;
  • Fixed broken GitHub links to the R script used to generate the datasets bundled with comorbidity.

BREAKING CHANGES

The score argument from comorbidity has been split into score and icd. For instance, the command comorbidity(x = x, id = "id", code = "code", score = "charlson_icd10") has to be modified as r comorbidity(x = x, id = "id", code = "code", score = "charlson", icd = "icd10"). The default value of icd is icd10, for ICD-10 codes, and possible values are icd10 and icd9.

comorbidity 0.1.3

  • Added nhds2010 and australia10 datasets, imported from Stata version 15.

Bug fix:

  • Fixed a bug in the regex for the ICD10 Charlson score;
  • Fixed a bug in the regex for the ICD10 Elixhauser score.

comorbidity 0.1.2

  • Added ICD10-CM data (version 2017 and 2018).

comorbidity 0.1.1

  • Documented variables that were missing among those returned by comorbidity() (@corinne-riddell, #5);
  • Added CITATION file: citation("comorbidity") now returns a properly formatted entry.

comorbidity 0.1.0

  • Added support for the ICD-9-CM version of Charlson and Elixhauser scores
  • Added vignette with information on the scores computed by comorbidity
  • sample_diag_icd10() function renamed back to sample_diag(), as now can simulate ICD-9-CM codes too

comorbidity 0.0.3

  • Added datasets icd10_2009 and icd10_2011 with ICD-10 codes, 2009 and 2011 versions (respectively)
  • sample_diag is now sample_diag_icd10 and simulates proper ICD-10 codes
  • Added Elixhauser comorbidity score
  • Renamed the package to comorbidity as it now can compute more than just the Charlson score
  • Added formal testing: codes for the Charlson score are properly identified
  • Added formal testing: codes for the Elixhauser score are properly identified

charlson 0.0.2

  • Running computations in parallel now should work on every platform
  • Improved code coverage
  • charlson is marginally faster

charlson 0.0.1

  • Rebooted charlson using only base R functions
  • Added a NEWS.md file to track changes to the package
  • Added CI with Travis and AppVeyor
  • Added automated testing with testthat
  • Added code coverage with Codecov