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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).
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.).
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).
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.
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 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 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).
data.table that only occurred when the input dataset had
extra columns other than id and code.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 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.
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 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").
assign0 argument of comorbidity now
defaults to FALSE;comorbidity function:
assign0 now explains in details what hierarchy of
comorbidities is applied;comorbidity is faster, with a conservative estimated
speed-up of >60%;comorbidity.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.
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() (@corinne-riddell, #5);citation("comorbidity") now
returns a properly formatted entry.comorbiditysample_diag_icd10() function renamed back to
sample_diag(), as now can simulate ICD-9-CM codes tooicd10_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 codescomorbidity as it now can
compute more than just the Charlson scorecharlson is marginally fastercharlson using only base R functionsNEWS.md file to track changes to the
packagetestthatThese binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.