-
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.
- Fixed bug in regex patterns (#10, thanks to @francisco003 for reporting it and @salmasian for the pull request).
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 val 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")
.
- Fixed bug in weighting algorithm of Elixhauser comorbidity score;
- The
assign0
argument ofcomorbidity
now defaults toFALSE
; - 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
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
.
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
.
- Added
nhds2010
andaustralia10
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.
- Added ICD10-CM data (version 2017 and 2018).
- Documented variables that were missing among those returned by
comorbidity()
(@corinne-riddell, #5); - Added CITATION file:
citation("comorbidity")
now returns a properly formatted entry.
- 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 tosample_diag()
, as now can simulate ICD-9-CM codes too
- Added datasets
icd10_2009
andicd10_2011
with ICD-10 codes, 2009 and 2011 versions (respectively) sample_diag
is nowsample_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
- Running computations in parallel now should work on every platform
- Improved code coverage
charlson
is marginally faster
- 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