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 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")
.
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.comorbidity
sample_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 packagetestthat