comorbidity

1.1.0

Computing Comorbidity Scores

2packages depend

21.3Kdownloads / year

95.1%test coverage

13/13checks pass

Overview

About

Maintained by Alessandro GaspariniFirst published 2018-01-0816 releasesCRAN page ↗GitHub ↗

Computing comorbidity indices and scores such as the weighted Charlson score (Charlson, 1987 doi:10.1016/0021-9681(87)90171-8) and the Elixhauser comorbidity score (Elixhauser, 1998 doi:10.1097/00005650-199801000-00004) using ICD-9-CM or ICD-10 codes (Quan, 2005 doi:10.1097/01.mlr.0000182534.19832.83). Australian and Swedish modifications of the Charlson Comorbidity Index are available as well (Sundararajan, 2004 doi:10.1016/j.jclinepi.2004.03.012 and Ludvigsson, 2021 doi:10.2147/CLEP.S282475), together with different weighting algorithms for both the Charlson and Elixhauser comorbidity scores.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("comorbidity", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ellessenne/comorbidity")

Development version from ellessenne/comorbidity. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-comorbidity

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-comorbidity

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-comorbidity

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 4.6 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 1.49

95.1%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 380 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 75%
References docs: 15%

Downloads

21.3K

CRAN downloads in the past year

Rank #3,312 · ~58/day · ~1.8K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.1K30 days

3.6K90 days

21.3K1 year

Compare downloads with other packages →

Also on210 r2u37 autocran943 conda_forge

Repository

GitHub ↗ ellessenne/comorbidity

92Stars

23Forks

10Open issues

4Open PRs

4Releases

418Commits

9Contributors

comorbidityrrstats

License GPL-3.0 · 418 commits · Last activity 2024-07-16 · +1.1% stars, 30d

Stars over time

2025-07-11 · 832026-07-07 · 92

Repository practices

Upstream repositoryBeta

7 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/ellessenne/comorbidity on 2026-07-30.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (2)

data-raw/Makefile

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (5)

checkmate data.tablestatsstringiutils

LinkingTo (0)

none

Suggests (4)

covr knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

TreeMineR ciecl

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

Alessandro Gasparini

Author, Maintainer

Authors (1)

Alessandro Gasparini

Author, Maintainer

Contributors (5)

Sing Yi Chia

Contributor · added in 1.0.0

Desi Quintans

Contributor · added in 1.1.0

Hojjat Salmasian

Contributor · added in 0.1.0

Edmund Teo

Contributor · added in 1.0.0

Jonathan Williman

Contributor · added in 0.5.0

Package Timeline

16 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.1.0Latest
2024-07-16 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.7
2023-05-01 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.5
2022-09-26 · diff ↗
1.0.3
2022-07-12 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.2
2022-04-06 · diff ↗
1.0.0
2022-01-17 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.5.3
2020-01-09 · diff ↗
0.5.2
2019-10-20 · diff ↗
0.5.1
2019-10-16 · diff ↗

Show 10 earlier events

0.5.0
2019-08-20 · diff ↗
0.4.1
2019-06-27 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.3.0
2019-03-22 · diff ↗
0.2.0
2018-10-08 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.1.1
2018-03-30 · diff ↗
0.1.0
2018-03-07 · diff ↗
0.0.3
2018-01-08
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-01-08
Total releases: 16 / 8 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 1.9 MB / 8 files
Download size: 1.9 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →