cfr

0.2.0

Estimate Disease Severity and Case Ascertainment

0packages depend

3.7Kdownloads / year

100.0%test coverage

13/13checks pass

Overview

About

Maintained by Adam KucharskiFirst published 2023-11-214 releasesCRAN page ↗GitHub ↗

Estimate the severity of a disease and ascertainment of cases, as discussed in Nishiura et al. (2009) doi:10.1371/journal.pone.0006852.

Install

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

install.packages("cfr", 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("epiverse-trace/cfr")

Development version from epiverse-trace/cfr. 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-cfr

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

# 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-cfr

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

Health

CRAN checks

13OK

Slowest check: 3.2 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 1.14

100.0%

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 · 844 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 33%

Downloads

3.7K

CRAN downloads in the past year

Rank #11,431 · ~10/day · ~308/mo

Releases R versions

Daily download trend is not available in this view yet.

31030 days

91290 days

3.7K1 year

Compare downloads with other packages →

Also on144 r2u34 autocran

Repository

GitHub ↗ epiverse-trace/cfr

15Stars

5Forks

13Open issues

8Open PRs

4Releases

560Commits

8Contributors

rr-packagecase-fatality-rateepidemiologyhealth-outcomesepidemic-modellingoutbreak-analysisepiverse

560 commits · Last activity 2026-01-01

Repository practices

Upstream repositoryBeta

11 development-tooling and community-health practices detected across 8 families in the upstream repository

Checks run against github.com/epiverse-trace/cfr on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Research and citation (1)

CITATION.cff

Lint, format, editor (2)

lintrRStudio project

Coverage (1)

Codecov

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (2)

checkmatestats

LinkingTo (0)

none

Suggests (16)

bookdown data.table distcrete distributional dplyr forcats ggplot2 incidence2 knitr magrittr purrr rmarkdown scales spelling testthat tidyr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (9)

Maintainer (1)

Adam Kucharski

Author, Copyright holder, Maintainer

Authors (3)

Adam Kucharski

Author, Copyright holder, Maintainer

Pratik R. Gupte

Author, Copyright holder

Tim Russell

Author, Copyright holder

Adam Kucharski

Author, Copyright holder, Maintainer

Pratik R. Gupte

Author, Copyright holder

Tim Russell

Author, Copyright holder

Reviewers (6)

James M. Azam

Reviewer

Abdoelnaser M. Degoot

Reviewer

Reviewer

Reviewer

Reviewer

Reviewer

Package Timeline

4 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
0.2.0Latest
2025-02-21 · current release · diff ↗
0.1.2
2024-09-26 · diff ↗
0.1.1
2024-06-12 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.1.0
2023-11-21
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-11-21
Total releases: 4 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 73 KB / 2 files
Download size: 872 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Epidemiology

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