linelistBayes

1.0

Bayesian Analysis of Epidemic Data Using Line List and Case Count Approaches

0packages depend

6.9Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Chad MilandoFirst published 2024-05-031 releasesCRAN page ↗

Provides tools for performing Bayesian inference on epidemiological data to estimate the time-varying reproductive number and other related metrics. These methods were published in Li and White (2021) doi:10.1371/journal.pcbi.1009210. This package supports analyses based on aggregated case count data and individual line list data, facilitating enhanced surveillance and intervention planning for infectious diseases like COVID-19.

Install

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

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

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

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-linelistbayes

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-linelistBayes

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-linelistBayes

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

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 4.6 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 25 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 84%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 5%

Downloads

6.9K

CRAN downloads in the past year

Rank #6,016 · ~19/day · ~572/mo

Releases R versions

Daily download trend is not available in this view yet.

24630 days

1.5K90 days

6.9K1 year

Compare downloads with other packages →

Also on398 r2u7 autocran

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (5)

Rcpp magrittr lubridate coda dplyr

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Chad Milando

Author, Maintainer

Authors (1)

Chad Milando

Author, Maintainer

Contributors (2)

Tenglong Li

Contributor

Laura White

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2024-05-03
Total releases: 1 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.10
Bundled data: 7.3 KB / 6 files
Download size: 167 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Epidemiology

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