vaccine

1.4.0

Statistical Tools for Immune Correlates Analysis of Vaccine Clinical Trial Data

0packages depend

5.4Kdownloads / year

55.7%test coverage

13/13checks pass

Overview

About

Maintained by Avi KennyFirst published 2023-07-088 releasesCRAN page ↗GitHub ↗

Various semiparametric and nonparametric statistical tools for immune correlates analysis of vaccine clinical trial data. This includes calculation of summary statistics and estimation of risk, vaccine efficacy, controlled effects (controlled risk and controlled vaccine efficacy), and mediation effects (natural direct effect, natural indirect effect, proportion mediated). See Gilbert P, Fong Y, Kenny A, and Carone, M (2022) doi:10.1093/biostatistics/kxac024 and Fay MP and Follmann DA (2023) doi:10.48550/arXiv.2208.06465.

Install

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

install.packages("vaccine", 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("Avi-Kenny/vaccine")

Development version from Avi-Kenny/vaccine. 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-vaccine

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-vaccine

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-vaccine

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

Health

CRAN checks

13OK

Slowest check: 11.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.06

55.7%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 130 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 85%
Documented parameters: 92%
Return-value docs: 100%
References docs: 13%

Downloads

5.4K

CRAN downloads in the past year

Rank #7,901 · ~15/day · ~453/mo

Releases R versions

Daily download trend is not available in this view yet.

21630 days

1.2K90 days

5.4K1 year

Compare downloads with other packages →

Also on114 r2u

Repository

GitHub ↗ avi-kenny/vaccine

4Stars

1Forks

4Open issues

0Open PRs

2Releases

373Commits

3Contributors

License GPL-3.0 · 373 commits · Last activity 2026-07-06 · 0% stars, 30d

Stars over time

2024-02-27 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/avi-kenny/vaccine on 2026-08-02.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (18)

dplyr fdrtool ggplot2 ggpubrmethodsrlang RsolnpsplinesstatsSuperLearnersurvivalsurvML truncnorm e1071 gam rangerutilsMASS

LinkingTo (0)

none

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 (1)

Maintainer (1)

Avi Kenny

Author, Maintainer

Authors (1)

Avi Kenny

Author, Maintainer

Package Timeline

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

1.4.0Latest
2026-07-05 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.3.1
2025-09-08 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.3.0
2025-01-07 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.2.1
2024-02-17 · diff ↗
1.2.0
2024-02-14 · diff ↗
1.1.0
2023-12-04 · diff ↗
1.0.0
2023-10-20 · diff ↗
0.1.0
2023-07-08
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-07-08
Total releases: 8 / 3 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.10
Bundled data: 21 KB / 1 file
Download size: 583 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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