denvax

0.1.2

Simple Dengue Test and Vaccinate Cost Thresholds

0packages depend

2.9Kdownloads / year

15.6%test coverage

11/13checks pass

Overview

About

Maintained by Carl A. B. PearsonFirst published 2019-07-193 releasesCRAN page ↗GitLab ↗

Provides the mathematical model described by "Serostatus Testing & Dengue Vaccine Cost-Benefit Thresholds" in doi:10.1098/rsif.2019.0234. Using the functions in the package, that analysis can be repeated using sample life histories, either synthesized from local seroprevalence data using other functions in this package (as in the manuscript) or from some other source. The package provides a vignette which walks through the analysis in the publication, as well as a function to generate a project skeleton for such an analysis.

Install

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

install.packages("denvax", 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("cabp_LSHTM/denvax")

Development version from cabp_LSHTM/denvax. 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-denvax

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-denvax

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-denvax

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

Health

CRAN checks

2NOTE11OK

Failing flavors

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

Slowest check: 1.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.09

15.6%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 0%
Return-value docs: 100%
References docs: 0%

Downloads

2.9K

CRAN downloads in the past year

Rank #17,399 · ~8/day · ~241/mo

Releases R versions

Daily download trend is not available in this view yet.

20830 days

62590 days

2.9K1 year

Compare downloads with other packages →

Also on88 r2u2 autocran

Repository

GitLab ↗ cabp_lshtm/denvax

Repository practices

Upstream repositoryBeta

Repository gitlab.com/cabp_lshtm/denvax is linked, but repository-practices checks have not run for it yet. Checks are GitHub-only for now.

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (0)

none

LinkingTo (0)

none

Suggests (11)

data.table testthat usethis devtools roxygen2 jsonlite ggplot2 cowplot directlabels rmarkdown knitr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Carl A. B. Pearson

Author, Maintainer

Authors (5)

Carl A. B. Pearson

Author, Maintainer

Kaja M. Abbas

Author · added in 0.1.1

Samuel Clifford

Author · added in 0.1.1

Stefan Flasche

Author · added in 0.1.1

Thomas J. Hladish

Author · added in 0.1.1

Package Timeline

3 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
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.1.2Latest
2019-12-01 · current release · diff ↗
0.1.1
2019-08-21 · diff ↗
0.1.0
2019-07-19
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-07-19
Total releases: 3 / 7 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5
Bundled data: 0.8 KB / 2 files
Download size: 31 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →