R Observatory: Metrics for inctools version 1.0.15

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

inctools

1.0.15

Incidence Estimation Tools

0packages depend

3.2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Eduard GrebeFirst published 2016-05-187 releasesCRAN page ↗GitHub ↗

Tools for estimating incidence from biomarker data in cross- sectional surveys, and for calibrating tests for recent infection. Implements and extends the method of Kassanjee et al. (2012) doi:10.1097/EDE.0b013e3182576c07.

Install

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

install.packages("inctools", 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("SACEMA/inctools")

Development version from SACEMA/inctools. 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-inctools

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-inctools

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-inctools

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

Health

CRAN checks

13OK

Slowest check: 3.1 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

16

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 86%
References docs: 0%

Downloads

3.2K

CRAN downloads in the past year

Rank #14,546 · ~9/day · ~267/mo

Releases R versions

Daily download trend is not available in this view yet.

20730 days

71390 days

3.2K1 year

Compare downloads with other packages →

Also on119 r2u14 autocran996 conda_forge

Repository

GitHub ↗ sacema/inctools

6Stars

4Forks

8Open issues

0Open PRs

9Releases

546Commits

10Contributors

epidemiologyincidence-estimationincidence-inferenceincidencebiomarkershivcranbiostatistics

License GPL-3.0 · 546 commits · Last activity 2025-11-27 · 0% stars, 30d

Stars over time

2022-08-01 · 52026-07-07 · 6

Repository practices

Upstream repositoryBeta

Checks run against github.com/sacema/inctools on 2026-08-09.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.4.0

Imports (16)

statsutilsmagrittr rlang dplyr tibble cubature tmvtnorm ggplot2 glm2 plyr pracma foreachparalleldoParallel binom

LinkingTo (0)

none

Suggests (3)

survey knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (12)

Maintainer (1)

Eduard Grebe

Maintainer, Author

Authors (5)

Maintainer, Author

Author

Author

Author

Author

Contributors (7)

Contributor

Contributor

Contributor

Contributor · added in 1.0.11

Reshma Kassanjee

Contributor

Yuruo Li

Contributor

Cari Van Schalkwyk

Contributor · added in 1.0.5

Package Timeline

7 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
1.0.15Latest
2019-11-07 · current release · diff ↗
R
R 3.6.0 released · 2019-04-26
1.0.14
2018-09-22 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.11
2018-01-03 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.0.10
2017-04-13 · diff ↗
1.0.7
2016-09-13 · diff ↗
1.0.5
2016-05-26 · diff ↗

Show 2 earlier events

1.0.3
2016-05-18
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-05-18
Total releases: 7 / 10 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.4.0
Bundled data: 25 KB / 1 file
Download size: 202 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("inctools")

Format

Grebe, E., Asai, Y., Brand, H., Bäumler, P., Daniel, S., Eaton, J., Kassanjee, R., Li, Y., McIntosh, A., Ongarello, S., Van Schalkwyk, C., & Welte, A. (2019). inctools: Incidence Estimation Tools (Version 1.0.15) [Computer software]. https://doi.org/10.32614/CRAN.package.inctools

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for inctools version 1.0.15 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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