R Observatory: Metrics for inctools version 1.0.15

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

inctools

1.0.15Package record

Incidence Estimation Tools

0packages depend

3.5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Eduard GrebeCRAN page ↗GitHub ↗Website ↗Issues ↗

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.15

READMENoVignettesYes · 4 · dynamicNEWSNoCitation fileNoWebsiteYes

Help pages: 9includes a package overview page
Examples that run: 100%7 run in a plain check
Exported functions with examples: 100%
Documented parameters: 98%
Return-value docs: 86%
Help pages citing references: 0%

Vignettes (4)

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #10,773 · ~10/day · ~290/mo

Releases R versions

Daily download trend is not available in this view yet.

39930 days

95990 days

3.5K1 year

Compare downloads with other packages →

Also on88 r2u7 autocran862 conda_forge

How downloads are counted

Repository

sacema/inctools ↗Organization: SACEMA

6Stars

4Forks

8Open issues

0Open PRs

9Releases

546Commits

10Commit identities

epidemiologyincidence-estimationincidence-inferenceincidencebiomarkershivcranbiostatistics

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

Responsiveness

How these are sampled

PRs merged (all time): 81%
Median days to close, 50 most recently updated closed issues: 7
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2022-08-01 · 52026-07-07 · 6

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/sacema/inctools on 2026-10-18.

Docs source (1)

GitHub Pages site last deployed 2025-11-13

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing inctools adds 39 packages (20 with compiled code, 27 MB of source tarballs). Heaviest: ggplot2 6.0 MB, cubature 3.2 MB, Rcpp 1.8 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (12)

Eduard Grebe

Maintainer since 1.0.3 (2016), Author

Author

Author

Author

Author

Contributor

Contributor

Contributor

Contributor · added in 1.0.11

Reshma Kassanjee

Contributor

Yuruo Li

Contributor

Cari Van Schalkwyk

Contributor · added in 1.0.5

Releases (7)

Pick two releases to compare their code metrics.

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

Show 2 earlier eventsHide 2 earlier events

1.0.3
record
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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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