R Observatory: Metrics for mitey version 0.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

mitey

0.2.0Package record

Serial Interval and Case Reproduction Number Estimation

0packages depend

2.4Kdownloads / year

77.7%test coverage

13/13flavors OK

Overview

About

Maintained by Kylie AinslieCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides methods to estimate serial intervals and time-varying case reproduction numbers from infectious disease outbreak data. Serial intervals measure the time between symptom onset in linked transmission pairs, while case reproduction numbers quantify how many secondary cases each infected individual generates over time. These parameters are essential for understanding transmission dynamics, evaluating control measures, and informing public health responses. The package implements the maximum likelihood framework from Vink et al. (2014) doi:10.1093/aje/kwu209 for serial interval estimation and the retrospective method from Wallinga & Lipsitch (2007) doi:10.1098/rspb.2006.3754 for reproduction number estimation. Originally developed for scabies transmission analysis but applicable to other infectious diseases including influenza, COVID-19, and emerging pathogens. Designed for epidemiologists, public health researchers, and infectious disease modelers working with outbreak surveillance data.

Install

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

install.packages("mitey", 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("kylieainslie/mitey")

Development version from kylieainslie/mitey. 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-mitey

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-mitey

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-mitey

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: 5.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
WARNING11 OK, 1 NOTE, 2 WARNING2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.0

READMEYes · 1,216 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.2.0Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 22 (1 internal)includes a package overview page
Examples that run: 100%17 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 36%

Vignettes (1)

Quick Start Guide: Estimating Epidemiological Parameters with `mitey`

How these are measured

Downloads

2.4K

CRAN downloads in the past year

Rank #17,170 · ~7/day · ~198/mo

Releases R versions

Daily download trend is not available in this view yet.

28230 days

74690 days

2.4K1 year

Compare downloads with other packages →

Also on69 r2u3 autocran

How downloads are counted

Repository

kylieainslie/mitey ↗Account: kylieainslie

7Stars

0Forks

9Open issues

0Open PRs

5Releases

506Commits

2Commit identities

506 commits · Last activity 2026-06-04 · 0% stars, 30d · Default branch at 0.4.0, ahead of CRAN 0.2.0 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 80%
Median days to close, 50 most recently updated closed issues: 84
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-02 · 62026-07-07 · 7

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/kylieainslie/mitey on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-06-04 · The repository has a site deploy workflow

pkgdown site last built 2026-06-04

Coverage (1)

Coverage reporting

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen on or before 2026-01-07
Named in .Rbuildignore: .claude
Pull request it wrote: opened by a project member
Commits: at least 17 crediting it in the message

Models named in its commits

Claude Opus 4.511 commits · Jan 2026
Claude Sonnet 4.66 commits · Feb to Jun 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

Installing mitey adds 18 packages (8 with compiled code, 14 MB of source tarballs). Heaviest: ggplot2 6.0 MB, isoband 1.5 MB, farver 1.2 MB.

Depends (1)

R >= 3.5.0

Imports (3)

fdrtool ggplot2stats

LinkingTo (0)

none

Suggests (25)

brms broom cowplot dplyr EpiLPS flextable forcats ftExtra ggridges gt here ISOweek knitr lubridate officer openxlsx outbreaks purrr rmarkdown stringr testthat tidybayes tidyr viridis zoo

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 (1)

Kylie Ainslie

Releases (1)

R
R 4.6.0 released · 2026-04-24
0.2.0Latest
record
2025-09-02 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-09-02
Total releases: 1 / 1 yrs
License: EUPL-1.2
Minimum R: ≥ 3.5.0
Download size: 4.6 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("mitey")

Format

Ainslie, K. (2025). mitey: Serial Interval and Case Reproduction Number Estimation (Version 0.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.mitey

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 mitey version 0.2.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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