R Observatory: Metrics for nbTransmission version 1.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

nbTransmission

1.2.0

Naive Bayes Transmission Analysis

0packages depend

6.6Kdownloads / year

92.0%test coverage

13/13checks pass

Overview

About

Maintained by Sarah V LeavittFirst published 2020-07-135 releasesCRAN page ↗GitHub ↗

Estimates the relative transmission probabilities between cases in an infectious disease outbreak or cluster using naive Bayes. Included are various functions to use these probabilities to estimate transmission parameters such as the generation/serial interval and reproductive number as well as finding the contribution of covariates to the probabilities and visualizing results. The ideal use is for an infectious disease dataset with metadata on the majority of cases but more informative data such as contact tracing or pathogen whole genome sequencing on only a subset of cases. For a detailed description of the methods see Leavitt et al. (2020) doi:10.1093/ije/dyaa031.

Install

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

install.packages("nbTransmission", 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("sarahleavitt/nbTransmission")

Development version from sarahleavitt/nbTransmission. 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-nbtransmission

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-nbTransmission

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-nbTransmission

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

Health

CRAN checks

13OK

Slowest check: 3.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.25

92.0%

Coverage · measured lines

100%

Documentation · exports

9

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 439 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 82%
Documented parameters: 100%
Return-value docs: 77%
References docs: 38%

Downloads

6.6K

CRAN downloads in the past year

Rank #6,414 · ~18/day · ~546/mo

Releases R versions

Daily download trend is not available in this view yet.

20730 days

1.3K90 days

6.6K1 year

Compare downloads with other packages →

Also on119 r2u15 autocran25 c2d4u

Repository

GitHub ↗ sarahleavitt/nbtransmission

4Stars

1Forks

0Open issues

0Open PRs

6Releases

199Commits

2Contributors

199 commits · Last activity 2025-05-14

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/sarahleavitt/nbtransmission on 2026-08-16.

Continuous integration (1)

Travis CI

CRAN release process (1)

CRAN-SUBMISSION

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.4.0

Imports (9)

dplyr rlang caret lubridate poisbinomstatstidyrutilsbroom

LinkingTo (0)

none

Suggests (9)

ggplot2 Hmisc igraph knitrmethodspheatmap RColorBrewer rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Sarah V Leavitt

Author, Maintainer

Authors (2)

Sarah V Leavitt

Author, Maintainer

Anne Shapiro

Author · added in 1.2.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.2.0Latest
2025-05-14 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.1.4
2024-01-30 · diff ↗
1.1.3
2024-01-10 · diff ↗
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
1.1.2
2021-01-06 · diff ↗
1.1.1
2020-07-13
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-07-13
Total releases: 5 / 6 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.4.0
Bundled data: 256 KB / 3 files
Download size: 446 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("nbTransmission")

Format

Leavitt, S. V., & Shapiro, A. (2025). nbTransmission: Naive Bayes Transmission Analysis (Version 1.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.nbTransmission

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 nbTransmission version 1.2.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →