Package: nbTransmission 1.2.0

Sarah V Leavitt

nbTransmission: Naive Bayes Transmission Analysis

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>.

Authors:Sarah V Leavitt [aut, cre], Anne Shapiro [aut]

nbTransmission_1.2.0.tar.gz
nbTransmission_1.2.0.tar.gz(r-4.7-any)nbTransmission_1.2.0.tar.gz(r-4.6-any)
nbTransmission_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
nbTransmission/json (API)

# Install 'nbTransmission' in R:
install.packages('nbTransmission', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sarahleavitt/nbtransmission/issues

Pkgdown/docs site:https://sarahleavitt.github.io

Datasets:
  • indData - Individual-level simulated outbreak dataset
  • nbResults - Dataset with results of 'nbProbabilities'
  • pairData - Pair-level simulated outbreak dataset

On CRAN:

Conda:

3.26 score 18 scripts 602 downloads 13 exports 76 dependencies

Last updated from:fb16333b02. Checks:4 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK168
source / vignettesOK225
linux-release-x86_64OK152
wasm-releaseOK143

Exports:clusterInfectorsestimateRestimateRiestimateRtestimateRtAvgestimateSIindToPairnbHeatmapnbNetworknbProbabilitiesperformNBperformPEMplotRt

Dependencies:backportsbroomcaretclasscliclockcodetoolscpp11data.tablediagramdigestdplyre1071farverforeachfuturefuture.applygenericsggplot2globalsgluegowergtablehardhatipredisobanditeratorsKernSmoothlabelinglatticelavalifecyclelistenvlubridatemagrittrMASSMatrixModelMetricsnlmennetnumDerivparallellypillarpkgconfigplyrpoisbinompROCprodlimprogressrproxypurrrR6RColorBrewerRcpprecipesreshape2rlangrpartS7scalesshapesparsevctrsSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithr

Adjusted Odds Ratio Example

Anne N. Shapiro

Rendered fromadjusted-odds-ratio-example-vignette.Rmdusingknitr::rmarkdownon May 10 2026.

Last update: 2025-05-14
Started: 2025-05-14

Introductory tutorial for R Package nbTransmission

Sarah V. Leavitt

Rendered fromnbTransmission-vignette.Rmdusingknitr::rmarkdownon May 10 2026.

Last update: 2020-07-13
Started: 2020-07-13