Package: nbTransmission 1.2.0

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

# Install 'nbTransmission' in R:
install.packages('nbTransmission', repos = c('https://sarahleavitt.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:

4.88 score 4 stars 19 scripts 645 downloads 13 exports 76 dependencies

Last updated from:fb96900dfd. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK168
source / vignettesOK240
linux-release-x86_64OK167
macos-release-arm64OK134
macos-oldrel-arm64OK153
windows-develOK144
windows-releaseOK108
windows-oldrelOK142
wasm-releaseOK128

Exports:clusterInfectorsestimateRestimateRiestimateRtestimateRtAvgestimateSIindToPairnbHeatmapnbNetworknbProbabilitiesperformNBperformPEMplotRt

Dependencies:backportsbroomcaretclasscliclockcodetoolscpp11data.tablediagramdigestdplyre1071farverforeachfuturefuture.applygenericsggplot2globalsgluegowergtablehardhatipredisobanditeratorsKernSmoothlabelinglatticelavalifecyclelistenvlubridatemagrittrMASSMatrixModelMetricsnlmennetnumDerivparallellypillarpkgconfigplyrpoisbinompROCprodlimprogressrproxypurrrR6RColorBrewerRcpprecipesreshape2rlangrpartS7scalesshapesparsevctrsSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithr

Adjusted Odds Ratio Example
Introduction | Using nbTransmission for modeling | Creating a Dataset of Pairs | Running the unadjusted model | Unadjusted model results | Table of contribution of covariates | Forest plot of contribution of covariates | Identifying significant variables for the adjusted model | Running the adjusted model | Conclusion
Rendered fromadjusted-odds-ratio-example-vignette.Rmdusingknitr::rmarkdown

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

Introductory tutorial for R Package nbTransmission
Introduction | Creating a Dataset of Pairs | Estimating Relative Transmission Probabilties | Covariates Associated with Probable Transmission | Table of contribution of covariates | Forest plot of contribution of covariates | Finding the Most Likely Infectors | Clustering Illustration | Visualizing Results | Network with all pairs | Network with only top probability pairs | Heatmap with stars on top cluster | Estimating the Reproductive Number | Estimating the Serial Interval | Conclusion
Rendered fromnbTransmission-vignette.Rmdusingknitr::rmarkdown

Last update: 2020-07-06
Started: 2019-11-19