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nbTransmission
View on CRAN: Click
here
Download and install nbTransmission package within the R console
Install from CRAN:
install.packages("nbTransmission")
Install from Github:
library("remotes")
install_github("cran/nbTransmission") Install by package version:
library("remotes")
install_version("nbTransmission", "1.2.0") Attach the package and use:
library("nbTransmission")
Maintained by
Sarah V Leavitt
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-07-13
Latest Update: 2025-05-14
Description:
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) .
How to cite:
Sarah V Leavitt (2020). nbTransmission: Naive Bayes Transmission Analysis. R package version 1.2.0, https://cran.r-project.org/web/packages/nbTransmission. Accessed 15 Jul. 2026.
Previous versions and publish date:
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Complete documentation for nbTransmission
Functions, R codes and Examples using
the nbTransmission R package
Some associated functions: clusterInfectors . estimateR . estimateRi . estimateRt . estimateRtAvg . estimateSI . indData . indToPair . nbHeatmap . nbNetwork . nbProbabilities . nbResults . pairData . performNB . performPEM . plotRt .
Some associated R codes: calcProbabilities.R . calcR.R . calcSI.R . clusterInfectors.R . indData.R . indToPair.R . nbResults.R . pairData.R . performNB.R . visualizeResults.R . Full nbTransmission package functions and examples
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