Package: nbTransmission
Title: Naive Bayes Transmission Analysis
Version: 1.2.0
Date: 2025-05-14
Authors@R: c(
	person("Sarah V", "Leavitt", email = "sv1205@bu.edu", role = c("aut", "cre")),
	person("Anne", "Shapiro", email = "anshap@bu.edu", role = "aut"))
Maintainer: Sarah V Leavitt <sv1205@bu.edu>
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)
        <doi:10.1093/ije/dyaa031>.
Depends: R (>= 3.4.0)
RoxygenNote: 7.3.2
Encoding: UTF-8
License: MIT + file LICENSE
URL: https://sarahleavitt.github.io/nbTransmission/
BugReports: https://github.com/sarahleavitt/nbTransmission/issues
LazyData: true
Imports: dplyr, rlang, caret, lubridate, poisbinom, stats, tidyr,
        utils, broom
Suggests: ggplot2, Hmisc, igraph, knitr, methods, pheatmap,
        RColorBrewer, rmarkdown, testthat
VignetteBuilder: knitr
Config/pak/sysreqs: libfftw3-dev libicu-dev
Repository: https://sarahleavitt.r-universe.dev
Date/Publication: 2025-05-14 17:20:38 UTC
RemoteUrl: https://github.com/sarahleavitt/nbtransmission
RemoteRef: HEAD
RemoteSha: fb96900dfd0ab08ff6c88cf82bef794abb606ec9
NeedsCompilation: no
Packaged: 2026-06-20 07:58:31 UTC; root
Author: Sarah V Leavitt [aut, cre],
  Anne Shapiro [aut]