Package: nbTransmission 1.1.4

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, cph]

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nbTransmission.pdf |nbTransmission.html✨
nbTransmission/json (API)

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

Peer review:

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

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

On CRAN:

13 exports 4 stars 1.19 score 76 dependencies 14 scripts 279 downloads

Last updated 8 months agofrom:5469d371b4. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 27 2024
R-4.5-winOKAug 27 2024
R-4.5-linuxOKAug 27 2024
R-4.4-winOKAug 27 2024
R-4.4-macOKAug 27 2024
R-4.3-winOKAug 27 2024
R-4.3-macOKAug 27 2024

Exports:clusterInfectorsestimateRestimateRiestimateRtestimateRtAvgestimateSIindToPairnbHeatmapnbNetworknbProbabilitiesperformNBperformPEMplotRt

Dependencies:caretclasscliclockcodetoolscolorspacecpp11data.tablediagramdigestdplyre1071fansifarverforeachfuturefuture.applygenericsggplot2globalsgluegowergtablehardhatipredisobanditeratorsKernSmoothlabelinglatticelavalifecyclelistenvlubridatemagrittrMASSMatrixmgcvModelMetricsmunsellnlmennetnumDerivparallellypillarpkgconfigplyrpoisbinompROCprodlimprogressrproxypurrrR6RColorBrewerRcpprecipesreshape2rlangrpartscalesshapeSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithr

Introductory tutorial for R Package nbTransmission

Sarah V. Leavitt

Rendered fromnbTransmission-vignette.Rmdusingknitr::rmarkdownon Aug 27 2024.

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