Package: nbTransmission 1.1.4

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, cph]

nbTransmission_1.1.4.tar.gz
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nbTransmission.pdf |nbTransmission.html✨
nbTransmission/json (API)

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

4.75 score 4 stars 14 scripts 251 downloads 13 exports 76 dependencies

Last updated 10 months agofrom:5469d371b4. Checks:OK: 7. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 09 2024
R-4.5-winOKNov 09 2024
R-4.5-linuxOKNov 09 2024
R-4.4-winOKNov 09 2024
R-4.4-macOKNov 09 2024
R-4.3-winOKNov 09 2024
R-4.3-macOKNov 09 2024

Exports:clusterInfectorsestimateRestimateRiestimateRtestimateRtAvgestimateSIindToPairnbHeatmapnbNetworknbProbabilitiesperformNBperformPEMplotRt

Dependencies:caretclasscliclockcodetoolscolorspacecpp11data.tablediagramdigestdplyre1071fansifarverforeachfuturefuture.applygenericsggplot2globalsgluegowergtablehardhatipredisobanditeratorsKernSmoothlabelinglatticelavalifecyclelistenvlubridatemagrittrMASSMatrixmgcvModelMetricsmunsellnlmennetnumDerivparallellypillarpkgconfigplyrpoisbinompROCprodlimprogressrproxypurrrR6RColorBrewerRcpprecipesreshape2rlangrpartscalesshapeSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithr

Introductory tutorial for R Package nbTransmission

Sarah V. Leavitt

Rendered fromnbTransmission-vignette.Rmdusingknitr::rmarkdownon Nov 09 2024.

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