Package: bayestransmission 0.1.1

Andrew Redd

bayestransmission: Bayesian Transmission Models

Provides Bayesian inference methods for infectious disease transmission models in healthcare settings. Implements Markov Chain Monte Carlo (MCMC) algorithms for estimating transmission parameters from patient-level data including admission, discharge, and testing events as described in Thomas et al. (2015) <doi:10.1093/imammb/dqt021>.

Authors:Andrew Redd [aut, cre], Alun Thomas [aut], University of Utah [cph], CDC's Center for Forecasting and Outbreak Analytics [fnd]

# Install 'bayestransmission' in R:

install.packages('bayestransmission', repos = c('https://epiforesite.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/epiforesite/bayestransmission/issues

Pkgdown/docs site:https://epiforesite.github.io

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

simulated.data - Simulated Transmission Data
simulated.data_sorted - Simulated Transmission Data

On CRAN:

openblas cpp

5.11 score 3 stars 32 scripts 1 downloads 25 exports 18 dependencies

Last updated from:b30d1e0059. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	299
linux-devel-x86_64	OK	276
source / vignettes	OK	380
linux-release-arm64	OK	271
linux-release-x86_64	OK	293
macos-release-arm64	OK	156
macos-release-x86_64	OK	432
macos-oldrel-arm64	OK	169
macos-oldrel-x86_64	OK	359
windows-devel	OK	364
windows-release	OK	367
windows-oldrel	OK	360
wasm-release	OK	281

Exports:ABXInUnitParams AbxParams AbxRateParams ClearanceParams ClinicalTestParams CodeToEvent EventToCode getCppModelParams getExposureFlags InsituParams InUnitParams LinearAbxAcquisitionParams LinearAbxModel LogNormalAcquisitionParams LogNormalModelParams mcmc_to_dataframe newCppModel newModelExport OutOfUnitInfectionParams Param ParamWRate ProgressionParams RandomTestParams runMCMC SurveillanceTestParams

Dependencies:assertthat cli dplyr generics glue lifecycle magrittr pillar pkgconfig R6 Rcpp RcppArmadillo rlang tibble tidyselect utf8 vctrs withr

Bayesian Transmission Modeling

Rendered frombayesian-transmission.Rmdusingknitr::rmarkdown

Last update: 2026-01-05
Started: 2025-02-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Antibiotic Parameters	AbxParams
Antibiotic Administration Rate Parameters	AbxRateParams
Clearance Parameters	ClearanceParams
Convert coded events to string events	CodeToEvent
Convert string events to coded events	EventToCode
Extract Model Parameters from C++ Model Object	getCppModelParams
Get compilation flags for exposed classes	getExposureFlags
InSitu Parameters	InsituParams
In Unit Parameters	ABXInUnitParams InUnitParams
Linear Antibiotic Acquisition Parameters	LinearAbxAcquisitionParams
Log-Normal Acquisition Parameters	LogNormalAcquisitionParams
Model Parameters for a Log Normal Model	LinearAbxModel LogNormalModelParams
Convert MCMC Parameters to Data Frame	mcmc_to_dataframe
Create a new C++ model object with parameters	newCppModel
Create a new model object	newModelExport
Out of Unit Infection Parameters	OutOfUnitInfectionParams
Construct a parameter with a prior, weight and an update flag.	Param
Specify a random testing parameter with a rate.	ParamWRate
Progression Parameters	ProgressionParams
Random Testing Parameter Set	ClinicalTestParams RandomTestParams
Run Bayesian Transmission MCMC	runMCMC
Simulated Transmission Data	simulated.data
Simulated Transmission Data (Sorted)	simulated.data_sorted
Surveillance Test Parameters	SurveillanceTestParams