Introduction | Data Structure | Model Specification | Model Choice | Parameters | Specifying parameters | Abx Antibiotic use | AbxRate Antibiotic rates | InUnit In unit infection rate | Acquisition Model | Progression Model | Clearance Model | Out of Unit Importation | In Situ | Testing | Surveillance Testing | Clinical Testing | All Together | Running the Model | Analyzing MCMC Results | Converting Parameters to Data Frame | Trace Plots | Posterior Distributions | Summary Statistics
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:
bayestransmission_0.1.1.tar.gz
bayestransmission_0.1.1.zip(r-4.7-x86_64)bayestransmission_0.1.1.zip(r-4.7-arm64)bayestransmission_0.1.1.zip(r-4.6-x86_64)bayestransmission_0.1.1.zip(r-4.6-arm64)bayestransmission_0.1.1.zip(r-4.5-x86_64)
bayestransmission_0.1.1.tgz(r-4.6-x86_64)bayestransmission_0.1.1.tgz(r-4.6-arm64)bayestransmission_0.1.1.tgz(r-4.5-x86_64)bayestransmission_0.1.1.tgz(r-4.5-arm64)
bayestransmission_0.1.1.tar.gz(r-4.7-arm64)bayestransmission_0.1.1.tar.gz(r-4.7-x86_64)bayestransmission_0.1.1.tar.gz(r-4.6-arm64)bayestransmission_0.1.1.tar.gz(r-4.6-x86_64)
bayestransmission_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bayestransmission/json (API)
| # 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
Datasets:
- simulated.data - Simulated Transmission Data
- simulated.data_sorted - Simulated Transmission Data
Last updated from:b30d1e0059. Checks:15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 232 | ||
| linux-devel-x86_64 | OK | 234 | ||
| source / vignettes | OK | 412 | ||
| linux-release-arm64 | OK | 249 | ||
| linux-release-x86_64 | OK | 330 | ||
| macos-release-arm64 | OK | 205 | ||
| macos-release-x86_64 | OK | 430 | ||
| macos-oldrel-arm64 | OK | 223 | ||
| macos-oldrel-x86_64 | OK | 708 | ||
| windows-devel-arm64 | OK | 569 | ||
| windows-devel-x86_64 | OK | 317 | ||
| windows-release-arm64 | OK | 546 | ||
| windows-release-x86_64 | OK | 328 | ||
| windows-oldrel-x86_64 | OK | 327 | ||
| wasm-release | OK | 188 |
Exports:ABXInUnitParamsAbxParamsAbxRateParamsClearanceParamsClinicalTestParamsCodeToEventEventToCodegetCppModelParamsgetExposureFlagsInsituParamsInUnitParamsLinearAbxAcquisitionParamsLinearAbxModelLogNormalAcquisitionParamsLogNormalModelParamsmcmc_to_dataframenewCppModelnewModelExportOutOfUnitInfectionParamsParamParamWRateProgressionParamsRandomTestParamsrunMCMCSurveillanceTestParams
Dependencies:assertthatclidplyrgenericsgluelifecyclemagrittrpillarpkgconfigR6RcppRcppArmadillorlangtibbletidyselectutf8vctrswithr
