Overview | Part 1: Study Setup | 1.1 Study Timeline | 1.2 Surveillance Data (Community Forcing) | 1.3 Contact Matrix (Role Mixing Weights) | 1.4 Household Composition | 1.5 Intervention Strategies (Covariates) | Part 2: Simulation | 2.1 Run the Simulator | 2.2 Inspect the Output | 2.3 Summarize Attack Rates | 2.4 Plot the Epidemic Curve | Part 3: Preparing Data for Stan | 3.1 Join Covariates to Diagnostic Data | 3.2 Define Priors | 3.3 Viral Load Imputation Parameters | 3.4 Build the Stan Input | Part 4: Fitting the Bayesian Model | 4.1 Run HMC Sampling | 4.2 View Summary | 4.3 Convergence Diagnostics | Part 5: Visualization | 5.1 Posterior Distributions | 5.2 Covariate Effects (Forest Plot) | 5.3 Transmission Chain Reconstruction | 5.4 Household Timeline | Appendix A: Complete Script | Session Info
Package: HHBayes 0.0.0.9000
Ke Li
HHBayes: Bayesian Household Transmission Modeling
Provides a streamlined pipeline to simulate household infection dynamics, estimate transmission parameters, and visualize epidemic timelines. Uses a Bayesian approach with Stan that models transmission probability as a Function of viral load, seasonality and infectivity, multiple infection episodes (reinfections), and waning immunity modeling.
Authors:
HHBayes_0.0.0.9000.tar.gz
HHBayes_0.0.0.9000.zip(r-4.7-x86_64)HHBayes_0.0.0.9000.zip(r-4.7-arm64)HHBayes_0.0.0.9000.zip(r-4.6-x86_64)HHBayes_0.0.0.9000.zip(r-4.6-arm64)HHBayes_0.0.0.9000.zip(r-4.5-x86_64)
HHBayes_0.0.0.9000.tgz(r-4.6-arm64)HHBayes_0.0.0.9000.tgz(r-4.6-x86_64)HHBayes_0.0.0.9000.tgz(r-4.5-x86_64)HHBayes_0.0.0.9000.tgz(r-4.5-arm64)
HHBayes_0.0.0.9000.tar.gz(r-4.7-arm64)HHBayes_0.0.0.9000.tar.gz(r-4.7-x86_64)HHBayes_0.0.0.9000.tar.gz(r-4.6-arm64)HHBayes_0.0.0.9000.tar.gz(r-4.6-x86_64)
HHBayes_0.0.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
HHBayes/json (API)
| # Install 'HHBayes' in R: |
| install.packages('HHBayes', repos = c('https://keli5734.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/keli5734/hhbayes/issues
Last updated from:3a26683b82. Checks:15 OK. Indexed: yes.
The latest version of this package failed to build. Look at thebuild logs for more information.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 249 | ||
| linux-devel-x86_64 | OK | 312 | ||
| source / vignettes | OK | 374 | ||
| linux-release-arm64 | OK | 269 | ||
| linux-release-x86_64 | OK | 288 | ||
| macos-release-arm64 | OK | 284 | ||
| macos-release-x86_64 | OK | 587 | ||
| macos-oldrel-arm64 | OK | 300 | ||
| macos-oldrel-x86_64 | OK | 694 | ||
| windows-devel-arm64 | OK | 426 | ||
| windows-devel-x86_64 | OK | 334 | ||
| windows-release-arm64 | OK | 469 | ||
| windows-release-x86_64 | OK | 297 | ||
| windows-oldrel-x86_64 | OK | 267 | ||
| wasm-release | OK | 182 |
Exports:calculate_sar_quickcalculate_sar_robustfill_missing_viral_datafit_household_modelplot_covariate_effectsplot_epidemic_curveplot_household_timelineplot_posterior_distributionsprepare_stan_datareconstruct_transmission_chainssimulate_multiple_households_commsummarize_attack_rates
Dependencies:abindbackportsBHbootbroomcallrcarcarDatacheckmateclicolorspacecorrplotcowplotcpp11DerivdescdeSolvedistributionaldoBydplyrfarverforecastFormulafracdiffgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtableinlineisobandlabelinglatticelifecyclelme4lmtestloomagrittrMASSMatrixMatrixModelsmatrixStatsmgcvminqamodelrnlmenloptrnnetnumDerivotelpbkrtestpillarpkgbuildpkgconfigpolynomposteriorprocessxpspurrrquantregQuickJSRR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRdpackreformulasrlangrstanrstantoolsrstatixS7scalesSparseMStanHeadersstringistringrsurvivaltensorAtibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Quick SAR Calculator (Convenience Wrapper) | calculate_sar_quick |
| Calculate Secondary Attack Rate (Robust) | calculate_sar_robust |
| Fill Missing Viral Data (Ct or Log10) based on Episode Start | fill_missing_viral_data |
| Fit Household Transmission Model | fit_household_model |
| Generate Household Contact Matrix from Role Rules | generate_contact_matrix_from_roles |
| ODE System for Within-Host Dynamics | ode_system_func |
| Plot Covariate Coefficients (Forest Plot) | plot_covariate_effects |
| Plot Dual-Axis Epidemic Curve (Binned) | plot_epidemic_curve |
| Plot Household Timeline with Person-Centric Reinfections | plot_household_timeline |
| Plot Posterior Distributions (Phi and Kappa) | plot_posterior_distributions |
| Prepare Data for Stan Model | prepare_stan_data |
| Reconstruct Transmission Chains | reconstruct_transmission_chains |
| Simulate Household Transmission | simulate_multiple_households_comm |
| Summarize Attack Rates & Reinfections | summarize_attack_rates |