Package: SimBIID 0.2.1
Trevelyan J. McKinley
SimBIID: Simulation-Based Inference Methods for Infectious Disease Models
Provides some code to run simulations of state-space models, and then use these in the Approximate Bayesian Computation Sequential Monte Carlo (ABC-SMC) algorithm of Toni et al. (2009) <doi:10.1098/rsif.2008.0172> and a bootstrap particle filter based particle Markov chain Monte Carlo (PMCMC) algorithm (Andrieu et al., 2010 <doi:10.1111/j.1467-9868.2009.00736.x>). Also provides functions to plot and summarise the outputs.
Authors:
SimBIID_0.2.1.tar.gz
SimBIID_0.2.1.tar.gz(r-4.5-noble)SimBIID_0.2.1.tar.gz(r-4.4-noble)
SimBIID.pdf |SimBIID.html✨
SimBIID/json (API)
NEWS
| # Install 'SimBIID' in R: |
| install.packages('SimBIID', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tjmckinley/simbiid/issues
Last updated 4 years agofrom:e372cdcf7b. Checks:OK: 1 NOTE: 1. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 15 2024 |
| R-4.5-linux-x86_64 | NOTE | Nov 15 2024 |
Exports:ABCRefABCSMCcompileRcppmparseRcppPMCMCrun
Dependencies:clicodacolorspacecpp11dplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellmvtnormnlmepillarpkgconfigpurrrR6RColorBrewerRcppRcppArmadilloRcppXPtrUtilsrlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Simulation-based inference for infectious disease models | SimBIID-package |
| Produces ABC reference table | ABCRef |
| Runs ABC-SMC algorithm | ABCSMC ABCSMC.ABCSMC ABCSMC.default |
| Compiles 'SimBIID_model' object | compileRcpp |
| Time series counts of ebola cases | ebola |
| Parse custom model using 'SimInf' style markup | mparseRcpp |
| Plots 'ABCSMC' objects | plot.ABCSMC |
| Plots 'PMCMC' objects | plot.PMCMC |
| Plots 'SimBIID_runs' objects | plot.SimBIID_runs |
| Runs particle MCMC algorithm | PMCMC PMCMC.default PMCMC.PMCMC |
| Predicts future course of outbreak from 'PMCMC' objects | predict.PMCMC |
| Prints 'ABCSMC' objects | print.ABCSMC |
| Prints 'PMCMC' objects | print.PMCMC |
| Prints 'SimBIID_model' objects | print.SimBIID_model |
| Prints 'SimBIID_runs' objects | print.SimBIID_runs |
| Runs 'SimBIID_model' object | run |
| Time series counts of smallpox cases | smallpox |
| Summarises 'ABCSMC' objects | summary.ABCSMC |
| Summarises 'PMCMC' objects | summary.PMCMC |
| Time windows for 'PMCMC' objects | window.PMCMC |
