Package: hestia 0.1.0

Claire Perrin Smith

hestia: Bayesian Compartmental Infection Models from Individual Outcomes

Fit Bayesian compartmental infection models (such as susceptible-infected-recovered and multi-compartment hidden Markov variants) from individual-level outcome data. Models are composed from infection-process and observation-process components and fit using Stan via 'rstan'.

Authors:Claire Perrin Smith [aut, cre], Jack Goodall [aut]

hestia_0.1.0.tar.gz
hestia_0.1.0.zip(r-4.7-x86_64)hestia_0.1.0.zip(r-4.7-arm64)hestia_0.1.0.zip(r-4.6-x86_64)hestia_0.1.0.zip(r-4.6-arm64)
hestia_0.1.0.tar.gz(r-4.7-arm64)hestia_0.1.0.tar.gz(r-4.7-x86_64)hestia_0.1.0.tar.gz(r-4.6-arm64)hestia_0.1.0.tar.gz(r-4.6-x86_64)
hestia_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
hestia/json (API)

# Install 'hestia' in R:
install.packages('hestia', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/accidda/hestia/issues

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

Uses libs:
  • onetbb– Parallelism library for C++
  • c++– GNU Standard C++ Library v3
Datasets:
  • siir - Simulated SIIR household data
  • siir_res - Fitted draws for the SIIR model
  • sir - Simulated SIR household data
  • sir_cov - Simulated SIR household data with covariates
  • sir_cov_res - Fitted draws for the SIR model with covariates
  • sir_res - Fitted draws for the basic SIR model

On CRAN:

Conda:

onetbbcpp

3.22 score 11 scripts 7 exports 56 dependencies

Last updated from:36831c95f0. Checks:10 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK261
linux-devel-x86_64OK323
source / vignettesOK519
linux-release-arm64OK266
linux-release-x86_64OK326
windows-devel-arm64OK370
windows-devel-x86_64OK413
windows-release-arm64OK385
windows-release-x86_64OK379
wasm-releaseOK249

Exports:get_transmission_detailsmake_infection_modelmake_observation_modelprogressrun_modelstan_optionstransmit

Dependencies:abindbackportsBHcallrcheckmateclicpp11descdistributionaldplyrfarverflexstanrgenericsggplot2gluegridExtragtableinlineisobandlabelinglifecycleloomagrittrmatrixStatsnumDerivotelparallellypillarpkgbuildpkgconfigposteriorprocessxpspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsS7scalesStanHeadersstringistringrtensorAtibbletidyrtidyselectutf8vctrsviridisLitewithr

Basic SIR Model
SIR model | Simulate data | Model specification | Infection process model | Observation process model | Add in covariates
Rendered fromSIR.Rmdusingknitr::rmarkdown

Last update: 2026-10-20
Started: 2026-10-20

Multiple Infection Compartments
SIIR model (multiple infection compartments) | Simulate data | Model specification | Infection process model | Observation process model
Rendered frommultiple_infection_compartments.Rmdusingknitr::rmarkdown

Last update: 2026-10-20
Started: 2026-10-20

Parallel and threaded fitting (including HPC)
Why threading helps a hestia fit | Turning it on
Rendered fromparallel-hpc.Rmdusingknitr::rmarkdown

Last update: 2026-10-20
Started: 2026-10-20