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.zip(r-4.5-x86_64)
hestia_0.1.0.tgz(r-4.6-x86_64)hestia_0.1.0.tgz(r-4.6-arm64)hestia_0.1.0.tgz(r-4.5-x86_64)hestia_0.1.0.tgz(r-4.5-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://accidda.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

On CRAN:

Conda:

onetbbcpp

6.43 score 3 stars 11 scripts 7 exports 56 dependencies

Last updated from:f7592871ba. Checks:13 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING242
linux-devel-x86_64WARNING354
source / vignettesOK461
linux-release-arm64WARNING244
linux-release-x86_64WARNING245
macos-release-arm64WARNING194
macos-release-x86_64WARNING531
macos-oldrel-arm64WARNING248
macos-oldrel-x86_64WARNING633
windows-devel-arm64WARNING506
windows-devel-x86_64WARNING386
windows-release-arm64WARNING513
windows-release-x86_64WARNING345
windows-oldrel-x86_64WARNING355
wasm-releaseOK247

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

Last update: 2026-09-17
Started: 2025-09-18

Multiple Infection Compartments
SIIR model (multiple infection compartments) | Simulate data | Model specification | Infection process model | Observation process model

Last update: 2026-09-17
Started: 2026-03-16

Parallel and threaded fitting (including HPC)
Why threading helps a hestia fit | Turning it on

Last update: 2026-08-07
Started: 2026-07-21