EpiNow2 - Estimate and Forecast Real-Time Infection Dynamics

Estimates the time-varying reproduction number, rate of spread, and doubling time using a renewal equation approach combined with Bayesian inference via Stan. Supports Gaussian process and random walk priors for modelling changes in transmission over time. Accounts for delays between infection and observation (incubation period, reporting delays), right-truncation in recent data, day-of-week effects, and observation overdispersion. Can estimate relationships between primary and secondary outcomes (e.g., cases to hospitalisations or deaths) and forecast both. Runs across multiple regions in parallel. Based on Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1> and Gostic et al. (2020) <doi:10.1101/2020.06.18.20134858>.

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backcalculationcovid-19gaussian-processesopen-sourcereproduction-numberstancpp

12.28 score 138 stars 331 scripts 477 downloads

socialmixr - Social Mixing Matrices for Infectious Disease Modelling

Methods for sampling contact matrices from diary data for use in infectious disease modelling, as discussed in Mossong et al. (2008) <doi:10.1371/journal.pmed.0050074>.

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10.76 score 43 stars 2 dependents 288 scripts 1.0k downloads

rbi - Interface to 'LibBi'

Provides a complete interface to 'LibBi', a library for Bayesian inference (see <https://libbi.org> and Murray, 2015 <doi:10.18637/jss.v067.i10> for more information). This includes functions for manipulating 'LibBi' models, for reading and writing 'LibBi' input/output files, for converting 'LibBi' output to provide traces for use with the coda package, and for running 'LibBi' to conduct inference.

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8.53 score 25 stars 1 dependents 380 scripts 259 downloads

rbi.helpers - 'rbi' Helper Functions

Contains a collection of helper functions to use with 'rbi', the R interface to 'LibBi', described in Murray et al. (2015) <doi:10.18637/jss.v067.i10>. It contains functions to adapt the proposal distribution and number of particles in particle Markov-Chain Monte Carlo, as well as calculating the Deviance Information Criterion (DIC) and converting between times in 'LibBi' results and R time/dates.

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6.76 score 4 stars 363 scripts 246 downloads

contactsurveys - Download Contact Surveys for Use in Infectious Disease Modelling

Download, cache, and manage social contact survey data from the social contact data community on Zenodo (<https://zenodo.org/communities/social_contact_data>) for use in infectious disease modelling. Provides functions to list available surveys, download survey files with automatic caching, and retrieve citations. Contact survey data describe who contacts whom in a population and are used to parameterise age-structured transmission models, for example via the 'socialmixr' package. The surveys available include those from the POLYMOD study (Mossong et al. (2008) <doi:10.1371/journal.pmed.0050074>) and other social contact data shared on Zenodo.

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5.90 score 2 stars 12 scripts 316 downloads

qrensemble - Forecast ensembles using Quantile Regression Average (QRA)

Performs quantile regression average

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4.32 score 3 stars 1 scripts

forecastbaselines - R Interface to ForecastBaselines.jl

Provides an R interface to the ForecastBaselines.jl Julia package, enabling access to 10 baseline forecasting models including ARMA, ETS, STL, and others. Supports probabilistic forecasting with multiple interval methods and seamless integration with the scoringutils evaluation framework.

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2.00 score 10 scripts

stanedit - Facilitate editing of stan models

Provides functionality for extracting particular bits of stan models as well as removing and adding lines.

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probabilistic-programmingstan

2.00 score 2 stars 1 scripts