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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

12.35 score 140 stars 388 scripts 586 downloads

scoringutils - Utilities for Scoring and Assessing Predictions

Facilitate the evaluation of forecasts in a convenient framework based on data.table. It allows user to to check their forecasts and diagnose issues, to visualise forecasts and missing data, to transform data before scoring, to handle missing forecasts, to aggregate scores, and to visualise the results of the evaluation. The package mostly focuses on the evaluation of probabilistic forecasts and allows evaluating several different forecast types and input formats. Find more information about the package in the Vignettes as well as in the accompanying paper, <doi:10.48550/arXiv.2205.07090>.

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forecast-evaluationforecasting

11.35 score 61 stars 7 dependents 384 scripts 1.2k 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

epinowcast - A Bayesian Framework for Real-time Infectious Disease Surveillance

A modular Bayesian framework for real-time infectious disease surveillance. Provides tools for nowcasting, reproduction number estimation, delay estimation, and forecasting from data subject to reporting delays, right-truncation, missing data, and incomplete ascertainment. Users can build models suited to their setting using a flexible formula interface supporting fixed effects, random effects, random walks, and time-varying parameters, with options including parametric and non-parametric delay distributions with optional modifiers (via discrete-time hazard models), renewal processes, observation models, missing data imputation, and stratified analyses with partial pooling. By jointly estimating disease dynamics and reporting patterns, our framework enables earlier and more reliable detection of trends. While designed with epidemiological applications in mind, the framework can be applied to any right-truncated time series count data.

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cmdstanreffective-reproduction-number-estimationepidemiologyinfectious-disease-surveillancenowcastingoutbreak-analysispandemic-preparednessreal-time-infectious-disease-modellingstan

8.96 score 65 stars 98 scripts

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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8.59 score 25 stars 1 dependents 432 scripts 223 downloads

ringbp - Simulate and Evaluate Targeted Interventions in Infectious Disease Outbreaks

Branching process simulation model of infectious disease transmission with flexible parameterisation of epidemiology and targeted interventions, including isolation, contact tracing and quarantine, to reduce transmission, together with functions to evaluate outbreak control. Introduced in Hellewell et al. (2020) <doi:10.1016/S2214-109X(20)30074-7>.

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controlling-outbreakstransmission

6.99 score 17 stars 24 scripts

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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6.83 score 4 stars 418 scripts 219 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 215 downloads

quantgen - Tools for generalized quantile modeling

Tools for generalized quantile modeling: regularized quantile regression (with generalized lasso penalties and noncrossing constraints), cross-validation, quantile extrapolation, and quantile ensembles.

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5.36 score 1 dependents 36 scripts

lopensemble - Create Mixture Models From Predictive Samples

Combines predictions from individual time series or panel data models into an ensemble using stacking (Yao, Vehtari, Simpson, and Gelman (2018) <doi:10.1214/17-BA1091>) based on the Continuous Ranked Probability Score (CRPS) (Gneiting and Raftery (2007) <doi:10.1198/016214506000001437>) over k-step ahead predictions. Predictions must be predictive distributions represented by samples, typically posterior predictive simulation draws from a Markov chain Monte Carlo (MCMC) algorithm. Given training data with observed values and predictive samples from different models, optimal stacking weights are computed to minimize expected cross-validation predictive error. These weights can then be used to generate samples from the mixture model by drawing from individual model predictions in the correct proportions.

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crpsensemblesforecastingstacking

5.32 score 7 stars 1 dependents 1 scripts

nfidd - Material to support course on nowcasting and forecasting of infectious disease dynamics

Resources to support a short course on nowcasting and forecasting of infectious disease dynamics.

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delay-estimationepidemicsforecastinginfectious-disease-dynamicslearningnowcastingoutbreak-analysisoutbreaks

5.07 score 24 stars 10 scripts

EpiSoon - Forecast Cases Using Reproduction Numbers

To forecast the time-varying reproduction number and use this to forecast reported case counts. Includes tools to evaluate a range of models across samples and time series using proper scoring rules.

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case-forecastsforecasts

4.79 score 7 stars 25 scripts

qrensemble - Forecast ensembles using Quantile Regression Average (QRA)

Performs quantile regression average

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4.32 score 3 stars 1 scripts

EpiAwareR - R Interface to the 'EpiAware' Infectious Disease Modelling Framework

Provides an R interface to the 'Julia'-based 'EpiAware' compositional infectious disease modelling framework. Enables users to build flexible epidemiological models by composing reusable components for latent processes, infection dynamics, and observation models without requiring 'Julia' expertise.

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3.65 score 6 stars 7 scripts

ringbp - Simulate and Evaluate Targeted Interventions in Infectious Disease Outbreaks

Branching process simulation model of infectious disease transmission with flexible parameterisation of epidemiology and targeted interventions, including isolation, contact tracing and quarantine, to reduce transmission, together with functions to evaluate outbreak control. Introduced in Hellewell et al. (2020) <doi:10.1016/S2214-109X(20)30074-7>.

Last updated

3.56 score 24 scripts

RtD3 - Rt Visualization in D3

An R interface for the JavaScript library rt_vis(<https://github.com/hamishgibbs/rt_vis>).

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2.95 score 6 stars 7 scripts 36 downloads

idbrms - Infectious Disease Modelling Using brms

Infectious disease modelling using brms.

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brmsinfectious-disease-modelsopensource

2.70 score 5 stars 3 scripts

epimixr - Epidemiological analysis using social mixing matrices

Provides methods to conduct epidemiological analysis using social mixing matrices, such as calculating contact-adjusted immunity levels or age distributions of epidemics.

Last updated

2.30 score 4 stars 2 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