EpiNow2 - Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters

Estimates the time-varying reproduction number, rate of spread, and doubling time using a range of open-source tools (Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1>), and current best practices (Gostic et al. (2020) <doi:10.1101/2020.06.18.20134858>). It aims to help users avoid some of the limitations of naive implementations in a framework that is informed by community feedback and is actively supported.

Last updated 21 days ago

backcalculationcovid-19gaussian-processesopen-sourcereproduction-numberstan

11.75 score 114 stars 209 scripts 977 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>.

Last updated 21 days ago

forecast-evaluationforecasting

11.11 score 48 stars 5 packages 272 scripts 1.0k downloads

socialmixr - Social Mixing Matrices for Infectious Disease Modelling

Provides 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>.

Last updated 1 months ago

9.67 score 38 stars 1 packages 215 scripts 692 downloads

epinowcast - Flexible Hierarchical Nowcasting

Tools to enable flexible and efficient hierarchical nowcasting of right-truncated epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes. Nowcasting, in this context, is gaining situational awareness using currently available observations and the reporting patterns of historical observations. This can be useful when tracking the spread of infectious disease in real-time: without nowcasting, changes in trends can be obfuscated by partial reporting or their detection may be delayed due to the use of simpler methods like truncation. While the package has been designed with epidemiological applications in mind, it could be applied to any set of right-truncated time-series count data.

Last updated 7 months ago

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

8.49 score 57 stars 71 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.

Last updated 1 years ago

8.30 score 24 stars 1 packages 350 scripts 414 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.

Last updated 1 years ago

6.44 score 4 stars 348 scripts 279 downloads

covidregionaldata - Subnational Data for COVID-19 Epidemiology

An interface to subnational and national level COVID-19 data sourced from both official sources, such as Public Health England in the UK, and from other COVID-19 data collections, including the World Health Organisation (WHO), European Centre for Disease Prevention and Control (ECDC), John Hopkins University (JHU), Google Open Data and others. Designed to streamline COVID-19 data extraction, cleaning, and processing from a range of data sources in an open and transparent way. This allows users to inspect and scrutinise the data, and tools used to process it, at every step. For all countries supported, data includes a daily time-series of cases. Wherever available data is also provided for deaths, hospitalisations, and tests. National level data are also supported using a range of sources.

Last updated 3 years ago

covid-19dataopen-sciencer6regional-data

5.67 score 37 stars 121 scripts 128 downloads

forecast.vocs - Forecast Case and Sequence Notifications using Variant of Concern Strain Dynamics

Contains models and tools to produce short-term forecasts for both case and sequence notifications assuming circulation of either one or two variants. Tools are also provided to allow the evaluation of the use of sequence data for short-term forecasts in both real-world settings and in user generated scenarios.

Last updated 2 years ago

5.25 score 8 stars 22 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.

Last updated 17 days ago

delay-estimationepidemicsforecastinginfectious-disease-dynamicslearningnowcastingoutbreak-analysisoutbreaks

4.76 score 11 stars

EpiNow - Estimate Realtime Case Counts and Time-varying Epidemiological Parameters

To identify changes in the reproduction number, rate of spread, and doubling time during the course of outbreaks whilst accounting for potential biases due to delays in case reporting.

Last updated 5 years ago

4.74 score 33 stars 111 scripts

covid19.nhs.data - Covid 19 England Hospital Admissions

Facilitates access to data on English Covid-19 hospital admissions aggregated to a range of spatial scales.

Last updated 4 years ago

covid19hospitalisationslocal-authoritynhsopenscienceuk

4.61 score 8 stars 17 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.

Last updated 2 years ago

case-forecastsforecasts

4.26 score 7 stars 1 packages 25 scripts

stackr - Create Mixture Models From Predictive Samples

The `stackr` package provides an easy way to combine predictions from individual time series or panel data models to an ensemble. `stackr` stacks (Yuling Yao, Aki Vehtari, Daniel Simpson, and Andrew Gelman (2018) <doi:10.1214/17-BA1091>) Models according to the Continuous Ranked Probability Score (CRPS) (Tilmann Gneiting & Adrian E Raftery (2007) <doi:10.1198/016214506000001437>) over k-step ahead predictions. It is therefore especially suited for timeseries and panel data. A function for leave-one-out CRPS may be added in the future. Predictions need to be predictive distributions represented by predictive samples. Usually, these will be sets of posterior predictive simulation draws generated by an MCMC algorithm. Given some training data with true observed values as well as predictive samples generated from different models, `crps_weights` finds the optimal (in the sense of minimizing expected cross-validation predictive error) weights to form an ensemble from these models. Using these weights, `mixture_from_samples` can then provide samples from the optimal model mixture by drawing from the predictice samples of the individual models in the correct proportion. This gives a mixture model solely based on predictive samples and is in this regard superior to other ensembling techniques like Bayesian Model Averaging.

Last updated 20 days ago

crpsensemblesforecastingstacking

4.25 score 4 stars 44 scripts

qrensemble - Forecast ensembles using Quantile Regression Average (QRA)

Performs quantile regression average

Last updated 15 days ago

3.78 score 3 stars 1 scripts

RtD3 - Rt Visualization in D3

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

Last updated 4 years ago

2.78 score 6 stars 7 scripts 44 downloads

idbrms - Infectious Disease Modelling Using brms

Infectious disease modelling using brms.

Last updated 2 years ago

brmsinfectious-disease-modelsopensource

2.60 score 4 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 20 days ago

2.18 score 3 stars 2 scripts

stanedit - Facilitate editing of stan models

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

Last updated 7 days ago

probabilistic-programmingstan

1.70 score 1 scripts