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 3 days ago

backcalculationcovid-19gaussian-processesopen-sourcereproduction-numberstan

112 stars 11.86 score 68 dependencies

scoringutils - Utilities for Scoring and Assessing Predictions

scoringutils facilitates 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 6 days ago

forecast-evaluationforecasting

48 stars 11.06 score 41 dependencies 5 dependents

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 5 days ago

38 stars 9.71 score 35 dependencies 1 dependents

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 6 days ago

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

57 stars 8.87 score 52 dependencies

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 4 months ago

24 stars 8.33 score 16 dependencies 1 dependents

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

4 stars 6.47 score 23 dependencies

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 4 years ago

33 stars 5.74 score 104 dependencies

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 2 years ago

covid-19dataopen-sciencer6regional-data

37 stars 5.67 score 46 dependencies

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 1 years ago

8 stars 5.25 score 71 dependencies

covid19.nhs.data - NHS Trust Level COVID-19 Data Aggregated to a Range of Spatial Scales

Facilitates access to data on NHS trust level COVID-19 data aggregated to a range of spatial scales.

Last updated 2 years ago

covid19hospitalisationslocal-authoritynhsopenscienceuk

8 stars 4.61 score 58 dependencies

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

7 stars 4.26 score 63 dependencies 1 dependents

RtD3 - Rt Visualization in D3

Create interactive visualisations of Rt estimates using 'D3.js' (Gibbs et al. (2020) <doi:10.5281/zenodo.4011842>). Developed primarily targeting Rt estimates generated by the 'EpiNow2' package, 'RtD3' aims to make simple, beautiful visualisations that help researchers explore their results and share them with others.

Last updated 2 years ago

6 stars 2.78 score 37 dependencies

idbrms - Infectious Disease Modelling Using brms

Infectious disease modelling using brms.

Last updated 2 years ago

brmsinfectious-disease-modelsopensource

4 stars 2.60 score 76 dependencies

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 1 years ago

3 stars 2.18 score 38 dependencies