![](https://github.com/epiforecasts/epinowcast/raw/HEAD/man/figures/logo.png)
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 5 days ago
cmdstanreffective-reproduction-number-estimationepidemiologyinfectious-disease-surveillancenowcastingoutbreak-analysispandemic-preparednessreal-time-infectious-disease-modellingstan
56 stars 4.10 score 52 dependencies![](https://github.com/epinowcast/epinowcast/raw/v0.3.0/man/figures/logo.png)
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 5 months ago
cmdstanreffective-reproduction-number-estimationepidemiologyinfectious-disease-surveillancenowcastingoutbreak-analysispandemic-preparednessreal-time-infectious-disease-modellingstan
54 stars 3.87 score 52 dependencies![](https://github.com/epiforecasts/covidregionaldata/raw/HEAD/man/figures/logo.png)
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 3.14 score 46 dependenciesEpiNow - 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 2.46 score 104 dependenciesEpiSoon - 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 1.58 score 63 dependencies 1 dependents![](https://github.com/epiforecasts/forecast.vocs/raw/HEAD/man/figures/README-unnamed-chunk-8-1.png)
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 1.08 score 71 dependencies![](https://github.com/epinowcast/primarycensoreddist/raw/v0.3.0/man/figures/logo.png)
primarycensoreddist - Primary Event Censored Distributions in R and Stan
This package provides both R functions for working with primary event censored distributions and Stan implementations for use in Bayesian modeling. Primary event censored distributions are useful for modeling delayed reporting scenarios in epidemiology and other fields. It provides support for arbitrary delay distributions, a range of common primary distributions, and allows for truncation and secondary event censoring to be accounted for.
Last updated 1 days ago
censoringdistributionstruncation
4 stars 0.91 score 0 dependenciesidbrms - Infectious Disease Modelling Using brms
Infectious disease modelling using brms.
Last updated 2 years ago
brmsinfectious-disease-modelsopensource
4 stars 0.71 score 76 dependencies