Software
R packages and other software developed by the group
Reusable tools and packages developed by the group. See also our ongoing projects and publications.
Most packages are on CRAN. The rest can be installed from our r-universe:
install.packages(
"packagename",
repos = c("https://epiforecasts.r-universe.dev", getOption("repos"))
)
EpiNow2
Estimate Realtime Case Counts and Time-varying Epidemiological Parameters
epinowcast
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
scoringutils
Utilities for Scoring and Assessing Predictions
rbi
Bayesian inference with state-space models using LibBi.
ringbp
Simulate infectious disease transmission with contact tracing
baselinenowcast
Baseline nowcasting methods for correcting reporting delays in epidemiological data.
epichains
Methods for simulating and analysing the sizes and lengths of infectious disease transmission chains from branching process models
lopensemble
Model stacking for predictive ensembles
epimixr
Epidemiological analysis using social mixing matrices
rbi.helpers
Helper functions for inference with LibBi. Building on the rbi library.
qrensemble
Function and example for quantile regression average
contactsurveys
Download and access social contact data
cfrnow
Real-time case fatality ratio from a line list via a Bayesian mixture-cure survival model
distspec
Define probability distributions with certain or uncertain parameters
forecastbaselines
forecastbaselines: R interface to ForecastBaselines.jl
socialmixr
Derive social mixing matrices from survey data.