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 22 days ago

backcalculationcovid-19gaussian-processesopen-sourcereproduction-numberstan

11.75 score 114 stars 209 scripts 977 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

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 6 months ago

8.01 score 24 stars 1 packages 352 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 249 downloads

qrensemble - Forecast ensembles using Quantile Regression Average (QRA)

Performs quantile regression average

Last updated 16 days ago

3.78 score 3 stars 1 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 8 days ago

probabilistic-programmingstan

1.70 score 1 scripts