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 1 months ago

backcalculationcovid-19gaussian-processesopen-sourcereproduction-numberstancpp

11.86 score 123 stars 210 scripts 1.1k 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 6 months ago

9.74 score 38 stars 1 dependents 227 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 10 months ago

8.35 score 24 stars 1 dependents 390 scripts 358 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 2 years ago

6.48 score 4 stars 380 scripts 265 downloads

qrensemble - Forecast ensembles using Quantile Regression Average (QRA)

Performs quantile regression average

Last updated 5 months 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 5 months ago

probabilistic-programmingstan

2.00 score 2 stars 1 scripts