Package 'jointlyr'

Title: Joint estimation of initial incidence and reproduction number
Description: Provides a Stan implementation of a method to jointly estimate incidence and reproduction number.
Authors: Sangeeta Bhatia [aut, cre], Pierre Nouvellet [aut], Anne Cori [aut], Jack Wardle [aut]
Maintainer: Sangeeta Bhatia <[email protected]>
License: MIT
Version: 0.0.1
Built: 2024-11-25 04:41:00 UTC
Source: https://github.com/mrc-ide/jointlyr

Help Index


The 'jointlyr' package.

Description

A DESCRIPTION OF THE PACKAGE

References

Stan Development Team (2020). RStan: the R interface to Stan. R package version 2.21.2. https://mc-stan.org


Jointly estimate I0 and Rt

Description

Joint estimation of initial incidence and reproduction number

Usage

jointly_estimate(window, window_back, incid, si_distr, ...)

Arguments

window

length of the window used for estimation. If you have the full incidence time-series, only data in this window are used for estimatiom.

window_back

length of time for which incidence should be estimated.

incid

Incidence used to fit the model. Numeric vector of length window

si_distr

Discretised serial interval distribution

...

Arguments passed to rstan::fit (e.g. iter, chains).

Value

an object of class stanfit

Author(s)

Sangeeta Bhatia