Package 'jointlyr' reference manual

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:	2024-10-26 04:43:13 UTC
Source:	https://github.com/mrc-ide/jointlyr

The 'jointlyr' package.

A DESCRIPTION OF THE PACKAGE

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

Joint estimation of initial incidence and reproduction number

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

`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).

an object of class stanfit

Sangeeta Bhatia