stan_pathfinder_opts

<a href="https://lifecycle.r-lib.org/articles/stages.html#experimental"><img src="figures/lifecycle-experimental.svg?package=EpiNow2&version=1.6.1" alt="[Experimental]"></a>
Defines a list specifying the arguments passed to <code>cmdstanr::laplace()</code>.

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.

Sebastian Funk

EpiNow2

Estimate Real-Time Case Counts and Time-Varying Epidemiological
Parameters

Sam Abbott

Joel Hellewell

Katharine Sherratt

Katelyn Gostic

Joe Hickson

Hamada S. Badr

Michael DeWitt

James M. Azam

Robin Thompson

Sophie Meakin

James Munday

Nikos Bosse

Paul Mee

Peter Ellis

Pietro Monticone

Lloyd Chapman

Andrew Johnson

Kaitlyn Johnson

EpiForecasts 

stan_pathfinder_opts function

<dl><dt>backend</dt>
<dd>Character string indicating the backend to use for fitting
stan models. Supported arguments are "rstan" (default) or "cmdstanr".</dd>
<dt>samples</dt>
<dd>Numeric, default 2000. Overall number of posterior samples.
When using multiple chains iterations per chain is samples / chains.</dd>
<dt>trials</dt>
<dd>Numeric, defaults to 10. Number of attempts to use
rstan::vb()] before failing.</dd>
<dt>...</dt>
<dd>Additional parameters to pass to <code>cmdstanr::laplace()</code>.</dd></dl>

Arguments

<a href='https://lifecycle.r-lib.org/articles/stages.html#experimental'><img src='figures/lifecycle-experimental.svg' alt='[Experimental]' /></a>
Defines a list specifying the arguments passed to <code>cmdstanr::laplace()</code>.

Stan pathfinder algorithm Options — stan_pathfinder_opts

<dl>

<dt>backend</dt>
<dd>Character string indicating the backend to use for fitting
stan models. Supported arguments are "rstan" (default) or "cmdstanr".</dd>


<dt>samples</dt>
<dd>Numeric, default 2000. Overall number of posterior samples.
When using multiple chains iterations per chain is samples / chains.</dd>


<dt>trials</dt>
<dd>Numeric, defaults to 10. Number of attempts to use
rstan::vb()] before failing.</dd>


<dt>...</dt>
<dd>Additional parameters to pass to <code>cmdstanr::laplace()</code>.</dd>

</dl>

Stan pathfinder algorithm Options

stan_pathfinder_opts: Stan pathfinder algorithm Options

Description

Usage

Value

Arguments

Examples