solve_de

A Bayesian framework for parameter inference in differential equations.
This approach offers a rigorous methodology for parameter inference as well as
modeling the link between unobservable model states and parameters, and
observable quantities. Provides templates for the DE model, the
observation model and data likelihood, and the model parameters and their prior
distributions. A Markov chain Monte Carlo (MCMC) procedure processes these inputs
to estimate the posterior distributions of the parameters and any derived
quantities, including the model trajectories. Further functionality is provided
to facilitate MCMC diagnostics and the visualisation of the posterior distributions
of model parameters and trajectories.

Philipp H Boersch-Supan

deBInfer

Bayesian Inference for Differential Equations

Leah R Johnson

Sadie J Ryan

solve_de function

<dl><dt>sim</dt>
<dd>function; solver compatible specification of the DE</dd>
<dt>params</dt>
<dd>numeric; named vector of parameter values</dd>
<dt>inits</dt>
<dd>numeric; initial values. Must be in the same order as specified within sim!</dd>
<dt>Tmax</dt>
<dd>numeric; maximum timestep</dd>
<dt>numsteps</dt>
<dd>numeric</dd>
<dt>solver</dt>
<dd>Choice of solver to use 1 or "ode" = deSolve::ode, 2 or "dde" = PBSddesolve::dde, 3 or "dede" = deSolve::dede</dd>
<dt>sizestep</dt>
<dd>for solver</dd>
<dt>verbose</dt>
<dd>passed to deSolve::ode</dd>
<dt>data.times</dt>
<dd>numeric a vector of times at which the ODE is to be evaluated. Defaults to NULL. If value is supplied it takes precedence over any value supplied to <code>numsteps</code> or <code>sizesteps</code>.</dd>
<dt>method</dt>
<dd>solver method</dd>
<dt>...</dt>
<dd>additional arguments to solver</dd></dl>

Arguments

solve_de — solve_de

<dl>

<dt>sim</dt>
<dd>function; solver compatible specification of the DE</dd>


<dt>params</dt>
<dd>numeric; named vector of parameter values</dd>


<dt>inits</dt>
<dd>numeric; initial values. Must be in the same order as specified within sim!</dd>


<dt>Tmax</dt>
<dd>numeric; maximum timestep</dd>


<dt>numsteps</dt>
<dd>numeric</dd>


<dt>solver</dt>
<dd>Choice of solver to use 1 or "ode" = deSolve::ode, 2 or "dde" = PBSddesolve::dde, 3 or "dede" = deSolve::dede</dd>


<dt>sizestep</dt>
<dd>for solver</dd>


<dt>verbose</dt>
<dd>passed to deSolve::ode</dd>


<dt>data.times</dt>
<dd>numeric a vector of times at which the ODE is to be evaluated. Defaults to NULL. If value is supplied it takes precedence over any value supplied to <code>numsteps</code> or <code>sizesteps</code>.</dd>


<dt>method</dt>
<dd>solver method</dd>


<dt>...</dt>
<dd>additional arguments to solver</dd>

</dl>

solve_de: solve_de

Description

Usage

Value

Arguments