# de_mcmc: de_mcmc In pboesu/debinfer: Bayesian Inference for Differential Equations

## Description

Bayesian inference for a deterministic DE model (with models solved via an DE solver) with an observation model.

## Usage

 ```1 2 3 4``` ```de_mcmc(N, data, de.model, obs.model, all.params, ref.params = NULL, ref.inits = NULL, Tmax, data.times, cnt = 10, plot = TRUE, sizestep = 0.01, solver = "ode", verbose.mcmc = TRUE, verbose = FALSE, ...) ```

## Arguments

 `N` integer, number of MCMC iterations `data` data.frame of time course observations to fit the model to. The observations must be ordered ascending by time. `de.model` a function defining a DE model, compliant with the solvers in deSolve or PBSddesolve `obs.model` a function defining an observation model. Must be a function with arguments 'data', 'sim.data', 'samp'. `all.params` debinfer_parlist containing all model, MCMC, and observation `ref.params` an optional named vector containing a set of reference parameters, e.g. the true parameters underlying a simulated data set `ref.inits` an optional named vector containing a set of reference initial values, e.g. the true initial values underlying a simulated data set `Tmax` maximum timestep for solver `data.times` time points for which observations are available `cnt` integer interval at which to print and possibly plot information on the current state of the MCMC chain `plot` logical, plot traces for all parameters at the interval defined by `cnt` `sizestep` timestep for solver to return values at, only used if data.times is missing `solver` the solver to use. 1 or "ode" = deSolve::ode; 2 or "dde" = PBSddesolve::dde; 3 or "dede" = deSolve::dde `verbose.mcmc` logical display MCMC progress messages `verbose` logical display verbose solver output `...` further arguments to the solver

## Value

a debinfer_result object containing input parameters, data and MCMC samples

pboesu/debinfer documentation built on Oct. 26, 2018, 11:08 a.m.