trajectory {pomp}R Documentation

Trajectory of a deterministic model

Description

Compute trajectories of the deterministic skeleton of a Markov process.

Usage

## S4 method for signature 'pomp'
trajectory(object, params, times, t0,
  format = c("array", "data.frame"), ...,
  verbose = getOption("verbose", FALSE))

## S4 method for signature 'traj_match_objfun'
trajectory(object, ...,
  verbose = getOption("verbose", FALSE))

Arguments

object

an object of class ‘pomp’, or of a class that extends ‘pomp’. This will typically be the output of pomp, simulate, or one of the pomp inference algorithms.

params

a npar x nrep matrix of parameters. Each column is treated as an independent parameter set, in correspondence with the corresponding column of x.

times

a numeric vector (length ntimes) containing times at which the itineraries are desired. These must be in non-decreasing order with times[1]>t0.

t0

the time at which the initial conditions are assumed to hold.

format

the format in which to return the results.

format = "array" causes the trajectories to be returned in a rank-3 array with dimensions nvar x ncol(params) x ntimes. Here, nvar is the number of state variables and ntimes the length of the argument times.

format = "data.frame" causes the results to be returned as a single data frame containing the time and states. An ordered factor variable, ‘.id’, distinguishes the trajectories from one another.

...

Additional arguments are passed to the ODE integrator (if the skeleton is a vectorfield) and are ignored if it is a map. See ode for a description of the additional arguments accepted by the ODE integrator.

verbose

logical; if TRUE, diagnostic messages will be printed to the console.

Details

In the case of a discrete-time system, the deterministic skeleton is a map and a trajectory is obtained by iterating the map. In the case of a continuous-time system, the deterministic skeleton is a vector-field; trajectory uses the numerical solvers in deSolve to integrate the vectorfield.

Note that the handling of ... in trajectory differs from that of most other functions in pomp. In particular, it is not possible to modify the model structure in a call to trajectory.

Value

trajectory returns an array of dimensions nvar x nrep x ntimes. If x is the returned matrix, x[i,j,k] is the i-th component of the state vector at time times[k] given parameters params[,j].

See Also

skeleton, flow


[Package pomp version 2.3 Index]