BSL (version 3.0.0)

BSLMODEL-class: S4 class ``BSLMODEL''

Description

The S4 class contains the simulation and summary statistics function and other necessary arguments for a model to run in the main bsl function.

BSLModel is the constructor function for a BSLMODEL object.

initialize.BSLMODEL initialises a ``BSLMODEL'' object.

validBSLModelObject check the validity of a ``BSLMODEL'' object.

Usage

BSLModel(fnSim, fnSimVec, fnSum, fnLogPrior, simArgs, sumArgs, theta0,
  thetaNames, test = TRUE)
initialize.BSLMODEL(.Object, fnSim, fnSimVec, simArgs, fnSum, sumArgs,
  fnLogPrior, theta0, thetaNames, test = TRUE)
validBSLModelObject(object)
# S4 method for BSLMODEL
fn(.Object)
# S4 method for BSLMODEL
setns(.Object)

Arguments

fnSim

A function that simulates data for a given parameter value. The first argument should be the parameters. Other necessary arguments (optional) can be specified with simArgs.

fnSimVec

A vectorised function that simulates a number of datasets simultaneously for a given parameter value. The first two arguments should be the number of simulations to run and parameters, respectively. Other necessary arguments (optional) can be specified with simArgs. The output must be a list of each simulation result.

fnSum

A function for computing summary statistics of data. The first argument should be the observed or simulated dataset. Other necessary arguments (optional) can be specified with sumArgs.

fnLogPrior

A function that computes the log of prior density for a parameter. If this is missing, the prior by default is an improper flat prior over the real line for each parameter. The function must have a single input: a vector of parameter values.

simArgs

A list of additional arguments to pass into the simulation function. Only use when the input fnSim requires additional arguments.

sumArgs

A list of additional arguments to pass into the summary statistics function. Only use when the input fnSum requires additional arguments.

theta0

Initial guess of the parameter value.

thetaNames

A string vector of parameter names, which must have the same length as the parameter vector.

test

Logical, whether a short simulation test will be ran upon initialisation.

.Object

A ``BSLMODEL'' object.

object

A ``BSLMODEL'' object.

Methods (by generic)

• fn: Generate the generic simulation and summary statistics function for n simulations and fixed theta (for internal use).

• setns: Find and set the length of summary statistics with a test run (for internal use).

Slots

fnSim

A function that simulates data for a given parameter value. The first argument should be the parameters. Other necessary arguments (optional) can be specified with simArgs.

fnSimVec

A vectorised function that simulates a number of datasets simultaneously for a given parameter value. If this is not NULL, vectorised simulation function will be used instead of fnSim. The first two arguments should be the number of simulations to run and parameters, respectively. Other necessary arguments (optional) can be specified with simArgs. The output must be a list of each simulation result.

fnSum

A function for computing summary statistics of data. The first argument should be the observed or simulated dataset. Other necessary arguments (optional) can be specified with sumArgs. The users should code this function carefully so the output have fixed length and never contain any Inf value.

fnLogPrior

A function that computes the log of prior density for a parameter. The default is NULL, which uses an improper flat prior over the real line for each parameter. The function must have a single input: a vector of parameter values.

simArgs

A list of additional arguments to pass into the simulation function. Only use when the input fnSim or fnSimVec requires additional arguments. The default is NULL.

sumArgs

A list of additional arguments to pass into the summary statistics function. Only use when the input fnSum requires additional arguments. The default is NULL.

theta0

Initial guess of the parameter value, which is used as the starting value for MCMC.

thetaNames

Expression, parameter names.

ns

The number of summary statistics of a single observation. Note this will be generated automatically, thus is not required for initialisation.

test

Logical indicator of whether a short simulation test will be ran upon initialisation.

Examples

# NOT RUN {
data(ma2)
model <- BSLModel(fnSim = ma2_sim, fnSum = ma2_sum, simArgs = ma2$sim_options, theta0 = ma2$start,
                  fnLogPrior = ma2_logPrior)
validObject(model)
# }