Create a new C++ model object with parameters

Creates and initializes a C++ model object based on the provided parameters. This function wraps the underlying C++ model classes (LogNormalModel, LinearAbxModel, LinearAbxModel2, MixedModel) in appropriate R reference classes that expose the model's methods and properties.

Usage

newCppModel(modelParameters, verbose = FALSE)

Arguments

modelParameters

List of model parameters created using functions from constructors.R, such as:

• LogNormalModelParams() - Basic log-normal model

• LinearAbxModel() - Linear antibiotic model

• Or custom parameter lists containing:

  • modname: Model name ("LogNormalModel", "LinearAbxModel", "LinearAbxModel2", "MixedModel")

  • nstates: Number of states (2 or 3)

  • nmetro: Number of Metropolis-Hastings steps

  • forward: Forward simulation flag

  • cheat: Cheat flag for debugging

  • Insitu: In situ parameters from InsituParams()

  • SurveillanceTest: Surveillance test parameters from SurveillanceTestParams()

  • ClinicalTest: Clinical test parameters from ClinicalTestParams()

  • OutCol: Out-of-unit infection parameters from OutOfUnitInfectionParams()

  • InCol: In-unit parameters from InUnitParams() or ABXInUnitParams()

  • Abx: Antibiotic parameters from AbxParams()

  • AbxRate: Antibiotic rate parameters from AbxRateParams()

verbose

Logical flag to print progress messages during model creation and parameter setup (default: FALSE)

Value

A reference class object wrapping the C++ model. The specific class depends on modelParameters$modname:

• CppLogNormalModel - For "LogNormalModel"

• CppLinearAbxModel - For "LinearAbxModel"

• CppLinearAbxModel2 - For "LinearAbxModel2"

• CppMixedModel - For "MixedModel" (if exposed in C++)

All returned objects inherit from CppBasicModel and provide access to:

• Properties:

  • InColParams - In-unit colonization parameters

  • OutColParams - Out-of-unit colonization parameters

  • InsituParams - In situ parameters

  • SurveillanceTestParams - Surveillance test parameters

  • ClinicalTestParams - Clinical test parameters

  • AbxParams - Antibiotic parameters

• Methods:

  • logLikelihood(hist) - Calculate log likelihood for a SystemHistory

  • getHistoryLinkLogLikelihoods(hist) - Get individual link log likelihoods

  • forwardSimulate(...) - Perform forward simulation

  • initEpisodeHistory(...) - Initialize episode history

  • sampleEpisodes(...) - Sample episodes

  • setAbx(...) - Set antibiotic parameters

Details

The function uses the existing newModel C++ function to instantiate the model and configure all parameters, then wraps it in the appropriate R reference class based on the model type specified in modelParameters$modname.

See also

• LogNormalModelParams() for creating model parameters

• LinearAbxModel() for linear antibiotic model parameters

• InsituParams(), SurveillanceTestParams(), etc. for parameter components

• newModelExport() for extracting parameter values from a model

Examples

if (FALSE) { # \dontrun{
# Create a basic log-normal model
params <- LogNormalModelParams("LogNormalModel")
model <- newCppModel(params)

# Access model properties
inColParams <- model$InColParams
insituParams <- model$InsituParams

# Create a linear antibiotic model
params <- LinearAbxModel()
model <- newCppModel(params, verbose = TRUE)

# Get parameter values
inColParams <- model$InColParams
paramValues <- inColParams$values

# Use with a system history for likelihood calculation
# (requires data and SystemHistory object)
# ll <- model$logLikelihood(systemHistory)
} # }