MCSimMod Model class — Model-class • MCSimMod

A class for managing MCSimMod models.

Arguments

mName: Name of an MCSim model specification file, excluding the file name extension .model.
mString: A character string containing MCSim model specification text.

Details

Instances of this class represent ordinary differential equation (ODE) models. A Model object has both attributes (i.e., things the object “knows” about itself) and methods (i.e., things the object can “do”). Model attributes include: the name of the model (mName); a vector of parameter names and values (parms); and a vector of initial conditions (Y0). Model methods include functions for: translating, compiling, and loading the model (loadModel); updating parameter values (updateParms); updating initial conditions (updateY0); and running model simulations (runModel). So, for example, if mod is a Model object, it will have an attribute called parms that can be accessed using the R expression mod$parms. Similarly, mod will have a method called updateParms that can be accessed using the R expression mod$updateParms(). Use the createModel() function to create Model objects.

Fields

mName: Name of an MCSim model specification file, excluding the file name extension .model.
mString: Character string containing MCSim model specification text.
initParms: Function that initializes values of parameters defined for the associated MCSim model.
initStates: Function that initializes values of state variables defined for teh associated MCSim model..
Outputs: Names of output variables defined for the associated MCSim model.
parms: Named vector of parameter values for the associated MCSim model.
Y0: Named vector of initial conditions for the state variables of the associated MCSim model.
paths: List of character strings that are names of files associated with the model.
writeTemp: Boolean specifying whether to write model files to a temporary directory. If value is TRUE, model files will be Written to a temporary directory; if value is FALSE, model files will be Written to the same directory that contains the model specification file.

Methods

cleanup(deleteModel = FALSE): Delete files created during the translation and compilation steps performed by loadModel. If deleteModel = TRUE, delete the MCSim model specification file, as well.
initialize(...): Initialize the Model object using an MCSim model specification file (mName) or an MCSim model specification string (mString).
loadModel(force = FALSE): Translate (if necessary) the model specification text to C, compile (if necessary) the resulting C file to create a dynamic link library (DLL) file (on Windows) or a shared object (SO) file (on Unix), and then load all essential information about the Model object into memory (for use in the current R session).
runModel(times, ...): Perform a simulation for the Model object using the deSolve function ode for the specified times.
updateParms(new_parms = NULL): Update values of parameters for the Model object.
updateY0(new_states = NULL): Update values of initital conditions of state variables for the Model object.