R/NMSimModel_factory.R

In MangoTheCat/RNMImport: Tools for importing and manipulating NONMEM data.

#' Constructor for the NMSimModel class
#' @param controlStatements Set of parsed control statements 
#' @param path Path where the run is located
#' @param reportContents Parsed contents of the report file
#' @return Newly constructed object 
#' @author Mango Solutions

NMSimModel <- function(controlStatements, path, reportContents, versionInfo = c("major" = "VI", "minor" = 0))
{
	inData <- try(importModelData(dataStatement = controlStatements$Data,inputStatement = controlStatements$Input, path = path))
	# if we could not read data file for some reason, continue anyway
	if(inherits(inData, "try-error"))
	{
		msg <- paste("Could not import data file.  Error generated was:",
				inData, "\nWill continue importing other components\n")
		RNMImportWarning(msg)
		inData <- data.frame()
	} # end if(inherits(inData, "try-error"))

	outTables <- .importTablesSafely(controlStatements$Table, path = path  )

	# if the output tables are a "list", then there was a FIRSTONLY statment, or for some other reason
	# the number of rows of all of the output tables were not equivalent
	
	if(inherits(outTables, "list")) nDataRows <- max(sapply(outTables, nrow))
	else nDataRows <- nrow(outTables)
	seeds <- as.numeric(ifelse(controlStatements$Sim[c("Seed1", "Seed2")] == -1, NA,	
					controlStatements$Sim[c("Seed1", "Seed2")]))
	nSim <- as.numeric(controlStatements$Sim["nSub"])
	with(reportContents, 
		{	
			# check how many simulations there are.  If only one, the minimum of the objective funciton is stored
			# differently
			
			
			if(nSim == 1)
				objectiveFinal <- Objective.Minimum
			else
				objectiveFinal <- FinalEstimates$Objective.Minimum
			
			omegaFinal <- FinalEstimates$OMEGA
			# Use parameter labels for names, if any were supplied
			dimnames(omegaFinal)[1:2] <- dimnames(controlStatements$Omega)
			thetaFinal <- FinalEstimates$THETA
			colnames(thetaFinal) <- names(controlStatements$Theta[,"Est"])
			sigmaFinal <- FinalEstimates$SIGMA
			if(!is.null(sigmaFinal))
			{
				dimnames(sigmaFinal)[1:2] <- dimnames(controlStatements$Sigma)
			}
			else
				sigmaFinal <- array(c(0,0, nSim))
			
			new("NMSimModel", numSimulations = nSim, 
					seeds = seeds, inputData = inData, outputData = outTables, controlStatements = 
							controlStatements, problemStatement = controlStatements$Problem,
					thetaInitial = controlStatements$Theta[,"Est"], 
					omegaInitial = controlStatements$Omega, 
					sigmaInitial = controlStatements$Sigma,
					omegaFinal = omegaFinal,
					sigmaFinal = sigmaFinal,
					thetaFinal = thetaFinal,
					objectiveFinal = objectiveFinal,
					additionalVars = as.data.frame(matrix(ncol = 0, nrow = nDataRows)), 
					nmVersionMajor = versionInfo["major"],
					nmVersionMinor = as.numeric(versionInfo["minor"]), 
					reportStatements = reportContents)
		})
}