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#' Displays information about output data. Utility function for use with show methods
#' @param object NMProblem object
#' @title Show output table info
#' @return none
#' @author Mango Solutions
showOutput <- function(object)
{
controlStatements <- object@controlStatements
with( controlStatements,
{
# output data will be a list if there were "FIRSTONLY" tables
if(class(object@outputData) != "list")
{
if(all(dim(object@outputData) == c(0,0)))
cat("No output table data\n")
else
{
cat("Output table files: ")
cat(paste(Tables[,"File"], collapse = ","), "\n")
cat("Output table dimensions:\n")
cat(dim(object@outputData), "\n")
cat("Output table columns:\n")
cat(colnames(object@outputData), "\n")
}
}
else
{
cat("Output table files: ")
cat(paste(Tables[,"File"], collapse = ","), "\n")
cat("Output table dimensions:\n")
if(!is.null(object@outputData[["normal.tables"]]))
cat("Normal tables: ", dim(object@outputData[["normal.tables"]]), "\n")
if(!is.null(object@outputData[["firstonly.tables"]]))
cat("FIRSTONLY tables: ", dim(object@outputData[["firstonly.tables"]]), "\n")
cat("Output table columns:\n")
if(!is.null(object@outputData[["normal.tables"]]))
cat("Normal tables: ", colnames(object@outputData[["normal.tables"]]), "\n")
if(!is.null(object@outputData[["firstonly.tables"]]))
cat("FIRSTONLY tables: " , colnames(object@outputData[["firstonly.tables"]]), "\n")
}
})
}
# TODO: reduce amount of copy-paste code in this!
show.NMRun <- function(object)
{
fileInfo <- getFileinfo(object)
cat("Control file: \n")
print(fileInfo["controlFile",])
cat("Output report file: \n")
print(fileInfo["reportFile", ])
cat("Number of problems:", object@numProblems, "\n")
cat("Problems:\n******************* \n")
for(i in seq_along(object@problems))
{
cat("Problem ", i, "\n\n")
show(object@problems[[i]])
}
}
setMethod("show", signature(object = "NMRun"), show.NMRun )
show.NMBasicModel <- function(object)
{
controlStatements <- object@controlStatements
cat("Standard NONMEM problem:\n###############\n")
with( controlStatements,
{
cat("Problem statement: ", Problem, "\n")
cat("Data file:", Data[,"File"], "\n")
cat("Input table dimensions:\n")
cat(dim(object@inputData), "\n")
cat("Input table columns:\n")
cat(colnames(object@inputData), "\n")
if(!is.null(controlStatements$PRED))
{
cat("PRED:\n")
print(PRED)
cat("\n")
}
if(!is.null(controlStatements$PK))
{
cat("PK: \n")
print(PK)
cat("\n")
}
if(!is.null(controlStatements$Error))
{
cat("Error:\n")
print(Error)
}
cat("Parameter estimates:\n###############\n")
cat("THETAs:\n")
print(object@thetaFinal["estimates",])
cat("OMEGAs:\n")
print(object@omegaFinal[,,"estimates"])
cat("SIGMAs:\n")
print(object@sigmaFinal[,,"estimates"])
showOutput(object)
} ) # end with(controlStatements ...
}
setMethod("show", signature(object = "NMBasicModel"), show.NMBasicModel)
show.NMBasicModelNM7 <- function(object)
{
controlStatements <- object@controlStatements
cat("Standard NONMEM (7) problem:\n###############\n")
with( controlStatements,
{
cat("Problem statement: ", Problem, "\n")
cat("Data file:", Data[,"File"], "\n")
cat("Input table dimensions:\n")
cat(dim(object@inputData), "\n")
cat("Input table columns:\n")
cat(colnames(object@inputData), "\n")
if(!is.null(controlStatements$PRED))
{
cat("PRED:\n")
print(PRED)
cat("\n")
}
if(!is.null(controlStatements$PK))
{
cat("PK: \n")
print(PK)
cat("\n")
}
if(!is.null(controlStatements$Error))
{
cat("Error:\n")
print(Error)
}
cat("Methods used: \n")
print(object@methodNames)
cat("Parameter estimates:\n###############\n")
cat("THETAs:\n")
print(object@thetaFinal)
cat("OMEGAs:\n")
print(object@omegaFinal)
cat("SIGMAs:\n")
print(object@sigmaFinal)
showOutput(object)
} ) # end with(controlStatements ...
}
setMethod("show", signature(object = "NMBasicModelNM7"), show.NMBasicModelNM7)
show.NMSimDataGen <- function(object)
{
controlStatements <- object@controlStatements
with(controlStatements,
{
cat("NONMEM data simulation problem without model fitting step:\n###############\n")
cat("Problem statement: ", Problem, "\n")
cat("Data file:", Data[,"File"], "\n")
cat("Input table dimensions:\n")
cat(dim(object@inputData), "\n")
cat("Input table columns:\n")
cat(colnames(object@inputData), "\n")
showOutput(object)
cat("Number of simulations performed: ", Sim["nSub"], "\n")
cat("Seeds: ", na.omit(object@seeds), "\n" )
cat("Initial value of paremeters:\n")
cat("THETAs:\n")
print(object@thetaInitial)
cat("OMEGAs:\n")
print(object@omegaInitial)
cat("SIGMAs:\n")
print(object@sigmaInitial)
} ) # end with(controlStatments,
}
setMethod("show", signature(object = "NMSimDataGen"), show.NMSimDataGen)
show.NMSimModel <- function(object)
{
controlStatements <- object@controlStatements
with(controlStatements,
{
cat("NONMEM data simulation problem:\n###############\n")
cat("Problem statement: ", Problem, "\n")
if(!is.null(controlStatements$PRED))
{
cat("PRED:\n")
print(PRED)
cat("\n")
}
if(!is.null(controlStatements$PK))
{
cat("PK: \n")
print(PK)
cat("\n")
}
cat("Data file:", Data[,"File"], "\n")
cat("Input table dimensions:\n")
cat(dim(object@inputData), "\n")
cat("Input table columns:\n")
cat(colnames(object@inputData), "\n")
showOutput(object)
cat("Number of simulations performed: ", Sim["nSub"], "\n")
cat("Seeds: ", na.omit(object@seeds), "\n" )
# now display estimates
cat("Final estimates for each subproblem:\n\n")
cat("THETAs:\n")
print(object@thetaFinal)
cat("OMEGAs:\n")
print(object@omegaFinal)
cat("SIGMAs:\n")
print(object@sigmaFinal)
cat("Objective function(s): \n")
print(object@objectiveFinal)
})
}
setMethod("show", signature(object = "NMSimModel"), show.NMSimModel)
show.NMSimModelNM7 <- function(object)
{
controlStatements <- object@controlStatements
with(controlStatements,
{
cat("NONMEM (7) data simulation problem:\n###############\n")
cat("Problem statement: ", Problem, "\n")
if(!is.null(controlStatements$PRED))
{
cat("PRED:\n")
print(PRED)
cat("\n")
}
if(!is.null(controlStatements$PK))
{
cat("PK: \n")
print(PK)
cat("\n")
}
cat("Data file:", Data[,"File"], "\n")
cat("Input table dimensions:\n")
cat(dim(object@inputData), "\n")
cat("Input table columns:\n")
cat(colnames(object@inputData), "\n")
showOutput(object)
cat("Number of simulations performed: ", Sim["nSub"], "\n")
cat("Seeds: ", na.omit(object@seeds), "\n" )
cat("Methods used: \n")
print(object@methodNames)
# now display estimates
cat("Final estimates for each subproblem:\n\n")
cat("THETAs:\n")
print(object@thetaFinal)
cat("OMEGAs:\n")
print(object@omegaFinal)
cat("SIGMAs:\n")
print(object@sigmaFinal)
cat("Objective function(s): \n")
print(object@objectiveFinal)
})
}
setMethod("show", signature(object = "NMSimModelNM7"), show.NMSimModelNM7)
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