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# Xpose 4
# An R-based population pharmacokinetic/
# pharmacodynamic model building aid for NONMEM.
# Copyright (C) 1998-2004 E. Niclas Jonsson and Mats Karlsson.
# Copyright (C) 2005-2008 Andrew C. Hooker, Justin J. Wilkins,
# Mats O. Karlsson and E. Niclas Jonsson.
# Copyright (C) 2009-2010 Andrew C. Hooker, Mats O. Karlsson and
# E. Niclas Jonsson.
# This file is a part of Xpose 4.
# Xpose 4 is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
# as published by the Free Software Foundation, either version 3
# of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
# You should have received a copy of the GNU Lesser General Public License
# along with this program. A copy can be cound in the R installation
# directory under \share\licenses. If not, see http://www.gnu.org/licenses/.
#' Tabulate the population parameter estimates
#'
#' This function provides a summary of the model's parameter estimates and
#' precision.
#'
#'
#' @param object An xpose.data object.
#' @param prompt Ask before printing.
#' @param outfile file to output to (NULL means screen).
#' @param dir Which directory is the NONMEM output file located. \code{""} means
#' the current working directory \code{getwd()}.
#' @return A table summarizing the parameters and their precision.
#' @author Niclas Jonsson, Andrew Hooker & Justin Wilkins
#' @keywords methods
#' @examples
#'
#' od = setwd(tempdir()) # move to a temp directory
#' (cur.files <- dir()) # current files in temp directory
#'
#' simprazExample(overwrite=TRUE) # write files
#' (new.files <- dir()[!(dir() %in% cur.files)]) # what files are new here?
#' xpdb <- xpose.data(1) # read in files to xpose database
#'
#' tabulate.parameters(xpdb)
#'
#' file.remove(new.files) # remove these files
#' setwd(od) # restore working directory
#'
#' @export tabulate.parameters
#' @family data functions
tabulate.parameters <- function(object,prompt=FALSE,outfile=NULL,dir="")
{
if(prompt==TRUE){
listfile=paste("run",object@Runno,".lst",sep="")
## Get the name of the list file to use
cat("Type the name of the output file (0=cancel, return=",
listfile,")\n",sep="")
ans <- readline()
lstfile <- NULL
if(ans==0) {
return()
} else if (ans=="") {
if(is.readable.file(listfile)) {
lstfile <- listfile
}
} else {
if(is.readable.file(ans)) {
lstfile <- listfile
}
}
} else {
lstfile = paste(dir,"run",object@Runno,".lst",sep="")
}
if(is.null(lstfile)) {
cat("The specified file couldn't be found in the current directory.\n")
return()
}
parameter.list <- create.parameter.list(lstfile)
#attach(parameter.list,warn.conflicts=F)
## Set up matrix
if(any(parameter.list$separval!="" & parameter.list$separval!=0)) {
ret.mat <- matrix(0,
nrow=length(parameter.list$parval),
ncol=3,
dimnames=list(c(),c("Parameter","Value","RSE"))
)
ret.mat[,1] <- parameter.list$parnam
ret.mat[,2] <- parameter.list$parval
ret.mat[,3] <- parameter.list$separval
} else {
ret.mat <- matrix(0,
nrow=length(parameter.list$parval),
ncol=2,
dimnames=list(c(),c("Parameter","Value"))
)
ret.mat[,1] <- parameter.list$parnam
ret.mat[,2] <- parameter.list$parval
}
class(ret.mat) <- "char.matrix"
if(prompt==TRUE){
cat("Would you like to export the table(s) as a text file? n(y)\n")
ans <- readline()
} else {
if (is.null(outfile)){
ans = "n"
} else {
ans = "y"
}
}
if(ans != "y") {
Hmisc::print.char.matrix(ret.mat,col.names=TRUE)
}
else {
if(prompt==TRUE || is.null(outfile)){
cat("Please type a filename (excluding the .txt extension):\n"
)
ans <- readline()
} else {
ans <- outfile
}
print(ret.mat, file = paste(ans, ".txt", sep = ""))
}
#detach(parameter.list)
return(cat(""))
}
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