# 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/.
## Added by Andrew Hooker
## 21/12/2005
#' Plot parameters vs other parameters
#'
#' This function plots the parameter values stored in an Xpose data object
#' versus each other in a series of graphs. The mirror functionality is
#' available for this function.
#'
#' Each of the parameters in the Xpose data object, as specified in
#' \code{object@Prefs@Xvardef$parms}, is plotted against the rest, creating a
#' stack of plots.
#'
#' A wide array of extra options controlling \code{xyplots} are available. See
#' \code{\link{xpose.plot.default}} and \code{\link{xpose.panel.default}} for
#' details.
#'
#' @param object An xpose.data object.
#' @param onlyfirst Logical value indicating whether only the first row per
#' individual is included in the plot.
#' @param abline Allows for a line of identity.
#' @param smooth Logical value indicating whether an x-y smooth should be
#' superimposed. The default is TRUE.
#' @param type The plot type - defaults to points only.
#' @param main The title of the plot. If \code{"Default"} then a default title
#' is plotted. Otherwise the value should be a string like \code{"my title"} or
#' \code{NULL} for no plot title.
#' @param \dots Other arguments passed to \code{xpose.plot.default}.
#' @return Returns a stack of xyplots and histograms of parameters against
#' parameters.
#' @author Andrew Hooker
#' @keywords methods
#' @examples
#'
#' \dontrun{
#' ## We expect to find the required NONMEM run and table files for run
#' ## 5 in the current working directory
#' xpdb <- xpose.data(5)
#'
#'
#' parm.vs.parm(xpdb)
#'
#'
#' parm.vs.parm(xpdb,mirror=3)
#' }
#'
#' @export parm.vs.parm
#' @family specific functions
"parm.vs.parm" <-
function(object,
#xlb = NULL,
#ylb = NULL,
onlyfirst=TRUE,
#inclZeroWRES=FALSE,
#subset=xsubset(object),
#mirror=FALSE,
#seed = NULL,
#bins = NULL,
#samp = NULL,
abline= FALSE,
smooth=TRUE,
#prompt = FALSE,
type="p",
main="Default",
...) {
## is everything in place?
for (i in xvardef("parms", object)) {
if(is.null(i)) {
cat("Parameters are not properly set in the database!\n")
return()
}
}
## create enpty list for plots
number.of.plots <- 0
for (i in xvardef("parms", object)) {
for (j in xvardef("parms", object)) {
if (j!=i) {
if(!is.factor(object@Data[[i]])){
number.of.plots <- number.of.plots + 1
}
}
}
}
plotList <- vector("list",number.of.plots)
plot.num <- 0 # initialize plot number
## loop over params
for (i in xvardef("parms", object)) {
for (j in xvardef("parms", object)) {
if (j!=i) {
if(!is.factor(object@Data[[i]])){
xplot <- xpose.plot.default(j,
i,
object,
main=NULL,
#xlb = xlb,
#ylb = ylb,
abline=abline,
#abllwd=abllwd,
onlyfirst = onlyfirst,
#inclZeroWRES = inclZeroWRES,
#subset = subset,
smooth=smooth,
type=type,
pass.plot.list=TRUE,
...)
plot.num <- plot.num+1
plotList[[plot.num]] <- xplot
}
}
}
}
default.plot.title <- "Parameters vs. parameters "
plotTitle <- xpose.multiple.plot.title(object=object,
plot.text = default.plot.title,
main=main,
...)
obj <- xpose.multiple.plot(plotList,plotTitle,...)
return(obj)
}
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