# 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/.
#' Dependent variable vs individual predictions, conditioned on covariates, for
#' Xpose 4
#'
#' This is a plot of dependent variable (DV) vs individual predictions (IPRED)
#' conditioned by covariates, a specific function in Xpose 4. It is a wrapper
#' encapsulating arguments to the \code{xpose.plot.default} function. Most of
#' the options take their default values from xpose.data object but may be
#' overridden by supplying them as arguments.
#'
#' Each of the covariates in the Xpose data object, as specified in
#' \code{object@Prefs@Xvardef$Covariates}, is evaluated in turn, creating a
#' stack of plots.
#'
#' A wide array of extra options controlling \code{\link[lattice]{xyplot}} are
#' available. See \code{\link{xpose.plot.default}} and
#' \code{\link{xpose.panel.default}} for details.
#'
#' @param object An xpose.data object.
#' @param abline Vector of arguments to the \code{\link[lattice]{panel.abline}}
#' function. No abline is drawn if \code{NULL}.
#' @param smooth Logical value indicating whether an x-y smooth should be
#' superimposed. The default is TRUE.
#' @param main The title of the plot. If \code{"Default"} then a default title
#' is plotted. Otherwise the value should be a string like \code{"my title"} or
#' \code{NULL} for no plot title.
#' @param covs A vector of covariates to use in the plot. If "Default" the
#' the covariates defined in \code{object@Prefs@Xvardef$Covariates} are used.
#' @param \dots Other arguments passed to \code{link{xpose.plot.default}}.
#' @return Returns a stack of \code{xyplot}s of DV vs IPRED, conditioned on
#' covariates.
#' @author E. Niclas Jonsson, Mats Karlsson, Andrew Hooker & Justin Wilkins
#' @seealso \code{\link{dv.vs.ipred}}, \code{\link{xpose.plot.default}},
#' \code{\link{xpose.panel.default}}, \code{\link[lattice]{xyplot}},
#' \code{\link{xpose.prefs-class}}, \code{\link{xpose.data-class}}
#' @keywords methods
#' @examples
#' dv.vs.ipred.by.cov(simpraz.xpdb, covs=c("HCTZ","WT"), max.plots.per.page=2)
#'
#' @export dv.vs.ipred.by.cov
#' @family specific functions
dv.vs.ipred.by.cov <- function(
object,
covs="Default",
#xlb = NULL,
#ylb = NULL,
#onlyfirst=FALSE,
#inclZeroWRES=FALSE,
#subset=xsubset(object),
#mirror=FALSE,
#seed = NULL,
abline = c(0,1),
#abllwd = object@Prefs@Graph.prefs$abllwd,
#abllty = object@Prefs@Graph.prefs$abllty,
#ablcol = object@Prefs@Graph.prefs$ablcol,
#prompt = FALSE,
smooth=TRUE,
#main=NULL,
#samp = NULL,
#max.plots.per.page=1,
#scales=list(),
#aspect = object@Prefs@Graph.prefs$aspect,#"fill"
#mirror.aspect="fill",
#pass.plot.list=FALSE,
#x.cex=NULL,
#y.cex=NULL,
#main.cex=NULL,
main="Default",
...)
{
## Make sure we have the necessary variables defined in the
## object.
if(is.null(check.vars(c("dv","ipred"),object))) return(NULL)
# handle covs argument
if(all(covs == "Default")) {
if(is.null(check.vars(c("covariates"),object))) return(NULL)
covs <- xvardef("covariates", object)
} else {
if(is.null(check.vars(covs,object))) return(NULL)
}
## create plot list
plotList <- vector("list",length(covs))
plot.num <- 0 # initialize plot number
for (i in covs) {
xplot <- xpose.plot.default(xvardef("ipred",object),
xvardef("dv",object),
#xlb = xlb,
#ylb = ylb,
abline=abline,
#abllwd=abllwd,
#scales=scales,
#aspect=aspect,
object,
main=NULL,
by=i,
#subset=subset,
smooth=smooth,
#samp=samp,
pass.plot.list=TRUE,
...)
plot.num <- plot.num+1
plotList[[plot.num]] <- xplot
}
default.plot.title <- paste(xlabel(xvardef("dv",object),object)," vs ",
xlabel(xvardef("ipred",object),object),
sep="")
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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