R/cwres.vs.pred.R

In UUPharmacometrics/xpose4: Diagnostics for Nonlinear Mixed-Effect Models

# 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/.



#' Population conditional weighted residuals (CWRES) plotted against population
#' predictions (PRED) for Xpose 4
#' 
#' This is a plot of population conditional weighted residuals (cwres) vs
#' population predictions (PRED), 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.
#' 
#' 
#' Conditional weighted residuals (CWRES) require some extra steps to
#' calculate. See \code{\link{compute.cwres}} for details.
#' 
#' A wide array of extra options controlling xyplots are available. See
#' \code{\link{xpose.plot.default}} and \code{\link{xpose.panel.default}} for
#' details.
#' 
#' @param object An xpose.data object.
#' @param smooth Logical value indicating whether an x-y smooth should be
#' superimposed.  The default is TRUE.
#' @param abline Vector of arguments to the \code{\link[lattice]{panel.abline}}
#' function. No abline is drawn if \code{NULL}.
#' @param \dots Other arguments passed to \code{link{xpose.plot.default}}.
#' @return Returns an xyplot of CWRES vs PRED.
#' @author E. Niclas Jonsson, Mats Karlsson, Andrew Hooker & Justin Wilkins
#' @seealso \code{\link{xpose.plot.default}}, \code{\link[lattice]{xyplot}},
#' \code{\link{xpose.prefs-class}}, \code{\link{compute.cwres}},
#' \code{\link{xpose.data-class}}
#' @keywords methods
#' @examples
#' ## Here we load the example xpose database 
#' xpdb <- simpraz.xpdb
#' 
#' cwres.vs.pred(xpdb)
#' 
#' ## A conditioning plot
#' cwres.vs.pred(xpdb, by="HCTZ")
#' 
#' @export cwres.vs.pred
#' @family specific functions 
cwres.vs.pred <-
  function(object,
           abline=c(0,0),
           #main = NULL,
           #xlb  = NULL,
           #ylb  = NULL,
           #onlyfirst=FALSE,
           #inclZeroWRES=FALSE,
           #subset=xsubset(object),
           #mirror=FALSE,
           #seed  = NULL,
           smooth = TRUE,
           ...) {

    ## check for arguments in function
    if(is.null(check.vars(c("cwres","pred"),
                          object,silent=FALSE))) {      
      return()
    }
    
    xplot <- xpose.plot.default(xvardef("pred",object),
                                xvardef("cwres",object),
                                object,#main=main,
                                  #xlb = xlb,
                                  #ylb=ylb,
                                smooth = smooth,
                                abline=abline,#subset=subset,
                                ...)

      return(xplot)
    }