R/absval.iwres.vs.ipred.by.cov.R

In 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/.



#' Absolute individual weighted residuals vs individual predictions,
#' conditioned on covariates, for Xpose 4
#' 
#' This is a plot of absolute individual weighted residuals (|IWRES|) 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 xyplots are available. See
#' \code{\link{xpose.plot.default}} for details.
#' 
#' @param object An xpose.data object.
#' @param ylb A string giving the label for the y-axis. \code{NULL} if none.
#' @param idsdir Direction for displaying point labels. The default is "up",
#' since we are displaying absolute values.
#' @param type Type of plot. The default is points only ("p"), but lines ("l")
#' and both ("b") are also available.
#' @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 \dots Other arguments passed to \code{link{xpose.plot.default}}.
#' @return Returns a stack of xyplots of |IWRES| vs IPRED, conditioned by
#' covariates.
#' @author E. Niclas Jonsson, Mats Karlsson, Andrew Hooker & Justin Wilkins
#' @seealso \code{\link{absval.iwres.vs.ipred}},
#' \code{\link{xpose.plot.default}}, \code{\link[lattice]{xyplot}},
#' \code{\link{xpose.prefs-class}}, \code{\link{xpose.data-class}}
#' @keywords methods
#' @examples
#' 
#' \dontrun{
#' ## We expect to find the required NONMEM run and table files for run
#' ## 5 in the current working directory
#' xpdb5 <- xpose.data(5)
#' 
#' ## Here we load the example xpose database 
#' data(simpraz.xpdb)
#' xpdb <- simpraz.xpdb
#' 
#' ## A vanilla plot
#' absval.iwres.vs.ipred.by.cov(xpdb)
#' 
#' ## Custom axis labels
#' absval.iwres.vs.ipred.by.cov(xpdb, ylb="|IWRES|", xlb="IPRED")
#' 
#' ## Custom colours and symbols, no IDs
#' absval.iwres.vs.ipred.by.cov(xpdb, cex=0.6, pch=3, col=1, ids=FALSE)
#' }
#' @export absval.iwres.vs.ipred.by.cov
#' @family specific functions 
"absval.iwres.vs.ipred.by.cov" <-
  function(object,
           
           #xlb  = NULL,
           ylb  = "|IWRES|",
           #onlyfirst=FALSE,
           #inclZeroWRES=FALSE,
           #subset=xsubset(object),
           #mirror=FALSE,
           #seed  = NULL,
           idsdir="up",
           type="p",
           smooth=TRUE,
           #prompt = TRUE,
           main="Default",
           ...) {

    if(is.null(xvardef("iwres",object)) ||
       is.null(xvardef("ipred",object))) {
      
      return(cat("The required (IWRES and IPRED) variables are not set in the database!\n"))
    }
    
    if(any(is.null(xvardef("covariates",object)))) {
      
      return(cat("There are no covariates defined in the database!\n"))
    }

    
    ## create list for plots
    number.of.plots <- 0
    for (i in xvardef("covariates", object)) {
      number.of.plots <- number.of.plots + 1
    }
    plotList <- vector("list",number.of.plots)
    plot.num <- 0 # initialize plot number

    
    for (i in xvardef("covariates", object)) {

      xplot <- xpose.plot.default(xvardef("ipred",object),
                                  xvardef("iwres",object),
                                  object,
                                  main=NULL,
                                  funy="abs",
                                  #xlb = xlb,
                                  ylb=ylb,
                                  idsdir=idsdir,
                                  type=type,
                                  smooth=smooth,
                                  by=i,
                                  pass.plot.list=TRUE,
                                  #subset=subset,
                                  ...)
      plot.num <- plot.num+1
      plotList[[plot.num]] <- xplot
    }
    

    default.plot.title <- paste("|",xlabel(xvardef("iwres",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)
  
  }