R/absval.wres.vs.idv.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 value of (C)WRES vs. independent variable plot in Xpose4.
#' 
#' This is a plot of the absolute value of the CWRES (default, other residuals
#' as an option) vs independent variable, a specific function in Xpose 4. It is
#' a wrapper encapsulating arguments to the \code{\link{xpose.plot.default}}
#' function.  Most of the options take their default values from the xpose.data
#' object but may be overridden by supplying them as arguments.
#' 
#' 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 idv the independent variable.
#' @param wres Which weighted residual to use. \code{"Default"} is the CWRES.
#' @param ylb Y-axis label.
#' @param smooth Logical value indicating whether an x-y smooth should be
#' superimposed.  The default is TRUE.
#' @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 \dots Other arguments passed to \code{link{xpose.plot.default}}.
#' @return Returns an xyplot of |CWRES| vs idv (often TIME, defined by
#' \code{\link{xvardef}}).
#' @author Andrew Hooker
#' @seealso \code{\link{xpose.plot.default}},
#' \code{\link{xpose.panel.default}}, \code{\link[lattice]{xyplot}},
#' \code{\link{xpose.prefs-class}}, \code{\link{compute.cwres}},
#' \code{\link{xpose.data-class}} %% ~~objects to See Also as
#' \code{\link{help}}, ~~~
#' @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.wres.vs.idv(xpdb)
#' 
#' ## A conditioning plot
#' absval.wres.vs.idv(xpdb, by="HCTZ")
#' 
#' ## Custom heading and axis labels
#' absval.wres.vs.idv(xpdb, main="Hello World", ylb="|CWRES|", xlb="IDV")
#' 
#' ## Custom colours and symbols
#' absval.wres.vs.idv(xpdb, cex=0.6, pch=3, col=1)
#' 
#' ## using the NPDEs instead of CWRES
#' absval.wres.vs.idv(xpdb,wres="NPDE")
#' 
#' ## subsets
#' absval.wres.vs.idv(xpdb,subset="TIME<10")
#' 
#' 
#' @export absval.wres.vs.idv
#' @family specific functions 
"absval.wres.vs.idv" <-
  function(object,
           idv="idv",
           wres="Default",
           ylb  = "Default",
           smooth       = TRUE,
           idsdir       = "up",
           type         = "p",
           ...) {

    if(is.null(check.vars(idv,object,silent=FALSE))) {
      return()
    }

    if(!is.na(match(wres,"Default"))) {
      if(is.null(check.vars("cwres",object,silent=T))) {
        if(is.null(check.vars("wres",object,silent=F))){
          return()
        }else{
          wres="wres"
        }
      } else {
        wres = "cwres"
      }
    } else {
      if(is.null(check.vars(wres,object,silent=FALSE))) {
        return()
      }
    }
    
    
    if(is.null(xvardef(idv,object))){
      xvar <- idv
    }else{
      xvar <- xvardef(idv,object)
    }
    if(is.null(xvardef(wres,object))){
      yvar <- wres
    }else{
      yvar <- xvardef(wres,object)
    }

    if(!is.na(match(ylb,"Default"))) {
      ylb <- paste("|",yvar, "|", sep="")
    } 
    
    xplot <- xpose.plot.default(xvar,
                                yvar,
                                object,
                                ylb=ylb,
                                funy="abs",
                                idsdir=idsdir,
                                smooth=smooth,
                                type = type,
                                ...)
    
    return(xplot)
  }