R/parm.vs.cov.R

In andrewhooker/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/.

## Added by Justin Wilkins
## 9/11/2005
## edited by andrew Hooker fall 2006



#' Parameters plotted against covariates, for Xpose 4
#' 
#' This creates a stack of plots of Bayesian parameter estimates plotted
#' against covariates, and is 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 parameters in the Xpose data object, as specified in
#' \code{object@Prefs@Xvardef$parms}, is plotted against each covariate
#' present, as specified in \code{object@Prefs@Xvardef$covariates}, 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 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{link{xpose.plot.default}}.
#' @return Returns a stack of xyplots and histograms of parameters against
#' covariates.
#' @author E. Niclas Jonsson, Mats Karlsson, Andrew Hooker & Justin Wilkins
#' @seealso \code{\link{xpose.plot.default}},
#' \code{\link{xpose.plot.histogram}}, \code{\link[lattice]{xyplot}},
#' \code{\link[lattice]{histogram}}, \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
#' xpdb <- xpose.data(5)
#' 
#' ## A vanilla plot
#' parm.vs.cov(xpdb)
#' 
#' ## Custom colours and symbols, IDs
#' parm.vs.cov(xpdb, cex=0.6, pch=3, col=1, ids=TRUE)
#' }
#' 
#' @export parm.vs.cov
#' @family specific functions 
"parm.vs.cov" <-
  function(object,
           #xlb  = NULL,
           #ylb  = NULL,
           onlyfirst=TRUE,
           #inclZeroWRES=FALSE,
           #subset=xsubset(object),
           ## abline=c(0,1),
           smooth=TRUE,
           ##abllwd=2,
           #mirror=FALSE,
           #seed  = NULL,
           #prompt = FALSE,
           type="p",
           
           main="Default",
           ...) {

        

    ## is everything in place?
    if (is.null(xvardef("covariates", object))) {
      return(cat("Covariates are not properly set in the database!\n"))
    }
    
    if(is.null(xvardef("parms",object))) {
      return(cat("Parameters are not properly set in the database!\n"))    
    }
    
    ## create enpty list for plots
    number.of.plots <- 0
    for (i in xvardef("parms", object)) {
      for (j in xvardef("covariates", object)) {
        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

    ## big loop (parms)
    for (i in xvardef("parms", object)) {      

      ## small loop (covs
      for (j in xvardef("covariates", object)) {
                
        if(!is.factor(object@Data[[i]])){

          xplot <- xpose.plot.default(j,
                                      i,
                                      object,
                                      main=NULL,
                                      #xlb = xlb,
                                      #ylb = ylb,
                                      ##abline=abline,
                                      ##abllwd=abllwd,
                                      smooth=smooth,
                                      #subset=subset,
                                      type=type,
                                      onlyfirst=onlyfirst,
                                      pass.plot.list=TRUE,
                                      ...)
            
          plot.num <- plot.num+1
          plotList[[plot.num]] <- xplot
        }
      }
    }

    default.plot.title <- "Parameters vs. covariates "
    plotTitle <- xpose.multiple.plot.title(object=object,
                                           plot.text = default.plot.title,
                                           main=main,
                                           ...)

    obj <- xpose.multiple.plot(plotList,plotTitle,...)
    return(obj)

  }