Xpose 4 Changelog
-----------------

Latest
  * Fixed bug in xpose.VPC when asking for logx=T (didn't work
    previously).
  * Fixed dOFV.vs.id for when there are ties in individual dOFV drops.

2010-10-23
  * Updated read.nm.tables so that comma separated NONMEM 7 files
    can be read into Xpose.
  * Changing the behaviour of xpose.multiple.plot.default. Now
    multiple plots are returned as objects just like single plots are
    (no automatic printing from the function that created the plot
    list). This is accomplished by defining a new class -
    xpose.multiple.plots - and corresponding print and show methods for
    that class. 
  * Updated xpose.VPC, xpose.VPC.categorical and xpose.VPC.both to
    handle the new format of PsN vpc_results.csv
    files. 
  * xpose.VPC.categorical now has a new option: censored (T or F)
    which will create BLOQ VPC plots when TRUE.  
  * xpose.VPC.both tries to combine continuous and categorical BLOQ
    plots.
  * page numbers can be turned off in multiple page plots using the
    page.numbers option (T or F).



2009-11-27
  * Updated ind.plots(), the function is much more flexible now.
  * Added graphical options to xpose.VPC.categorical()
  * Fixed logy=T option for xpose.VPC(Pi.ci=T,logy=T).
  * Fixed logy=T and logx=T option (bug resulting in error).
  * VPC changed to require that y-axis be continuous as default.
  * Fixed classic version of parm.vs.parm() plot.
  * Fixed runsum(). Previous version had a line between each line in
    model file.
  * Added a new function change.xvardef(), which replaces much of the
    previous change functions. Thanks to Sbastien Bihorel for 
    input which helped create this function.
  * Added the ability to apply functions to the xaxis of plots. The
    function options are now called funx and funy.
  * Added support for reading NONMEM 7 table and output files. 
  * Added functions for odd type (categorical, TTE, count) plots including
    VPCs.
  * Updated handling of PsN vpc output file
  * Updated interpretation of categories in xpose.VPC.categorical()

14-12-2008:
  * cwres.vs.pred.bw() was fixed. Previously cwres.vs.pred.bw() gave the
    same result as cwres.vs.idv.bw(). 
  * Fixed xpose.VPC() bug causing plots to not be created in some
    situations.  
  * Added functionality to xpose.VPC() so that users can define their
    own titles for each subplot if stratification is used in the VPC.
    see ?xpose.VPC for more info.
  * Updated method for opening graphical devices in windows to be
    consistent with the new methods used in R version 2.8.0. 
  * Added functionality to allow the user to plot vertical and
    horizontal lines in histograms.  See ?xpose.panel.histogram for more
    information. 
  * Fixed small bug with xpose.panel.splom(). 

24-10-2008: Minor maintenance release
  * in compute.cwres() a debugging flag had been left in the file
    resulting in R going into debugging mode when this function was
    called. This has been fixed. 

04-10-2008: Maintenance release
  * Added ability to smooth the PI.ci "area" plots so that they match
    the "line" plots.  See 'PI.ci.area.smooth' in
    xpose.pandel.default()
  * Added 'logx' and 'logy' functionality to the PI plots.
  * Changed the par.summary and cov.summary routines and removed
    functions doing almost the same thing (adding that functionality
    to the current functions). 
  * fixed GAM plot problems in xp.plot() and added more support for
    GAM from the command line.
  * Fixed a problem with ind.plots() when the ID variable is not
    called ID.
  * Changed all functions in xpose4specific that began with "abs." to
    begin with "absval." to be consistant with the rules for generic
    function definitions in R.
  * Changed name of add.abs() to add.absval().
  * Changed name of par.summary() to parm.summary().   
  * Changed name of param.vs.cov() to parm.vs.cov().
  * Changed name of param.vs.param() to parm.vs.parm().


12-06-2008: Major release
  * Added functionality for visual predictive checks
  * Added functionality for numerical predictive checks

28-09-2006: Maintenance release
  * Added generic functions xpose.draw.table, xpose.draw.cell, xpose.get.c
      and xpose.get.r for drawing tables using the graphics device (JW)
  * Added specific function param.table to display parameter estimates 
      using the graphics device (e.g. in a PDF file) (JW)
  * Added additional specific functions for:
      - IWRES distribution (histogram) (iwres.dist.hist)
      - IWRES distribution (QQ) (iwres.dist.qq)
      - ETA distribution (histogram) (ranpar.dist.hist)
      - ETA scatterplot matrices (ranpar.splom)
      - ETAs vs covariates (ranpar.vs.cov)
      - Parameter tables on the graphics device (param.table)
  * Updated compute.cwres function so that it would work without xpose 4
      Just 'source' the file (compute.cwres.R) and it should work (AH)
  * fixed problems with the run summary function (AH)
  * added new general class of printing multiple plot objects on the
    same page (AH) 
  * Fixed bug with plotting results of GAM (AH)

21-08-2006: Maintenance release
  * Bugs in 'groups' argument fixed in xpose.plot.default,
      dv.vs.pred.ipred, dv.preds.vs.idv (multiple values of x or
      y not properly handled) (JW)
  * File devices (e.g. pdf, postscript, etc) now work correctly in
      all functions (JW)
  * Bug in multiple-page covariate plots fixed (only the first page 
      would display) (JW)
  * Bug in reading table files could sometimes leave file debris, 
      which could interfere with reading subsequent data - fixed (JW)
  * Bug in covariate checking could sometimes cause plot functions 
      to fail (e.g. abs.wres.vs.pred.by.cov) - fixed (JW)
  * Bug in the classic menu system prevented display of some plots -
      fixed (JW)
  * Bug in the classic menu system prevented display of some plots -
      fixed (JW)
  * Bug in CWRES calculation fixed (AH)
  * Bug in parameter histogram display fixed (JW)
  * Missing values (defaults to -99) now handled correctly (JW)
  * QQ plots no longer display categorical variables (JW)

24-07-2006: Maintenance release
  * Bug in 'subset' argument to individual plots corrected (JW)

21-07-2006: Maintenance release
  * Online documentation cleaned up (JW) 
  * Numerous small bugs fixed (JW)
  * *nix support added (JW)
  * Multipage plots now create stacks of display windows, rather than
      stacks of plots in a single window (JW)
  * Scatterplot matrices added (JW)
  * QQ plots for parameters and covariates added (JW)
  * Generic functions renamed for consistency (JW)
  
07-06-2006: Maintenance release
  * Bugs in CWRES application and documentation fixed (AH)
  * Bugs in histogram functions fixed
      - lack of defined covariates no longer causes crash
      - customization options now work

05-06-2006: Third release ("Midnight Sun")
  * GAM added (AH)
  * CWRES plots and functions added (AH)
  * gam package now required
  * Known bugs corrected

23-04-2006: Second release ("Easter Bunny")
  * SUBSET functionality fixed for all procedures
  * Preferences, summaries and data checkout implemented
  * Box and whisker plots now do what their preferences tell them to
  * 'label' function renamed to 'xlabel' for compatibility
  * Hmisc package now required
  * Many small additions and tweaks
  * R package functionality fixed

17-01-2006: Ind.plots.R updated (AH)

24-12-2005: Initial release ("Father Christmas")
  * Xpose 4 is a completely rewritten version of Xpose 3.1, and so
    everything has changed. 

