Fixed $PRIOR support and bugfix in shrinkage results handling

[PsN.git] / bin / vpc

#!/usr/bin/perl

use FindBin qw($Bin);
use lib "$Bin/../lib";

# Don't edit the line below, it must look exactly like this.
# Everything above this line will be replaced #

use PsN;
use model;
use tool::npc;
use strict;
use debug;
use Getopt::Long;
use common_options;
use ui;

my $cmd_line = $0 . " " . join( " ", @ARGV );

## Configure the command line parsing
Getopt::Long::config("auto_abbrev");

my %options;
## Declare the options

my %required_options = ('samples:i' => 'N');
my %optional_options = ( 'idv:s' => 'independent variable',
                         "stratify_on:s" => 'column' ,
                         'no_of_strata:i' => 'N',
                         'lst:s' => 'file',
                         'msfo:s' => 'file',
                         'bin_by_count:i' => '1|0',
                         'no_of_bins:i' => 'N',
                         'single_bin_size:s' => 'X',
                         'overlap:i' => 'N',
                         'bin_array:s' => 'x1,x2,...',
                         'mirrors:i' => 'N',
                         'dv:s' => 'variable',
                         'unstable_override_estimation:i' => '1');

my $res = GetOptions( \%options,
                      @common_options::get_opt_strings,
                      keys(%required_options),
                      keys(%optional_options) );
exit unless $res;

common_options::set_globals( \%options, 'vpc' );
common_options::get_defaults( \%options, 'vpc' );
common_options::sanity_checks( \%options, 'vpc' );

my %help_text;

$help_text{Pre_help_message} = <<'EOF';
  vpc

    Perl script for Visual Predictive Check.

  Usage:
EOF

$help_text{Options} = <<'EOF';      
    Options:

      The options are given here in their long form. Any option may be
      abbreviated to any nonconflicting prefix. The -threads option
      may be abbreviated to -t(or even -thr) but -debug may not be
      abbreviated to -d because it conflicts with -debug_packages and
      -debug_subroutines.

      The following options are valid:
EOF

$help_text{-h} = <<'EOF';
      -h | -?
      
      With -h or -? vpc will print a list of options and exit.
EOF
      
$help_text{-help} = <<'EOF';      
      -help
      
      With -help vpc will print this, longer, help message.
EOF

$help_text{-samples} = <<'EOF';
      -samples=number

      Number of simulated datasets to generate, required.
      Must be at least 20.
EOF


$help_text{-idv} = <<'EOF';
      -idv=VARIABLE

      Name of independent variable, optional, default TIME.
      The vpc will bin the observations based on the independent 
      variable, either on unique values of the specified variable 
      (default), or according to selected binning options.
EOF

$help_text{-bin_by_count} = <<'EOF';
      -bin_by_count= 1 | 0

      Decide whether binning should be done based on the number of 
      observations (1) in each bin or the width of the binning interval (0).
      Required unless only the independent variable is specified without any
      binning options, then forbidden.
EOF

$help_text{-no_of_bins} = <<'EOF';
      -no_of_bins=N

      Number of bins of approximately equal size to create. Optional.
      The number must be larger than 1.
      If used, the option -bin_by_count is required, while all other
      binning options are forbidden.
EOF

$help_text{-single_bin_size} = <<'EOF';
      -single_bin_size=X

      An scalar specifying the size of individual bins. The number 
      either specifies the number of observations in each bin or 
      the width of the binning interval, depending on whether the 
      option -bin_by_count is 1 or 0. If used, the option 
      -bin_by_count is required and -overlap is optional,
      while all other binning options are forbidden.
EOF

$help_text{-overlap} = <<'EOF';
      -overlap=Y

      An integer specifying the percent overlap between consecutive bins. 
      If used, the options -bin_by_count and -single_bin_size are required,
      while all other binning options are forbidden.
EOF

$help_text{-bin_array} = <<'EOF';
      -bin_array=x1,x2,...
      
      A comma-separated list of either the number of observations in each
      bin or the boundaries between bins, depending on whether the option 
      -bin_by_count is 1 or 0. If binning is done by count, the list 
      must contain at least 2 numbers, otherwise 1 number is enough.
      If used, the option -bin_by_count is required, while all other
      binning options are forbidden.
EOF

$help_text{-stratify_on} = <<'EOF';
      -stratify_on=VARIABLE

      Variable to stratify on. The variable must be independent, i.e. be
      the same for all simulations of a particular observation.
      The vpc will stratify the data on unique values of the specified
      variable, and perform separate analyses on each set.
EOF

$help_text{-no_of_strata} = <<'EOF';
      -no_of_strata=number

      Only allowed together with -stratify_on.
      An integer requesting the number of strata.
      The number must be equal to or less than the number of unique 
      values of the stratification variable.
      If the number is smaller than the number of unique values, the 
      observations will be grouped so that the number of observations in
      each group/strata is approximately equal.
EOF

$help_text{-lst} = <<'EOF';
      -lst=file

      The vpc will update initial parameter estimates in the model to
      the final values in the lst-file. Optional parameter.
      Cannot be used together with -msfo option nor with a model
      containing a $NONPARAMETRIC record.
EOF

$help_text{-lst} = <<'EOF';
      -msfo=file

      The vpc will use the NONMEM state defined in the update file.
      Cannot be used together with -lst option.
      If the modelfile contains a $NONPARAMETRIC record this parameter
      is required, otherwise it is optional.
EOF

$help_text{-mirrors} = <<'EOF';
      -mirrors=N

      Generate output data for N mirror plots.
EOF

$help_text{-dv} = <<'EOF';
      -dv=VARIABLE

      Name of dependent variable.
      Default is DV, but any dependent variable is allowed.
      Case sensitive, must be exactly the same case and spelling as in modelfile.
      Maximum of 4 letters because of NONMEM limitation, unless either IPRED or IWRES.
EOF

#$help_text{-unstable_override_estimation} = <<'EOF';
#      -unstable_override_estimation=1

#      Only for advanced users.
#      Override the safety checks of the program and refuse estimation when
#      -dv option is used. This option has not been tested and
#      crashes may occur.
#EOF

$help_text{Post_help_message} = <<'EOF';
      Also see 'execute -help' for a description of common options.
EOF

common_options::online_help( 'vpc', \%options, \%help_text, \%required_options, \%optional_options);

## Check that we do have a model file
if ( scalar(@ARGV) < 1 ) {
  print "A model file must be specified. Use 'vpc -h' for help.\n";
  exit;
}

if( scalar(@ARGV) > 1 ){
  print "VPC can only handle one modelfile. Check that all options begin with".
      " -.\nUse 'vpc -h' for help.\n";die;
  exit;
}

my @bin_array=();

if ( defined $options{'bin_array'} ){
  foreach my $v (split(/,/,$options{'bin_array'})){
    if (length($v)>0){
      push(@bin_array,$v);
    }
  }
  unless (scalar(@bin_array)>0){
    die "Error: Could not parse list bin_array.\n";
  }     
}

if ( defined $options{'no_of_strata'} ){
  unless (defined $options{'stratify_on'}){
    die "Error: The VPC does not allow option no_of_strata unless a ".
        "stratification column has been specified.\n";
  }     
}

if (defined $options{'msfo'}){
  if (defined $options{'extra_files'}){
    $options{'extra_files'} .= ','.$options{'msfo'};
  }else {
    $options{'extra_files'} = $options{'msfo'};
  }
}

my $eval_string = common_options::model_parameters(\%options);

my $model = model -> new ( eval( $eval_string ),
                           filename                    => $ARGV[0],
                           ignore_missing_output_files => 1,
                           cwres                       => ($options{'dv'} eq 'CWRES'));

my $do_estimation = ((defined $options{'dv'}) ||
                     ((defined $options{'idv'}) && ($options{'idv'} eq 'PRED')) ||
                     (defined $options{'stratify_on'} &&
                      ($options{'stratify_on'} eq 'PRED')));

if (defined $options{'unstable_override_estimation'} &&
    $options{'unstable_override_estimation'} == 1 &&
    defined $options{'dv'} &&
    !((defined $options{'idv'}) && ($options{'idv'} eq 'PRED'))&&
    !(defined $options{'stratify_on'} &&($options{'stratify_on'} eq 'PRED'))
    ){
  $do_estimation = 0;
}


my $vpc = tool::npc -> 
    new ( eval( $common_options::parameters ),
          models             => [ $model ],
          stratify_on        => $options{'stratify_on'},
          no_of_strata       => $options{'no_of_strata'},
          samples            => $options{'samples'},
          lst_file           => $options{'lst'},
          msfo_file          => $options{'msfo'},
          is_vpc             => 1,
          bin_on             => ((defined $options{'idv'})? $options{'idv'} :'TIME'),
          bin_by_count       => $options{'bin_by_count'},
          no_of_bins         => $options{'no_of_bins'},
          single_bin_size    => $options{'single_bin_size'},
          overlap_percent    => $options{'overlap'},
          bin_array          => \@bin_array ,
          mirrors            => $options{'mirrors'},
          dv                 => $options{'dv'},
          do_estimation      => $do_estimation
          );

my $restart = ( -e $vpc -> {'directory'}."/command.txt" ) ? 1 : 0;
unless ($restart){
  open(CMD, ">", $vpc -> directory . "/command.txt");
  print CMD $cmd_line, "\n";
  close(CMD);
}

$vpc -> run;
$vpc -> print_results;