bin/npc

   1 #!/usr/bin/perl
   2
   3 use FindBin qw($Bin);
   4 use lib "$Bin/../lib";
   5
   6 # Don't edit the line below, it must look exactly like this.
   7 # Everything above this line will be replaced #
   8
   9 use PsN;
  10 use model;
  11 use tool::npc;
  12 use strict;
  13 use debug;
  14 use Getopt::Long;
  15 use common_options;
  16 use ui;
  17
  18 my $cmd_line = $0 . " " . join( " ", @ARGV );
  19
  20 ## Configure the command line parsing
  21 Getopt::Long::config("auto_abbrev");
  22
  23 my %options;
  24 ## Declare the options
  25
  26 my %required_options = ('samples:i' => 'N' );
  27 my %optional_options = ( 'stratify_on:s' => 'column',
  28                          'no_of_strata:i' => 'N',
  29                          'lst:s' => 'file',
  30                          'msfo:s' => 'file',
  31                          'dv:s' => 'variable',
  32                          'unstable_override_estimation:i' => '1');
  33
  34 my $res = GetOptions( \%options,
  35                       @common_options::get_opt_strings,
  36                       keys(%required_options),
  37                       keys(%optional_options) );
  38 exit unless $res;
  39
  40 common_options::set_globals( \%options, 'npc' );
  41 common_options::get_defaults( \%options, 'npc' );
  42 common_options::sanity_checks( \%options, 'npc' );
  43
  44 my %help_text;
  45
  46 $help_text{Pre_help_message} = <<'EOF';
  47   npc
  48
  49     Perl script for Numerical Predictive Check.
  50
  51   Usage:
  52 EOF
  53
  54 $help_text{Options} = <<'EOF';
  55     Options:
  56
  57       The options are given here in their long form. Any option may be
  58       abbreviated to any nonconflicting prefix. The -threads option
  59       may be abbreviated to -t(or even -thr) but -debug may not be
  60       abbreviated to -d because it conflicts with -debug_packages and
  61       -debug_subroutines.
  62
  63       The following options are valid:
  64 EOF
  65
  66 $help_text{-h} = <<'EOF';
  67       -h | -?
  68
  69       With -h or -? npc will print a list of options and exit.
  70 EOF
  71
  72 $help_text{-help} = <<'EOF';
  73       -help
  74
  75       With -help npc will print this, longer, help message.
  76 EOF
  77
  78 $help_text{-samples} = <<'EOF';
  79       -samples=number
  80
  81       Number of simulated datasets to generate, required.
  82       Must be at least 20.
  83 EOF
  84
  85 $help_text{-stratify_on} = <<'EOF';
  86       -stratify_on=COLUMN_HEADER
  87
  88       Header of column to stratify on.
  89       The npc will stratify the data on unique values in the specified
  90       column, and perform separate analyses on each set.
  91 EOF
  92
  93 $help_text{-no_of_strata} = <<'EOF';
  94       -no_of_strata=number
  95
  96       Only allowed together with -stratify_on.
  97       An integer requesting the number of strata.
  98       The number must be equal to or less than the number of unique
  99       values in the stratification column.
 100       If the number is smaller than the number of unique values, the
 101       observations will be grouped so that the number of observations in
 102       each group/strata is approximately equal.
 103 EOF
 104
 105 $help_text{-lst} = <<'EOF';
 106       -lst=file
 107
 108       The npc will update initial parameter estimates in the model to
 109       the final values in the lst-file. Optional parameter.
 110       Cannot be used together with -msfo option nor with a model
 111       containing a $NONPARAMETRIC record.
 112 EOF
 113
 114 $help_text{-lst} = <<'EOF';
 115       -msfo=file
 116
 117       The npc will use the NONMEM state defined in the update file.
 118       Cannot be used together with -lst option.
 119       If the modelfile contains a $NONPARAMETRIC record this parameter
 120       is required, otherwise it is optional.
 121 EOF
 122
 123 $help_text{-dv} = <<'EOF';
 124       -dv=VARIABLE
 125
 126       Name of dependent variable.
 127       Default is DV, but any variable is allowed.
 128       Case sensitive, must be exactly the same case and spelling as in modelfile.
 129       Maximum of 4 letters because of NONMEM limitation, unless either IPRED or IWRES.
 130 EOF
 131
 132 #$help_text{-unstable_override_estimation} = <<'EOF';
 133 #      -unstable_override_estimation=1
 134
 135 #      Only for advanced users.
 136 #      Override the safety checks of the program and refuse estimation when
 137 #      -dv option is used. This option has not been tested and
 138 #      crashes may occur.
 139 #EOF
 140
 141 $help_text{Post_help_message} = <<'EOF';
 142       Also see 'execute -help' for a description of common options.
 143 EOF
 144
 145
 146
 147 common_options::online_help( 'npc', \%options, \%help_text, \%required_options, \%optional_options);
 148
 149 ## Check that we do have a model file
 150 if ( scalar(@ARGV) < 1 ) {
 151   print "A model file must be specified. Use 'npc -h' for help.\n";
 152   exit;
 153 }
 154
 155 if( scalar(@ARGV) > 1 ){
 156   print "NPC can only handle one modelfile. Check that all options begin with".
 157       " '-'.\nUse 'npc -h' for help.\n";die;
 158   exit;
 159 }
 160
 161 if ( defined $options{'no_of_strata'} ){
 162   unless (defined $options{'stratify_on'}){
 163     die "Error: The NPC does not allow option no_of_strata unless a ".
 164         "stratification column has been specified.\n";
 165   }
 166 }
 167
 168 if (defined $options{'msfo'}){
 169   if (defined $options{'extra_files'}){
 170     $options{'extra_files'} .= ','.$options{'msfo'};
 171   }else {
 172     $options{'extra_files'} = $options{'msfo'};
 173   }
 174 }
 175
 176 my $eval_string = common_options::model_parameters(\%options);
 177
 178 my $model = model -> new ( eval( $eval_string ),
 179                            filename                    => $ARGV[0],
 180                            ignore_missing_output_files => 1 ,
 181                            cwres                       => ($options{'dv'} eq 'CWRES'));
 182
 183
 184 my $do_estimation = ((defined $options{'dv'}) ||
 185                      (defined $options{'stratify_on'} &&
 186                       ($options{'stratify_on'} eq 'PRED')));
 187
 188 if (defined $options{'unstable_override_estimation'} &&
 189     $options{'unstable_override_estimation'} == 1 &&
 190     defined $options{'dv'} &&
 191     !(defined $options{'stratify_on'} &&($options{'stratify_on'} eq 'PRED'))
 192     ){
 193   $do_estimation = 0;
 194 }
 195
 196 my $npc = tool::npc ->
 197     new ( eval( $common_options::parameters ),
 198           models             => [ $model ],
 199           stratify_on        => $options{'stratify_on'},
 200           no_of_strata       => $options{'no_of_strata'},
 201           samples            => $options{'samples'},
 202           lst_file           => $options{'lst'},
 203           msfo_file          => $options{'msfo'},
 204           dv                 => $options{'dv'},
 205           do_estimation      => $do_estimation
 206           );
 207
 208 my $restart = ( -e $npc -> {'directory'}."/command.txt" ) ? 1 : 0;
 209 unless ($restart){
 210   open(CMD, ">", $npc -> directory . "/command.txt");
 211   print CMD $cmd_line, "\n";
 212   close(CMD);
 213 }
 214
 215 $npc -> run;
 216 $npc -> print_results;
 217