bin/mcs

   1 #!/usr/local/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::mc;
  12 use strict;
  13 use debug;
  14 use Getopt::Long;
  15 use common_options;
  16
  17 my $cmd_line = $0 . " " . join( " ", @ARGV );
  18
  19 ## Configure the command line parsing
  20 Getopt::Long::config("auto_abbrev");
  21
  22 my %options;
  23 ## Declare the options
  24
  25 my %required_options = ( 'case_column:s' => 'column_name|column_number',
  26                          'samples:i' => '100',
  27                          'alternative_model:s' => 'alt.mod' );
  28 my %optional_options = ( "bins:i" => '',
  29                          "selection_method:s" => '\'random\'|\'consecutive\'' );
  30
  31 my $res = GetOptions( \%options,
  32                       @common_options::get_opt_strings,
  33                       keys(%required_options),
  34                       keys(%optional_options) );
  35 exit unless $res;
  36
  37 my %help_text;
  38
  39 $help_text{Pre_help_message} = <<'EOF';
  40   mc
  41
  42     Perl script for Monte-carlo Simulation of Case-Deletion Diagnostics of NONMEM runs.
  43
  44   Usage:
  45 EOF
  46
  47 $help_text{Description} = <<'EOF';
  48     Description:
  49
  50       The Case Deletion Diagnostics tool is run from the command line
  51       with a few mandatory arguments. MC is run as a diagnostic after
  52       a model is regarded finished or at least mature enough to run
  53       validation tool on. You need to specify the NONMEM modelfile
  54       with a model that have successful termination. You also have to
  55       specify the number or name of the datafile column on which to
  56       select for deletion. You do so with the case_column option.
  57 EOF
  58
  59 $help_text{Examples} = <<'EOF';
  60     Example:
  61
  62       mc -model=run89.mod -case_column=10
  63
  64       This will perform a Case Deletion Diagnostic on the model
  65       specified in run89.mod based on the factors in column ten. If,
  66       for example, column ten holds the ids of the seven centers
  67       included in the study, this command will create seven copies of
  68       the dataset, each with individuals included in one specific
  69       center deleted. Say that the centers are numbered 1 to 7. Then
  70       dataset 1 will have individuals from center 1 excluded, dataset
  71       2 individuals from center 2 and so on.
  72 EOF
  73
  74 $help_text{Options} = <<'EOF';
  75     Options:
  76
  77       The options are given here in their long form. Any option may be
  78       abbreviated to any nonconflicting prefix. The -threads option
  79       may be abbreviated to -t(or even -thr) but -debug may not be
  80       abbreviated to -d because it conflicts with -debug_packages and
  81       -debug_subroutines.
  82
  83       The following options are valid:
  84 EOF
  85
  86 $help_text{-h} = <<'EOF';
  87       -h | -?
  88
  89       With -h or -? mc will print a list of options and exit.
  90 EOF
  91
  92 $help_text{-help} = <<'EOF';
  93       -help
  94
  95       With -help mc will print this, longer, help message.
  96 EOF
  97
  98 $help_text{-bins} = <<'EOF';
  99       -bins=$number
 100
 101       Sets the number of databins, or mc datasets, to use. If the
 102       number of unique values, or factors, in the based_on column is
 103       higher than the number of bins then one or more factors will be
 104       deleted in each mc dataset. Specifying $number as higher than
 105       the number of factors will have no effect. The bin number is
 106       then set to the number of factors.
 107       Default value = Number of unique values in the based_on column.
 108 EOF
 109
 110 $help_text{-selection_method} = <<'EOF';
 111       -selection_method='random' or 'consecutive'
 112
 113       Specifies whether the factors selected for exclusion should be
 114       drawn randomly or consecutively from the datafile.
 115       Default value = 'consecutive'
 116 EOF
 117
 118 $help_text{-case_column} = <<'EOF';
 119        -case_column=column_name|column_number
 120 EOF
 121
 122 $help_text{Post_help_message} = <<'EOF';
 123       Also see 'execute -help' for a description of common options.
 124 EOF
 125
 126 common_options::online_help( 'mc', \%options, \%help_text, \%required_options, \%optional_options);
 127
 128 debug -> level( $options{'debug'} );
 129 debug -> package( $options{'debug_package'} );
 130 debug -> subroutine( $options{'debug_subroutine'} );
 131 debug -> warn_with_trace( $options{'warn_with_trace'} );
 132
 133 ## Check that we do have a model file
 134 if ( scalar(@ARGV) < 1 ) {
 135   print "A model file must be specified. Use 'mc -h' for help.\n";
 136   exit;
 137 }
 138
 139 if( scalar(@ARGV) > 1 ){
 140   print "MC can only handle one modelfile. Use 'mc -h' for help.\n";die;
 141   exit;
 142 }
 143
 144 unless ( defined $options{'alternative_model'} ){
 145   print "alternative_model must be given\n" ;
 146   exit;
 147 }
 148
 149 unless ( defined $options{'samples'} ){
 150   print "samples must be given\n" ;
 151   exit;
 152 }
 153
 154 ui -> category( 'mc' );
 155 ui -> silent(1) if( $options{'silent'} );
 156
 157 my $eval_string = common_options::model_parameters(\%options);
 158
 159 my $model = model -> new ( eval( $eval_string ),
 160                            filename                    => $ARGV[0],
 161                            ignore_missing_output_files => 1 );
 162
 163 my $alternative_model = model ->
 164     new ( eval( $eval_string ),
 165           filename                    => $options{'alternative_model'},
 166           ignore_missing_output_files => 1 );
 167
 168 ## Create new Mc object:
 169 my $mc = tool::mc ->
 170     new ( eval( $common_options::parameters ),
 171           models             => [ $model ],
 172           alternative_models => [ $alternative_model ],
 173           samples            => $options{'samples'} );
 174
 175 open(CMD, ">", $mc -> directory . "/command.txt");
 176 print CMD $cmd_line, "\n";
 177 close(CMD);
 178
 179 $mc -> run;
 180 $mc -> print_results;
 181