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 = ( 'samples:i' => '100');
  26 my %optional_options = ( 'alternative_model:s' => 'alt1.mod,alt2.mod,...',
  27                          "bins:i" => '',
  28                          "selection_method:s" => '\'random\'|\'consecutive\'' );
  29
  30 my $res = GetOptions( \%options,
  31                       @common_options::get_opt_strings,
  32                       keys(%required_options),
  33                       keys(%optional_options) );
  34 exit unless $res;
  35
  36 my %help_text;
  37
  38 $help_text{Pre_help_message} = <<'EOF';
  39   mc
  40
  41     Perl script for Monte-Carlo Simulation of NONMEM runs.
  42
  43   Usage:
  44 EOF
  45
  46 $help_text{Options} = <<'EOF';
  47     Options:
  48
  49       The options are given here in their long form. Any option may be
  50       abbreviated to any nonconflicting prefix. The -threads option
  51       may be abbreviated to -t(or even -thr) but -debug may not be
  52       abbreviated to -d because it conflicts with -debug_packages and
  53       -debug_subroutines.
  54
  55       The following options are valid:
  56 EOF
  57
  58 $help_text{-h} = <<'EOF';
  59       -h | -?
  60
  61       With -h or -? mc will print a list of options and exit.
  62 EOF
  63
  64 $help_text{-help} = <<'EOF';
  65       -help
  66
  67       With -help mc will print this, longer, help message.
  68 EOF
  69
  70 $help_text{-alternative_model} = <<'EOF';
  71       -alternative_model=alt1.mod,alt2.mod,...
  72
  73       List of one or more alternative models to use for estimation
  74       with simulated datasets. The filenames must be comma-separated,
  75       no spaces.
  76 EOF
  77
  78 $help_text{-bins} = <<'EOF';
  79       -bins=$number
  80
  81       Sets the number of databins, or mc datasets, to use. If the
  82       number of unique values, or factors, in the based_on column is
  83       higher than the number of bins then one or more factors will be
  84       deleted in each mc dataset. Specifying $number as higher than
  85       the number of factors will have no effect. The bin number is
  86       then set to the number of factors.
  87       Default value = Number of unique values in the based_on column.
  88 EOF
  89
  90 $help_text{-selection_method} = <<'EOF';
  91       -selection_method='random' or 'consecutive'
  92
  93       Specifies whether the factors selected for exclusion should be
  94       drawn randomly or consecutively from the datafile.
  95       Default value = 'consecutive'
  96 EOF
  97
  98
  99 $help_text{Post_help_message} = <<'EOF';
 100       Also see 'execute -help' for a description of common options.
 101 EOF
 102
 103 common_options::online_help( 'mc', \%options, \%help_text, \%required_options, \%optional_options);
 104
 105 ## Check that we do have a model file
 106 if ( scalar(@ARGV) < 1 ) {
 107   print "A model file must be specified. Use 'mc -h' for help.\n";
 108   exit;
 109 }
 110
 111 if( scalar(@ARGV) > 1 ){
 112   print "MC can only handle one modelfile. Use 'mc -h' for help.\n";die;
 113   exit;
 114 }
 115
 116 unless ( defined $options{'samples'} ){
 117   print "samples must be given\n" ;
 118   exit;
 119 }
 120
 121 ui -> category( 'mc' );
 122 ui -> silent(1) if( $options{'silent'} );
 123
 124 debug -> level( $options{'debug'} );
 125 debug -> package( $options{'debug_package'} );
 126 debug -> subroutine( $options{'debug_subroutine'} );
 127 debug -> warn_with_trace( $options{'warn_with_trace'} );
 128
 129 my $eval_string = common_options::model_parameters(\%options);
 130
 131 my $model = model -> new ( eval( $eval_string ),
 132                            filename                    => $ARGV[0],
 133                            ignore_missing_output_files => 1 );
 134
 135
 136 my @alternatives=();
 137
 138 if ( defined $options{'alternative_model'} ){
 139     #split string, assume comma separated
 140     foreach my $altfile (split(/,/,$options{'alternative_model'})){
 141         if (length($altfile)>0){
 142             my $alternative_model = model ->
 143                 new ( eval( $eval_string ),filename => $altfile,ignore_missing_output_files => 1 );
 144             push(@alternatives,$alternative_model);
 145         }
 146     }
 147     if (scalar(@alternatives)<1){
 148         die "Error: Option alternative_model used, but list of filenames could not be parsed.\n";
 149     }
 150 }else{
 151     print "No alternative model given, will only estimate original model.\n" ;
 152
 153 }
 154
 155 my $mc = tool::mc ->
 156     new ( eval( $common_options::parameters ),
 157           models             => [ $model ],
 158           alternative_models => \@alternatives,
 159           samples            => $options{'samples'} );
 160 open(CMD, ">", $mc -> directory . "/command.txt");
 161 print CMD $cmd_line, "\n";
 162 close(CMD);
 163
 164 $mc -> run;
 165 $mc -> print_results;
 166