bin/sse

   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::sse;
  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_models:s' => 'alt1.mod,alt2.mod,...',
  27                          'ref_ofv:i' => '500',
  28                          'parallel_simulations:i' => '1',
  29                          'estimate_simulation!' => '1' );
  30                          #"bins:i" => '',
  31                          #"selection_method:s" => '\'random\'|\'consecutive\'' );
  32
  33 my $res = GetOptions( \%options,
  34                       @common_options::get_opt_strings,
  35                       keys(%required_options),
  36                       keys(%optional_options) );
  37 exit unless $res;
  38
  39 my %help_text;
  40
  41 $help_text{Pre_help_message} = <<'EOF';
  42   sse
  43
  44     Perl script for Stochastic Simulation and Estimation of NONMEM models.
  45
  46   Usage:
  47 EOF
  48
  49 $help_text{Options} = <<'EOF';
  50     Options:
  51
  52       The options are given here in their long form. Any option may be
  53       abbreviated to any nonconflicting prefix. The -threads option
  54       may be abbreviated to -t(or even -thr) but -debug may not be
  55       abbreviated to -d because it conflicts with -debug_packages and
  56       -debug_subroutines.
  57
  58       The following options are valid:
  59 EOF
  60
  61 $help_text{-h} = <<'EOF';
  62       -h | -?
  63
  64       With -h or -? mc will print a list of options and exit.
  65 EOF
  66
  67 $help_text{-help} = <<'EOF';
  68       -help
  69
  70       With -help mc will print this, longer, help message.
  71 EOF
  72
  73 $help_text{-alternative_models} = <<'EOF';
  74       -alternative_models=alt1.mod,alt2.mod,...
  75
  76       List of one or more alternative models to use for estimation
  77       with simulated datasets. The filenames must be comma-separated,
  78       no spaces.
  79 EOF
  80
  81 $help_text{-samples} = <<'EOF';
  82       -samples=N
  83
  84       The number of simulated datasets to generate.
  85 EOF
  86
  87 $help_text{-estimate_simulation} = <<'EOF';
  88       -estimate_simulation
  89
  90       By default, the simulation model is also used for estimation with
  91       the simulated datasets. The resulting OFV values are used as reference
  92       when evaluating the estimation results of alternative models. By setting
  93       -no-estimate_simulation the estimation of the simulation model is turned
  94       off, and the first alternative model is used as reference instead. See
  95       also -ref_ofv.
  96 EOF
  97
  98 $help_text{-ref_ofv} = <<'EOF';
  99       -ref_ofv=500
 100
 101       Instead of using the OFV values from the estimation of a model as
 102       reference when evaluating the other estimation results,
 103       it is possible to set a fixed reference OFV value. If using ref_ofv,
 104       it is not allowed to also estimate the simulation model.
 105 EOF
 106 $help_text{-parallel_simulations} = <<'EOF';
 107       -parallel_simulations=1
 108
 109       parallel_simulations govern the number of simulations that will
 110       be done in parallel. Normally simulations are quite fast and
 111       need only be run one at a time. See the threads option for
 112       controll over the number of estimations to do in parallel.
 113 EOF
 114
 115 $help_text{Post_help_message} = <<'EOF';
 116       Also see 'execute -help' for a description of common options.
 117 EOF
 118
 119 common_options::online_help( 'sse', \%options, \%help_text, \%required_options, \%optional_options);
 120
 121 ## Check that we do have a model file
 122 if ( scalar(@ARGV) < 1 ) {
 123   print "A simulation model file must be specified. Use 'mc -h' for help.\n";
 124   exit;
 125 }
 126
 127 if( scalar(@ARGV) > 1 ){
 128   print "SSE can only handle one modelfile, you listed: ",join(',',@ARGV),". Use 'mc -h' for help.\n";die;
 129   exit;
 130 }
 131
 132 unless ( defined $options{'samples'} ){
 133   print "samples must be given\n" ;
 134   exit;
 135 }
 136
 137 unless ( defined $options{'clean'} ){
 138   # Clean is by default much stricter in sse
 139   $options{'clean'} = 3;
 140 }
 141
 142 ui -> category( 'mc' );
 143 ui -> silent(1) if( $options{'silent'} );
 144
 145 debug -> level( $options{'debug'} );
 146 debug -> package( $options{'debug_package'} );
 147 debug -> subroutine( $options{'debug_subroutine'} );
 148 debug -> warn_with_trace( $options{'warn_with_trace'} );
 149
 150 my $eval_string = common_options::model_parameters(\%options);
 151
 152 my $model = model -> new ( eval( $eval_string ),
 153                            filename                    => $ARGV[0],
 154                            ignore_missing_output_files => 1 );
 155
 156
 157 my @alternatives=();
 158
 159 if ( defined $options{'alternative_models'} ){
 160   #split string, assume comma separated
 161   foreach my $altfile (split(/,/,$options{'alternative_models'})){
 162     if (length($altfile)>0){
 163       my $alternative_model = model ->
 164           new ( eval( $eval_string ),filename => $altfile,ignore_missing_output_files => 1 );
 165       push(@alternatives,$alternative_model);
 166     }
 167   }
 168   if (scalar(@alternatives)<1){
 169     die "Error: Option alternative_models used, but list of filenames could not be parsed.\n";
 170   }
 171 }else{
 172   print "No alternative model given, will only estimate simulation model.\n" ;
 173
 174 }
 175
 176 my $mc = tool::sse ->
 177     new ( eval( $common_options::parameters ),
 178           estimate_simulation => $options{'estimate_simulation'},
 179           ref_ofv            => $options{'ref_ofv'},
 180           parallel_simulations => $options{'parallel_simulations'},
 181           models             => [ $model ],
 182           top_tool           => 1,
 183           alternative_models => \@alternatives,
 184           samples            => $options{'samples'} );
 185 open(CMD, ">", $mc -> directory . "/command.txt");
 186 print CMD $cmd_line, "\n";
 187 close(CMD);
 188
 189 $mc -> run;
 190 $mc -> prepare_results;
 191 $mc -> print_results;
 192