bin/cdd

   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::cdd;
  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 my %optional_options = ( "bins:i"               => '',
  27                          "xv!"                  => '',
  28                          "rplots"               => '',
  29                          "selection_method:s"   => '\'random\'|\'consecutive\'',
  30                          "outside_n_sd_check:f" => '' );
  31
  32 my $res = GetOptions( \%options,
  33                       @common_options::get_opt_strings,
  34                       keys(%required_options),
  35                       keys(%optional_options) );
  36 exit unless $res;
  37
  38 common_options::set_globals( \%options );
  39 common_options::get_defaults( \%options, 'cdd' );
  40
  41 my %help_text;
  42
  43 $help_text{Pre_help_message} = <<'EOF';
  44 EOF
  45
  46 $help_text{Description} = <<'EOF';
  47 <h3 class=heading1>Description</h3>
  48
  49       The Case Deletion Diagnostics tool is run using the command from the command line
  50       with a few mandatory arguments. CDD is run as a diagnostic after
  51       a model is regarded finished or at least mature enough to run
  52       validation tool on. You need to specify the NONMEM modelfile
  53       with a model that have successful termination. You also have to
  54       specify the number or name of the datafile column on which to
  55       select for deletion. You do so with the case_column option.
  56 EOF
  57
  58 $help_text{Examples} = <<'EOF';
  59 <h3 class=heading1>Examples</h3>
  60
  61       cdd -model=run89.mod -case_column=10
  62
  63       This will perform a Case Deletion Diagnostic on the model
  64       specified in run89.mod based on the factors in column ten. If,
  65       for example, column ten holds the ids of the seven centers
  66       included in the study, this command will create seven copies of
  67       the dataset, each with individuals included in one specific
  68       center deleted. Say that the centers are numbered 1 to 7. Then
  69       dataset 1 will have individuals from center 1 excluded, dataset
  70       2 individuals from center 2 and so on.
  71 EOF
  72
  73 $help_text{Options} = <<'EOF';
  74       <h3 class=heading1>Options</h3>
  75
  76       The options are given here in their long form. Any option may be
  77       abbreviated to any nonconflicting prefix. The -threads option
  78       may be abbreviated to -t(or even -thr) but -debug may not be
  79       abbreviated to -d because it conflicts with -debug_packages and
  80       -debug_subroutines.
  81
  82       The following options are valid:
  83 EOF
  84
  85 $help_text{-h} = <<'EOF';
  86       <p class="option">-h | -?</p>
  87
  88       With -h or -? cdd will print a list of options and exit.
  89 EOF
  90
  91 $help_text{-help} = <<'EOF';
  92       <p class="option">-help</p>
  93
  94       With -help cdd will print this, longer, help message.
  95 EOF
  96
  97 $help_text{-bins} = <<'EOF';
  98       <p class="option">-bins=$number</p>
  99
 100       Sets the number of databins, or cdd datasets, to use. If the
 101       number of unique values, or factors, in the based_on column is
 102       higher than the number of bins then one or more factors will be
 103       deleted in each cdd dataset. Specifying $number as higher than
 104       the number of factors will have no effect. The bin number is
 105       then set to the number of factors.
 106       Default value = Number of unique values in the based_on column.
 107 EOF
 108
 109 $help_text{-selection_method} = <<'EOF';
 110       <p class="option">-selection_method='random' or 'consecutive'</p>
 111
 112       Specifies whether the factors selected for exclusion should be
 113       drawn randomly or consecutively from the datafile.
 114       Default value = 'consecutive'
 115 EOF
 116
 117 $help_text{-case_column} = <<'EOF';
 118       <p class="option">-case_column=column_name|column_number</p>
 119
 120       This flag is mandatory. Through this flag you set the column on
 121       which the case-deletion is done. You can either use the name of
 122       the column as specified in the $INPUT record in the model file
 123       or you can use the column number.
 124
 125 EOF
 126
 127 $help_text{-rplots} = <<'EOF';
 128       <p class="option">-rplots</p>
 129
 130       Generate R scripts for making various plots of the result.
 131 EOF
 132
 133 $help_text{-xv} = <<'EOF';
 134       <p class="option">-xv|-noxv</p>
 135
 136       Turns the cross-validation feature on (-xv) or off (-noxv). The
 137       default behavior is to run the cross-validation step.
 138 EOF
 139
 140 $help_text{Post_help_message} = <<'EOF';
 141       Also see 'execute -help' for a description of common options.
 142 EOF
 143
 144 common_options::online_help( 'cdd', \%options, \%help_text, \%required_options, \%optional_options);
 145
 146 ## Check that we do have a model file
 147 if ( scalar(@ARGV) < 1 ) {
 148   print "A model file must be specified. Use 'cdd -h' for help.\n";
 149   exit;
 150 }
 151
 152 if( scalar(@ARGV) > 1 ){
 153   print "CDD can only handle one modelfile. Use 'cdd -h' for help.\n";die;
 154   exit;
 155 }
 156
 157 unless ( defined $options{'case_column'} ){
 158   print "case_column must be given\n" ;
 159   exit;
 160 }
 161
 162 ui -> category( 'cdd' );
 163 ui -> silent(1) if( $options{'silent'} );
 164
 165 debug -> level( $options{'debug'} );
 166 debug -> package( $options{'debug_package'} );
 167 debug -> subroutine( $options{'debug_subroutine'} );
 168 debug -> warn_with_trace( $options{'warn_with_trace'} );
 169
 170 my $eval_string = common_options::model_parameters(\%options);
 171
 172 my $model = model -> new ( eval( $eval_string ),
 173                            filename                    => $ARGV[0],
 174                            ignore_missing_output_files => 1 );
 175
 176 if( $options{'shrinkage'} ) {
 177   $model -> shrinkage_stats( enabled => 1 );
 178 }
 179
 180 if( $options{'threads'} ){
 181   $options{'threads'} = [1,$options{'threads'}] ;
 182 }
 183
 184 ## Create new Cdd object:
 185 my $cdd = tool::cdd ->
 186     new ( eval( $common_options::parameters ),
 187           models             => [ $model ],
 188           bins               => $options{'bins'},
 189           selection_method   => $options{'selection_method'},
 190           case_columns       => $options{'case_column'},
 191           outside_n_sd_check => $options{'outside_n_sd_check'},
 192           cross_validate     => $options{'xv'} );
 193
 194 open(CMD, ">", $cdd -> directory . "/command.txt");
 195 print CMD $cmd_line, "\n";
 196 close(CMD);
 197
 198 if ( $options{'summarize'} ) {
 199   $cdd -> prepare_results();
 200   $cdd -> print_summary;
 201 } else {
 202   $cdd -> run;
 203   $cdd -> prepare_results();
 204   $cdd -> print_results;
 205 #  $cdd -> print_summary;
 206 }
 207
 208 if( $options{'rplots'} ){
 209   $cdd -> create_R_scripts();
 210 }