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, 'cdd' );
  39 common_options::get_defaults( \%options, 'cdd' );
  40 common_options::sanity_checks( \%options, 'cdd' );
  41
  42 my %help_text;
  43
  44 $help_text{Pre_help_message} = <<'EOF';
  45 EOF
  46
  47 $help_text{Description} = <<'EOF';
  48 <h3 class=heading1>Description</h3>
  49
  50       The Case Deletion Diagnostics tool is run using the command from the command line
  51       with a few mandatory arguments. CDD 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 <h3 class=heading1>Examples</h3>
  61
  62       cdd -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       <h3 class=heading1>Options</h3>
  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       <p class="option">-h | -?</p>
  88
  89       With -h or -? cdd will print a list of options and exit.
  90 EOF
  91
  92 $help_text{-help} = <<'EOF';
  93       <p class="option">-help</p>
  94
  95       With -help cdd will print this, longer, help message.
  96 EOF
  97
  98 $help_text{-bins} = <<'EOF';
  99       <p class="option">-bins=$number</p>
 100
 101       Sets the number of databins, or cdd 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 cdd 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       <p class="option">-selection_method='random' or 'consecutive'</p>
 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       <p class="option">-case_column=column_name|column_number</p>
 120
 121       This flag is mandatory. Through this flag you set the column on
 122       which the case-deletion is done. You can either use the name of
 123       the column as specified in the $INPUT record in the model file
 124       or you can use the column number.
 125
 126 EOF
 127
 128 $help_text{-rplots} = <<'EOF';
 129       <p class="option">-rplots</p>
 130
 131       Generate R scripts for making various plots of the result.
 132 EOF
 133
 134 $help_text{-xv} = <<'EOF';
 135       <p class="option">-xv|-noxv</p>
 136
 137       Turns the cross-validation feature on (-xv) or off (-noxv). The
 138       default behavior is to run the cross-validation step.
 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 common_options::online_help( 'cdd', \%options, \%help_text, \%required_options, \%optional_options);
 146
 147 ## Check that we do have a model file
 148 if ( scalar(@ARGV) < 1 ) {
 149   print "A model file must be specified. Use 'cdd -h' for help.\n";
 150   exit;
 151 }
 152
 153 if( scalar(@ARGV) > 1 ){
 154   print "CDD can only handle one modelfile. Use 'cdd -h' for help.\n";die;
 155   exit;
 156 }
 157
 158 unless ( defined $options{'case_column'} ){
 159   print "case_column must be given\n" ;
 160   exit;
 161 }
 162
 163 my $eval_string = common_options::model_parameters(\%options);
 164
 165 my $model = model -> new ( eval( $eval_string ),
 166                            filename                    => $ARGV[0],
 167                            ignore_missing_output_files => 1 );
 168
 169 if( $options{'shrinkage'} ) {
 170   $model -> shrinkage_stats( enabled => 1 );
 171 }
 172
 173 if( $options{'threads'} ){
 174   $options{'threads'} = [1,$options{'threads'}] ;
 175 }
 176
 177 ## Create new Cdd object:
 178 my $cdd = tool::cdd ->
 179     new ( eval( $common_options::parameters ),
 180           models             => [ $model ],
 181           bins               => $options{'bins'},
 182           selection_method   => $options{'selection_method'},
 183           case_columns       => $options{'case_column'},
 184           outside_n_sd_check => $options{'outside_n_sd_check'},
 185           cross_validate     => $options{'xv'} );
 186
 187 open(CMD, ">", $cdd -> directory . "/command.txt");
 188 print CMD $cmd_line, "\n";
 189 close(CMD);
 190
 191 if ( $options{'summarize'} ) {
 192   $cdd -> prepare_results();
 193   $cdd -> print_summary;
 194 } else {
 195   $cdd -> run;
 196   $cdd -> prepare_results();
 197   $cdd -> print_results;
 198 #  $cdd -> print_summary;
 199 }
 200
 201 if( $options{'rplots'} ){
 202   $cdd -> create_R_scripts();
 203 }