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                          "cross_validate:1" => '0|1',
  28                          "rplots" => '',
  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 common_options::set_globals( \%options );
  38
  39 my %help_text;
  40
  41 $help_text{Pre_help_message} = <<'EOF';
  42   cdd
  43
  44     Perl script for Case-Deletion Diagnostics of NONMEM runs.
  45
  46   Usage:
  47 EOF
  48
  49 $help_text{Description} = <<'EOF';
  50     Description:
  51
  52       The Case Deletion Diagnostics tool is run from the command line
  53       with a few mandatory arguments. CDD is run as a diagnostic after
  54       a model is regarded finished or at least mature enough to run
  55       validation tool on. You need to specify the NONMEM modelfile
  56       with a model that have successful termination. You also have to
  57       specify the number or name of the datafile column on which to
  58       select for deletion. You do so with the case_column option.
  59 EOF
  60
  61 $help_text{Examples} = <<'EOF';
  62     Example:
  63
  64       cdd -model=run89.mod -case_column=10
  65
  66       This will perform a Case Deletion Diagnostic on the model
  67       specified in run89.mod based on the factors in column ten. If,
  68       for example, column ten holds the ids of the seven centers
  69       included in the study, this command will create seven copies of
  70       the dataset, each with individuals included in one specific
  71       center deleted. Say that the centers are numbered 1 to 7. Then
  72       dataset 1 will have individuals from center 1 excluded, dataset
  73       2 individuals from center 2 and so on.
  74 EOF
  75
  76 $help_text{Options} = <<'EOF';
  77     Options:
  78
  79       The options are given here in their long form. Any option may be
  80       abbreviated to any nonconflicting prefix. The -threads option
  81       may be abbreviated to -t(or even -thr) but -debug may not be
  82       abbreviated to -d because it conflicts with -debug_packages and
  83       -debug_subroutines.
  84
  85       The following options are valid:
  86 EOF
  87
  88 $help_text{-h} = <<'EOF';
  89       -h | -?
  90
  91       With -h or -? cdd will print a list of options and exit.
  92 EOF
  93
  94 $help_text{-help} = <<'EOF';
  95       -help
  96
  97       With -help cdd will print this, longer, help message.
  98 EOF
  99
 100 $help_text{-bins} = <<'EOF';
 101       -bins=$number
 102
 103       Sets the number of databins, or cdd datasets, to use. If the
 104       number of unique values, or factors, in the based_on column is
 105       higher than the number of bins then one or more factors will be
 106       deleted in each cdd dataset. Specifying $number as higher than
 107       the number of factors will have no effect. The bin number is
 108       then set to the number of factors.
 109       Default value = Number of unique values in the based_on column.
 110 EOF
 111
 112 $help_text{-selection_method} = <<'EOF';
 113       -selection_method='random' or 'consecutive'
 114
 115       Specifies whether the factors selected for exclusion should be
 116       drawn randomly or consecutively from the datafile.
 117       Default value = 'consecutive'
 118 EOF
 119
 120 $help_text{-case_column} = <<'EOF';
 121        -case_column=column_name|column_number
 122 EOF
 123
 124     $help_text{-rplots} = <<'EOF';
 125       <p class="style2">-rplots</p>
 126
 127       Generate R scripts for making various plots of the result.
 128 EOF
 129
 130 $help_text{Post_help_message} = <<'EOF';
 131       Also see 'execute -help' for a description of common options.
 132 EOF
 133
 134 common_options::online_help( 'cdd', \%options, \%help_text, \%required_options, \%optional_options);
 135
 136 ## Check that we do have a model file
 137 if ( scalar(@ARGV) < 1 ) {
 138   print "A model file must be specified. Use 'cdd -h' for help.\n";
 139   exit;
 140 }
 141
 142 if( scalar(@ARGV) > 1 ){
 143   print "CDD can only handle one modelfile. Use 'cdd -h' for help.\n";die;
 144   exit;
 145 }
 146
 147 unless ( defined $options{'case_column'} ){
 148   print "case_column must be given\n" ;
 149   exit;
 150 }
 151
 152 ui -> category( 'cdd' );
 153 ui -> silent(1) if( $options{'silent'} );
 154
 155 debug -> level( $options{'debug'} );
 156 debug -> package( $options{'debug_package'} );
 157 debug -> subroutine( $options{'debug_subroutine'} );
 158 debug -> warn_with_trace( $options{'warn_with_trace'} );
 159
 160 my $eval_string = common_options::model_parameters(\%options);
 161
 162 my $model = model -> new ( eval( $eval_string ),
 163                            filename                    => $ARGV[0],
 164                            ignore_missing_output_files => 1 );
 165
 166 if( $options{'shrinkage'} ) {
 167   $model -> shrinkage_stats( enabled => 1 );
 168 }
 169
 170 ## Create new Cdd object:
 171 my $cdd = tool::cdd ->
 172     new ( eval( $common_options::parameters ),
 173           models           => [ $model ],
 174           bins             => $options{'bins'},
 175           selection_method => $options{'selection_method'},
 176           case_columns     => $options{'case_column'} );
 177
 178 open(CMD, ">", $cdd -> directory . "/command.txt");
 179 print CMD $cmd_line, "\n";
 180 close(CMD);
 181
 182 if ( $options{'summarize'} ) {
 183   $cdd -> prepare_results();
 184   $cdd -> print_summary;
 185 } else {
 186   $cdd -> run;
 187   $cdd -> prepare_results();
 188   $cdd -> print_results;
 189 #  $cdd -> print_summary;
 190 }
 191
 192 if( $options{'rplots'} ){
 193   $cdd -> create_R_scripts();
 194 }