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!"                  => '-xv|-noxv',
  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   cdd
  45
  46     Perl script for Case-Deletion Diagnostics of NONMEM runs.
  47
  48   Usage:
  49 EOF
  50
  51 $help_text{Description} = <<'EOF';
  52     Description:
  53
  54       The Case Deletion Diagnostics tool is run from the command line
  55       with a few mandatory arguments. CDD is run as a diagnostic after
  56       a model is regarded finished or at least mature enough to run
  57       validation tool on. You need to specify the NONMEM modelfile
  58       with a model that have successful termination. You also have to
  59       specify the number or name of the datafile column on which to
  60       select for deletion. You do so with the case_column option.
  61 EOF
  62
  63 $help_text{Examples} = <<'EOF';
  64     Example:
  65
  66       cdd -model=run89.mod -case_column=10
  67
  68       This will perform a Case Deletion Diagnostic on the model
  69       specified in run89.mod based on the factors in column ten. If,
  70       for example, column ten holds the ids of the seven centers
  71       included in the study, this command will create seven copies of
  72       the dataset, each with individuals included in one specific
  73       center deleted. Say that the centers are numbered 1 to 7. Then
  74       dataset 1 will have individuals from center 1 excluded, dataset
  75       2 individuals from center 2 and so on.
  76 EOF
  77
  78 $help_text{Options} = <<'EOF';
  79     Options:
  80
  81       The options are given here in their long form. Any option may be
  82       abbreviated to any nonconflicting prefix. The -threads option
  83       may be abbreviated to -t(or even -thr) but -debug may not be
  84       abbreviated to -d because it conflicts with -debug_packages and
  85       -debug_subroutines.
  86
  87       The following options are valid:
  88 EOF
  89
  90 $help_text{-h} = <<'EOF';
  91       -h | -?
  92
  93       With -h or -? cdd will print a list of options and exit.
  94 EOF
  95
  96 $help_text{-help} = <<'EOF';
  97       -help
  98
  99       With -help cdd will print this, longer, help message.
 100 EOF
 101
 102 $help_text{-bins} = <<'EOF';
 103       -bins=$number
 104
 105       Sets the number of databins, or cdd datasets, to use. If the
 106       number of unique values, or factors, in the based_on column is
 107       higher than the number of bins then one or more factors will be
 108       deleted in each cdd dataset. Specifying $number as higher than
 109       the number of factors will have no effect. The bin number is
 110       then set to the number of factors.
 111       Default value = Number of unique values in the based_on column.
 112 EOF
 113
 114 $help_text{-selection_method} = <<'EOF';
 115       -selection_method='random' or 'consecutive'
 116
 117       Specifies whether the factors selected for exclusion should be
 118       drawn randomly or consecutively from the datafile.
 119       Default value = 'consecutive'
 120 EOF
 121
 122 $help_text{-case_column} = <<'EOF';
 123        -case_column=column_name|column_number
 124 EOF
 125
 126     $help_text{-rplots} = <<'EOF';
 127       <p class="style2">-rplots</p>
 128
 129       Generate R scripts for making various plots of the result.
 130 EOF
 131
 132 $help_text{Post_help_message} = <<'EOF';
 133       Also see 'execute -help' for a description of common options.
 134 EOF
 135
 136 common_options::online_help( 'cdd', \%options, \%help_text, \%required_options, \%optional_options);
 137
 138 ## Check that we do have a model file
 139 if ( scalar(@ARGV) < 1 ) {
 140   print "A model file must be specified. Use 'cdd -h' for help.\n";
 141   exit;
 142 }
 143
 144 if( scalar(@ARGV) > 1 ){
 145   print "CDD can only handle one modelfile. Use 'cdd -h' for help.\n";die;
 146   exit;
 147 }
 148
 149 unless ( defined $options{'case_column'} ){
 150   print "case_column must be given\n" ;
 151   exit;
 152 }
 153
 154 ui -> category( 'cdd' );
 155 ui -> silent(1) if( $options{'silent'} );
 156
 157 debug -> level( $options{'debug'} );
 158 debug -> package( $options{'debug_package'} );
 159 debug -> subroutine( $options{'debug_subroutine'} );
 160 debug -> warn_with_trace( $options{'warn_with_trace'} );
 161
 162 my $eval_string = common_options::model_parameters(\%options);
 163
 164 my $model = model -> new ( eval( $eval_string ),
 165                            filename                    => $ARGV[0],
 166                            ignore_missing_output_files => 1 );
 167
 168 if( $options{'shrinkage'} ) {
 169   $model -> shrinkage_stats( enabled => 1 );
 170 }
 171
 172 if( $options{'threads'} ){
 173   $options{'threads'} = [1,$options{'threads'}] ;
 174 }
 175
 176 ## Create new Cdd object:
 177 my $cdd = tool::cdd ->
 178     new ( eval( $common_options::parameters ),
 179           models             => [ $model ],
 180           bins               => $options{'bins'},
 181           selection_method   => $options{'selection_method'},
 182           case_columns       => $options{'case_column'},
 183           outside_n_sd_check => $options{'outside_n_sd_check'},
 184           cross_validate     => $options{'xv'} );
 185
 186 open(CMD, ">", $cdd -> directory . "/command.txt");
 187 print CMD $cmd_line, "\n";
 188 close(CMD);
 189
 190 if ( $options{'summarize'} ) {
 191   $cdd -> prepare_results();
 192   $cdd -> print_summary;
 193 } else {
 194   $cdd -> run;
 195   $cdd -> prepare_results();
 196   $cdd -> print_results;
 197 #  $cdd -> print_summary;
 198 }
 199
 200 if( $options{'rplots'} ){
 201   $cdd -> create_R_scripts();
 202 }