bin/bootstrap

   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::bootstrap;
  12 use strict;
  13 use debug;
  14 use ui;
  15 use Getopt::Long;
  16 use common_options;
  17 use Data::Dumper;
  18
  19 my $cmd_line = $0 . " " . join( " ", @ARGV );
  20
  21 ## Configure the command line parsing
  22 Getopt::Long::config("auto_abbrev");
  23
  24 ## Declare the options
  25 my %options;
  26
  27 my %required_options = ();
  28 my %optional_options = ("bca"=>'',
  29                         "samples:i"=>'',
  30                         "sample_size:i"=>'',
  31                         "stratify_on:s"=>'',
  32                         "mplots"=>'',
  33                         "skip_minimization_terminated"=>'',
  34                         "skip_covariance_step_terminated"=>'',
  35                         "skip_with_covstep_warnings"=>'',
  36                         "skip_estimate_near_boundary"=>'' );
  37
  38 my $res = GetOptions( \%options,
  39                       @common_options::get_opt_strings,
  40                       keys(%required_options),
  41                       keys(%optional_options) );
  42
  43 exit unless $res;
  44
  45 common_options::set_globals( \%options );
  46
  47 my %help_text;
  48 $help_text{Pre_help_message} = <<'EOF';
  49     <h3 class="heading1">bootstrap</h3>
  50
  51       Perl script for nonparametric boostrap of NONMEM runs.
  52
  53     <h3 class="heading1">Usage:</h3>
  54 EOF
  55
  56     $help_text{Description} = <<'EOF';
  57    <h3 class="heading1">Description:</h3>
  58
  59       The Bootstrap can be used to calculate bias, standard errors and
  60       confidence intervals. It does so by resampling with replacement
  61       from the data, see Efron B, An Introduction to the Bootstrap,
  62       Chap. & Hall, London UK, 1993. To compute standard errors for
  63       all parameters of a model using the non-parametric bootstrap
  64       implemented here, roughly 200 model fits are necessary. To assess
  65       95% confidence intervals approximatly 2000 runs will suffice.
  66 EOF
  67     $help_text{Examples} = <<'EOF';
  68    <h3 class="heading1">Example:</h3>
  69
  70       <p class="style2">bootstrap -samples=200 run89.mod</p>
  71
  72       This will run a non-parametric bootstrap of 200 samples and give
  73       you good estimates of the standard errors of the parameter
  74       estimates. You may get some estimates for the confidence
  75       intervals too, but they will generally not be of high quality.
  76
  77
  78       <p class="style2">bootstrap -samples=2000 -bca run89.mod</p>
  79
  80       This will run a non-parametric bootstrap using the BCa technique
  81       (See An introduction to the bootstrap, Efron, 1993). The BCa is
  82       intended for caclulation of second-order correct confidence
  83       intervals.
  84
  85
  86       <p class="style2">bootstrap -samples=2000 -bca -stratify_on=5 run89.mod </p>
  87
  88       This is the same BCa approach as above but with stratification
  89       on the factors of column five.
  90 EOF
  91
  92     $help_text{Options} = <<'EOF';
  93    <h3 class="heading1">Options:</h3>
  94
  95       The options are given here in their long form. Any option may be
  96       abbreviated to any nonconflicting prefix. The -threads option
  97       may be abbreviated to <span class="style2">-t</span> (or even <span class="style2">-thr</span>) but -<span class="style2">debug</span> may not be
  98       abbreviated to <span class="style2">-d</span> because it conflicts with <span class="style2">-debug_packages</span> and
  99       <span class="style2">-debug_subroutines</span>.
 100
 101       The following options are valid:
 102 EOF
 103
 104     $help_text{-samples} = <<'EOF';
 105       <p class="style2">-samples</p>
 106
 107       The number of bootstrap samples.
 108 EOF
 109
 110     $help_text{-sample_size} = <<'EOF';
 111       <p class="style2">-sample_size</p>
 112
 113       The number of subjects in each bootstrap data set. The default
 114       value is set to the number of individuals in the original data
 115       set.
 116 EOF
 117
 118     $help_text{-bca} = <<'EOF';
 119       <p class="style2">-bca</p>
 120
 121       Using the <span class="style2">-bca </span>option, the bootstrap
 122       utility will calculate the confidence intervals through the BCa
 123       method. The default approach however, is not to use the BCa (see
 124       Efron B, An introduction to the Bootstrap, 1993). The BCa is
 125       intended for calculation of second-order correct confidence
 126       intervals.
 127 EOF
 128
 129     $help_text{-stratify_on} = <<'EOF';
 130       <p class="style2">-stratify_on=integer|string</p>
 131
 132       It may be necessary to use stratification in the resampling
 133       procedure. For example, if the original data consists of two
 134       groups of patients - say 10 patients with full pharmacokinetic
 135       profiles and 90 patients with sparse steady state concentration
 136       measurements - it may be wise to restrict the resampling
 137       procedure to resample within the two groups, producing bootstrap
 138       data sets that all contain 10 rich + 90 sparse data patients but
 139       with different compositions. The default is not to use
 140       stratification. Set <span class="style2">-stratify_on</span> to
 141       the column that defines the two groups. If a string is used with
 142       stratify_on the header in the datafile is used to map the string
 143       to a column number.
 144 EOF
 145
 146     $help_text{-mplots} = <<'EOF';
 147       <p class="style2">-mplots</p>
 148
 149       Generate matlab scripts for making various plots of the result.
 150 EOF
 151     $help_text{Post_help_message} = <<'EOF';
 152       Also see 'execute -help' for a description of common options.
 153 EOF
 154
 155 common_options::online_help('bootstrap',\%options, \%help_text, \%required_options, \%optional_options);
 156
 157
 158 ## Check that we do have a model file
 159 if ( scalar(@ARGV) < 1 ) {
 160   print "A model file must be specified. Use 'bootstrap -h' for help.\n";
 161   exit;
 162 }
 163
 164 if( scalar(@ARGV) > 1 ){
 165   print "Bootstrap can only handle one modelfile. Use 'boostrap -h' for help.\n";
 166   exit;
 167 }
 168
 169 'ui' -> category( 'bootstrap' );
 170 'ui' -> silent(1) if $options{'silent'};
 171
 172 debug -> level( $options{'debug'} );
 173 debug -> package( $options{'debug_package'} );
 174 debug -> subroutine( $options{'debug_subroutine'} );
 175 debug -> warn_with_trace( $options{'warn_with_trace'} );
 176
 177 my $eval_string = common_options::model_parameters(\%options);
 178
 179 my $model = model -> new ( eval( $eval_string ),
 180                            filename                    => @ARGV[0],
 181                            ignore_missing_output_files => 1 );
 182
 183 my $type = defined $options{'bca'} ? 'bca' : undef;
 184
 185 ## Create new Bootstrap object:
 186 my $bs = tool::bootstrap ->
 187   new ( eval( $common_options::parameters ),
 188         models                          => [ $model ],
 189         samples                         => $options{'samples'},
 190         subjects                        => $options{'sample_size'},
 191         type                            => $type,
 192         stratify_on                     => $options{'stratify_on'},
 193         skip_minimization_terminated    => $options{'skip_minimization_terminated'},
 194         skip_covariance_step_terminated => $options{'skip_covariance_step_terminated'},
 195         skip_with_covstep_warnings      => $options{'skip_with_covstep_warnings'},
 196         skip_estimate_near_boundary     => $options{'skip_estimate_near_boundary'} );
 197
 198 open(CMD, ">", $bs -> directory . "/command.txt");
 199 print CMD $cmd_line, "\n";
 200 close(CMD);
 201
 202 if ( $options{'summarize'} ) {
 203   $bs -> prepare_results();
 204   $bs -> print_results();
 205 #  $bs -> print_summary();
 206 } else {
 207   ui -> print(category => 'bootstrap',
 208               message  => "Starting execution of the bootstrap sets.");
 209   $bs -> run;
 210   $bs -> prepare_results();
 211   $bs -> print_results();
 212 #  $bs -> print_summary();
 213 }
 214
 215 if( $options{'mplots'} ){
 216   $bs -> create_matlab_scripts();
 217 }
 218
 219 ui -> print( category => 'bootstrap',
 220              message  => "Done");