lib/data_subs.pm

   1 This file contains the code for the subroutines in
   2 Perl-speaks-NONMEMs data module. It is not functional by itself.
   3 The code should be transferred to the module autogenerated by dia2code
   4 using the fill_diacode.pl script.
   5
   6 # {{{ include
   7
   8 start include statements
   9 use Digest::MD5 'md5_hex';
  10 use OSspecific;
  11 use File::Copy "cp";
  12 use Carp;
  13 use Carp qw(cluck);
  14 use Config;
  15 use Math::Random;
  16 use Storable;
  17 use debug;
  18 use ui;
  19 use status_bar;
  20 use Data::Dumper;
  21 use Time::HiRes qw(gettimeofday);
  22 my @primary_column_names = ('ID', 'DATE', 'DAT1', 'DAT2', 'DAT3' ,'L1', 'L2', 'DV', 'MDV', 'RAW_', 'MRG_', 'RPT_', 'TIME', 'DROP', 'SKIP', 'EVID', 'AMT', 'RATE', 'SS', 'II', 'ADDL', 'CMT', 'PCMT', 'CALL');
  23 end include
  24
  25 # }}} include statements
  26
  27 # {{{ description
  28
  29 start description
  30     # The structure of the data class is subject-centric, recognising that
  31     # the subjects included in a study often can be regarded as
  32     # independent. A class for the subject level exists within PsN and is
  33     # called the individual class. A data object consists of at least one
  34     # but probably many individual objects plus optional comments.
  35 end description
  36
  37 # }}} description
  38
  39 # {{{ synopsis
  40
  41 start synopsis
  42     #   use data;
  43     #
  44     #   my $data_obj = data -> new ( filename => 'test040314.dta' );
  45     #
  46     #   $data_obj -> renumber_ascending;
  47     #
  48     #   my $subsets_ref = $data_obj -> case_deletion( bins => 10 );
  49     #
  50     #   my @subsets = @{$subsets_ref};
  51 end synopsis
  52
  53 # }}} synopsis
  54
  55 # {{{ see_also
  56
  57 start see_also
  58     # =begin html
  59     #
  60     # <a HREF="model.html">model</a>, <a HREF="output.html">output</a>,
  61     # <a HREF="tool/modelfit.html">tool::modelfit</a>,
  62     # <a HREF="tool.html">tool</a>
  63     #
  64     # =end html
  65     #
  66     # =begin man
  67     #
  68     # model, output, tool::modelfit, tool
  69     #
  70     # =end man
  71 end see_also
  72
  73 # }}} see_also
  74
  75 # {{{ new
  76
  77 start new
  78       {
  79         # If the column holding the subject identifier is not the
  80         # first, it can be specified using the I<idcolumn> attribute
  81         #
  82         # I<ignoresign> determines which rows that are regarded as
  83         # comments. Corresponds to the IGNORE= option in the $DATA
  84         # record in a NONMEM model file.
  85
  86         $this -> {'use_data_table'} = 0;
  87
  88         ( $this -> {'directory'},
  89           $this -> {'filename'} ) = OSspecific::absolute_path( $this -> {'directory'},
  90                                                                $this->{'filename'} );
  91
  92         debug -> warn( level => 2,
  93                        message => "data -> new: Data object initialized from file: ".
  94                        $this -> full_name );
  95
  96 #       sub register_in_database {
  97 #         my $this = shift;
  98 #         # Backslashes messes up the sql syntax
  99 #         my $file_str = $this->{'filename'};
 100 #         my $dir_str = $this->{'directory'};
 101 #         $file_str =~ s/\\/\//g;
 102 #         $dir_str =~ s/\\/\//g;
 103
 104 #         # md5sum
 105 #         my $md5sum = md5_hex(OSspecific::slurp_file($this-> full_name ));
 106 #         my $dbh = DBI ->
 107 #             connect("DBI:mysql:host=".$PsN::config -> {'_'} -> {'database_server'}.
 108 #                     ";databse=".$PsN::config -> {'_'} -> {'project'},
 109 #                     $PsN::config -> {'_'} -> {'user'},
 110 #                     $PsN::config -> {'_'} -> {'password'},
 111 #                     {'RaiseError' => 1});
 112 #         my $sth;
 113 #         my $sth = $dbh -> prepare( "SELECT data_id FROM ".$PsN::config -> {'_'} -> {'project'}.
 114 #                              ".data ".
 115 #                                    "WHERE filename = '$file_str' AND ".
 116 #                                    "directory = '$dir_str' AND ".
 117 #                                    "md5sum = '".$md5sum."'" );
 118 #         $sth -> execute or debug -> die( message => $sth->errstr ) ;
 119 #         my $select_arr = $sth -> fetchall_arrayref;
 120 #         if ( scalar @{$select_arr} > 0 ) {
 121 #           debug -> warn( level   => 1,
 122 #                          message => "Found an old entry in the database matching the ".
 123 #                          "current data file" );
 124 #           if ( scalar @{$select_arr} > 1 ) {
 125 #             debug -> warn( level   => 1,
 126 #                            message => "Found more than one matching entry in database".
 127 #                            ", using the first" );
 128 #           }
 129 #           $this -> {'data_id'} = $select_arr->[0][0];
 130 #         } else {
 131 #           my ( $date_str, $time_str );
 132 #           if ( $Config{osname} eq 'MSWin32' ) {
 133 #             $date_str = `date /T`;
 134 #             $time_str = ' '.`time /T`;
 135 #           } else {
 136 #             # Assuming UNIX
 137 #             $date_str = `date`;
 138 #           }
 139 #           chomp($date_str);
 140 #           chomp($time_str);
 141 #           my $date_time = $date_str.$time_str;
 142 #           $sth = $dbh -> prepare("INSERT INTO ".$PsN::config -> {'_'} -> {'project'}.
 143 #                              ".data (filename,date,directory,md5sum) ".
 144 #                                  "VALUES ('$file_str', '$date_time', '$dir_str','".
 145 #                                  $md5sum."' )");
 146 #           $sth -> execute;
 147 #           $this -> {'data_id'} = $sth->{'mysql_insertid'};
 148 #         }
 149 #         $sth -> finish;
 150 #         $dbh -> disconnect;
 151 #         }
 152
 153
 154         unless ( ( defined $this -> {'header'} and
 155                    scalar @{$this -> {'header'}} > 0 ) or
 156                  ( defined $this -> {'individuals'} and
 157                    scalar @{$this -> {'individuals'}} > 0 ) ) {
 158           if ( -e $this -> full_name ) {
 159             if ( $this -> {'target'} eq 'mem' ) {
 160 #             &register_in_database( $this ) if ( $PsN::config -> {'_'} -> {'use_database'} and
 161 #                                                 $this -> {'use_data_table'} );
 162               $this -> _read_header;
 163               $this -> _read_individuals;
 164               $this -> {'synced'} = 1;
 165             } else {
 166               $this -> {'synced'} = 0;
 167             }
 168           } else {
 169             debug -> die(message => "No header, individuals, and no file " . $this -> full_name . " on disk.")
 170               unless $this -> {'ignore_missing_files'};
 171             $this ->  {'synced'} = 0;
 172           }
 173         } else {
 174           if ( $this -> {'target'} eq 'mem') {
 175             if ( -e $this -> {'filename'} ) {
 176               $this -> _read_header;
 177 #             &register_in_database if ( $PsN::config -> {'_'} -> {'use_database'} and
 178 #                                        $this -> {'use_data_table'} );
 179               $this -> _read_individuals;
 180               $this -> {'synced'} = 1;
 181             } else {
 182               debug -> die(message => "No file:".$this->{'filename'}." on disk" )
 183                   unless $this -> {'ignore_missing_files'};
 184               $this -> {'synced'} = 0;
 185             }
 186           } else {
 187             $this -> flush;
 188           }
 189         }
 190
 191         if ( $this -> {'synced'} ) {
 192           my $i = 1;
 193           foreach my $head ( @{$this -> {'header'}} ) {
 194             $this -> {'column_head_indices'} -> {$head} = $i;
 195             $i++;
 196           }
 197         }
 198 #       $Data::Dumper::Maxdepth = 3;
 199 #       die Dumper $this -> {'individuals'};
 200       }
 201 end new
 202
 203 # }}} new
 204
 205 # {{{ register_in_database
 206 start register_in_database
 207     if ( $PsN::config -> {'_'} -> {'use_database'} ) {
 208       # Backslashes messes up the sql syntax
 209       my $file_str = $self->{'filename'};
 210       my $dir_str = $self->{'directory'};
 211       $file_str =~ s/\\/\//g;
 212       $dir_str =~ s/\\/\//g;
 213
 214       my $project = $PsN::config -> {'_'} -> {'project'};
 215       # md5sum
 216       my $md5sum = md5_hex(OSspecific::slurp_file($self-> full_name ));
 217
 218       my $dbh = DBI -> connect("DBI:mysql:host=".$PsN::config -> {'_'} -> {'database_server'}.
 219                                ";databse=".$project,
 220                                $PsN::config -> {'_'} -> {'user'},
 221                                $PsN::config -> {'_'} -> {'password'},
 222                                {'RaiseError' => 1});
 223
 224       my $sth;
 225
 226       my $select_arr = [];
 227
 228       if ( not $force ) {
 229         my $sth = $dbh -> prepare( "SELECT data_id FROM ".$project.
 230                                    ".data ".
 231                                    "WHERE filename = '$file_str' AND ".
 232                                    "directory = '$dir_str' AND ".
 233                                    "md5sum = '".$md5sum."'" );
 234         $sth -> execute or debug -> die( message => $sth->errstr ) ;
 235         $select_arr = $sth -> fetchall_arrayref;
 236       }
 237
 238       if ( scalar @{$select_arr} > 0 ) {
 239         'debug' -> warn( level   => 1,
 240                          message => "Found an old entry in the database matching the ".
 241                          "current data file" );
 242         if ( scalar @{$select_arr} > 1 ) {
 243           'debug' -> warn( level   => 1,
 244                            message => "Found more than one data matching entry in database".
 245                            ", using the first" );
 246         }
 247         $self -> {'data_id'} = $select_arr->[0][0];
 248         # Find the id's
 249         my $sth = $dbh -> prepare( "SELECT individual_id FROM ".$project.".data_individual ".
 250                                    "WHERE data_id = '".$self -> {'data_id'}."'" );
 251         $sth -> execute or debug -> die( message => $sth->errstr ) ;
 252         my $id_arr = $sth -> fetchall_arrayref;
 253         map( $_ = $_ -> [0], @{$id_arr} );
 254         $self -> {'individual_ids'} = $id_arr;
 255       } elsif ( defined $self -> {'individuals'} ) {
 256         my ( $date_str, $time_str );
 257         if( $Config{osname} eq 'MSWin32' ){
 258           $date_str = `date /T`;
 259           $time_str = ' '.`time /T`;
 260         } else {
 261           # Assuming UNIX
 262           $date_str = `date`;
 263         }
 264         chomp($date_str);
 265         chomp($time_str);
 266         my $date_time = $date_str.$time_str;
 267         my ( $columns, $values );
 268         my $res_str = $resampled ? '1' : '0';
 269         if ( defined $model_id ) {
 270           $columns = '(model_id, filename, date, directory, md5sum, resampled)';
 271           $values = "('$model_id', '$file_str', '$date_time', '$dir_str','".
 272               $md5sum."', '$res_str' )";
 273         } else {
 274           $columns = '(filename, date, directory, md5sum, resampled)';
 275           $values = "('$file_str', '$date_time', '$dir_str','".$md5sum."', '$res_str' )";
 276         }
 277         $sth = $dbh -> prepare("INSERT INTO ".$PsN::config -> {'_'} -> {'project'}.
 278                                ".data $columns VALUES $values");
 279         $sth -> execute;
 280         $self -> {'data_id'} = $sth->{'mysql_insertid'};
 281
 282         if ( defined $self -> {'data_id'} ) {
 283           my $values;
 284           my $columns = "( id_key, id )";
 285           if( $#individual_ids >= 0 ) {
 286             $self -> register_di_relation( individual_ids => \@individual_ids );
 287           } else {
 288             my $inds = scalar @{$self -> {'individuals'}};
 289             $dbh -> do( "LOCK TABLES ".$PsN::config -> {'_'} -> {'project'}.
 290                         ".individual WRITE" );
 291 #           $sth = $dbh -> prepare( "SELECT MAX(individual_id)".
 292 #                                   " FROM ".$PsN::config -> {'_'} -> {'project'}.
 293 #                                   ".individual" );
 294             $dbh -> do( 'USE '.$PsN::config -> {'_'} -> {'project'} );
 295             $sth = $dbh -> prepare( "SHOW TABLE STATUS LIKE 'individual'" );
 296             $sth -> execute or debug -> die( message => $sth->errstr ) ;
 297             my $select_arr = $sth -> fetchall_arrayref;
 298             my $first_id_id = $select_arr -> [0][10] ?
 299                 $select_arr -> [0][10] : 0;
 300 #           my $first_id_id = $select_arr -> [0][0] ? ($select_arr -> [0][0] + 1) : 0;
 301             my $last_id_id = $first_id_id + $inds - 1;
 302             for( my $i = 0; $i < $inds; $i++ ) {
 303               if( defined $self -> {'individuals'}[$i] ) {
 304                 my $id_id = $self -> {'individuals'}[$i] -> idnumber;
 305                 $values = $values."," if ( defined $values );
 306                 $values = $values."( $i, $id_id )";
 307               }
 308             }
 309             $sth = $dbh -> prepare( "INSERT INTO ".$PsN::config -> {'_'} -> {'project'}.
 310                                     ".individual $columns VALUES $values" );
 311             $sth -> execute;
 312             $dbh -> do( "UNLOCK TABLES" );
 313             @individual_ids = ($first_id_id .. $last_id_id);
 314             $self -> register_di_relation( individual_ids => \@individual_ids );
 315           }
 316           $self -> {'individual_ids'} = \@individual_ids;
 317         }
 318         $sth -> finish;
 319         $dbh -> disconnect;
 320       }
 321       $data_id = $self -> {'data_id'}; # return the data_id
 322     }
 323 end register_in_database
 324 # }}} register_in_database
 325
 326 # {{{ register_di_relation
 327 start register_di_relation
 328   if ( $PsN::config -> {'_'} -> {'use_database'} and
 329        defined $self -> {'data_id'} and $#individual_ids >= 0 ) {
 330     my $dbh = DBI -> connect("DBI:mysql:host=".$PsN::config -> {'_'} -> {'database_server'}.
 331                              ";databse=".$PsN::config -> {'_'} -> {'project'},
 332                              $PsN::config -> {'_'} -> {'user'},
 333                              $PsN::config -> {'_'} -> {'password'},
 334                              {'raiseerror' => 1});
 335     my $sth;
 336     my $values;
 337     my $columns = "( data_id, individual_id )";
 338     foreach my $individual_id ( @individual_ids ) {
 339       if ( defined $individual_id ) {
 340         $values = $values."," if ( defined $values );
 341         $values = $values."(".$self -> {'data_id'}.", $individual_id )";
 342       }
 343     }
 344     $sth = $dbh -> prepare( "INSERT INTO ".$PsN::config -> {'_'} -> {'project'}.
 345                                ".data_individual $columns VALUES $values" );
 346     $sth -> execute;
 347     $sth -> finish if ( defined $sth );
 348     $dbh -> disconnect;
 349   }
 350 end register_di_relation
 351 # }}} register_di_relation
 352
 353 # {{{ full_name
 354
 355 start full_name
 356       {
 357         $full_name = $self -> {'directory'} . $self -> {'filename'};
 358       }
 359 end full_name
 360
 361 # }}}
 362
 363 # {{{ bootstrap
 364
 365 start bootstrap
 366       {
 367         # The bootstrap method draws I<samples> number of boostrap
 368         # samples from the data set. The I<subjects> arguments
 369         # determines the size of each sample (default equals to the
 370         # number of individuals in the original data set). The method
 371         # returns references to three arrays: I<boot_samples_ref>,
 372         # which holds the bootstrap data sets, I<incl_individuals_ref>
 373         # which holds arrays containing the subject identifiers (ID's)
 374         # for the included individuals of each bootstrap data set and
 375         # I<included_keys_ref> which holds the key or index of the
 376         # included individuals. The key or index is an integer
 377         # starting at 1 for the first individual in the original data
 378         # set and increasing by one for each following.
 379         $self -> synchronize;
 380         my @header      = @{$self -> {'header'}};
 381         my $individuals = $self -> {'individuals'};
 382         my $key_ref;
 383
 384         my $status_bar = status_bar -> new( steps => $samples );
 385         ui -> print( category => 'bootstrap',
 386                      message => $status_bar -> print_step,
 387                      newline => 0);
 388
 389         for ( my $i = 1; $i <= $samples; $i++ ) {
 390           my $new_name = defined $name_stub ? $name_stub."_$i.dta" : "bs$i.dta";
 391           $new_name = $directory.'/'.$new_name;
 392           my ( $boot, $incl_ind_ref, $incl_key_ref ) =
 393             $self -> resample( subjects    => \%subjects,
 394                                resume      => $resume,
 395                                new_name    => $new_name,
 396                                target      => $target,
 397                                stratify_on => $stratify_on,
 398                                model_id    => $model_ids[$i-1] );
 399           push( @included_keys, $incl_key_ref );
 400           push( @incl_individuals, $incl_ind_ref );
 401 #         $boot -> renumber_ascending;
 402           push( @boot_samples, $boot );
 403 #          $boot -> synchronize;
 404 #          $boot -> flush;
 405           if( $status_bar -> tick() ){
 406             ui -> print( category => 'bootstrap',
 407                          message => $status_bar -> print_step,
 408                          newline => 0,
 409                          wrap => 0);
 410           }
 411 #         print Dumper \@boot_samples;
 412 #         sleep(10);
 413         }
 414         ui -> print( category => 'bootstrap',
 415                      message => ' ... done' );
 416       }
 417 end bootstrap
 418
 419 # }}} bootstrap
 420
 421 # {{{ resample
 422
 423 start resample
 424       {
 425         $self -> synchronize;
 426         my ( @header, $individuals, @bs_inds, $key_ref, @id_ids, @bs_id_ids );
 427         @id_ids = @{$self -> {'individual_ids'}} if( defined $self -> {'individual_ids'} );
 428         my @subj_keys = keys( %subjects );
 429         if ( $#subj_keys < 0 ) {
 430           debug -> die( message => "sample_size must be defined" );
 431         }
 432         if ( defined $stratify_on ) {
 433           my %strata;
 434           if( $stratify_on =~ /\D/ ){
 435             %strata = %{$self -> factors( column_head => $stratify_on )};
 436             if ( $strata{'Non-unique values found'} eq '1' ) {
 437               debug -> die( message => "Individuals were found to have multiple values in the $stratify_on column. ".
 438                             "The column $stratify_on cannot be used for stratification of the resampling." );
 439             }
 440           } else {
 441             %strata = %{$self -> factors( column => $stratify_on )};
 442             if ( $strata{'Non-unique values found'} eq '1' ) {
 443               debug -> die( message => "Individuals were found to have multiple values in column number $stratify_on. ".
 444                             "Column $stratify_on cannot be used for stratification of the resampling." );
 445             }
 446           }
 447           if ( scalar keys( %subjects) != scalar keys( %strata ) and
 448                not ( $#subj_keys == 0 and defined $subjects{'default'} ) ) {
 449             debug -> die( message => "sample_size must be defined using one default value ".
 450                           "or exactly one value per strata:\n".
 451                           "resampling per STUD=1001,1002,1003\n".
 452                           "use -sample_size='1001=>10,1002=>25,1003=>12' or ".
 453                           "-sample_size='default=>10'");
 454           }
 455           unless ( $resume and -e $new_name ) {
 456             @header = @{$self -> {'header'}};
 457             $individuals = $self -> {'individuals'};
 458             while( my ( $factor, $key_list ) = each %strata ) {
 459               my $keys;
 460               if ( defined $subjects{$factor} ) {
 461                 $keys = $subjects{$factor};
 462               } elsif( defined $subjects{'default'} ) {
 463                 $keys = sprintf( "%.0f",($subjects{'default'}*
 464                                (scalar(@{$key_list}))/($self -> count_ind())) );
 465               } else {
 466                 debug -> die( message => "A sample size for strata $factor could not be found ".
 467                               "and no default sample size was set" );
 468               }
 469               for ( my $i = 0; $i < $keys; $i++ ) {
 470                 my $list_ref = random_uniform_integer(1,0,(scalar(@{$key_list}) - 1));
 471                 push( @bs_inds, $individuals ->
 472                       [ $key_list -> [$list_ref] ] -> copy );
 473                 push( @included_keys, $key_list -> [$list_ref] );
 474                 push( @incl_individuals, $individuals ->
 475                       [ $key_list -> [$list_ref] ] -> idnumber );
 476                 push( @bs_id_ids, $id_ids[ $key_list -> [$list_ref] ] );
 477               }
 478             }
 479
 480             $boot = data -> new( header      => \@header,
 481                                  idcolumn    => $self -> {'idcolumn'},
 482                                  ignoresign  => $self -> {'ignoresign'},
 483                                  individuals => \@bs_inds,
 484                                  filename    => $new_name,
 485                                  ignore_missing_files => 1,
 486                                  target      => 'mem' );
 487             $boot -> renumber_ascending;
 488             $boot -> _write;
 489             $boot -> flush;
 490             #$boot -> target( $target );
 491           } else {
 492             # If we are resuming, we still need to generate the
 493             # pseudo-random sequence and initiate a data object
 494             while( my ( $factor, $key_list ) = each %strata ) {
 495               my $keys;
 496               if ( defined $subjects{$factor} ) {
 497                 $keys = $subjects{$factor};
 498               } elsif( defined $subjects{'default'} ) {
 499                 $keys = sprintf( "%.0f",($subjects{'default'}*
 500                                (scalar(@{$key_list}))/($self -> count_ind())) );
 501               } else {
 502                 debug -> die( message => "A sample size for strata $factor could not be found ".
 503                               "and no default sample size was set" );
 504               }
 505               for ( my $i = 0; $i < $keys; $i++ ) {
 506                 my $list_ref = random_uniform_integer(1,0,(scalar(@{$key_list}) - 1));
 507               }
 508             }
 509             $boot = data -> new( idcolumn    => $self -> {'idcolumn'},
 510                                  ignoresign  => $self -> {'ignoresign'},
 511                                  filename    => $new_name,
 512                                  ignore_missing_files => 1,
 513                                  target      => $target );
 514
 515             $boot -> _write;
 516             $boot -> flush;
 517           }
 518         } else {
 519           my $size;
 520           if( defined $subjects{'default'} ) {
 521             $size = $subjects{'default'};
 522           } else {
 523             debug -> die( message => "No default sample size was set" );
 524           }
 525           unless ( $resume and -e $new_name ) {
 526             @header = @{$self -> {'header'}};
 527             $individuals = $self -> {'individuals'};
 528             for ( my $i = 1; $i <= $size; $i++ ) {
 529               $key_ref = random_uniform_integer(1,0,scalar @{$individuals}-1);
 530               push( @bs_inds, $individuals -> [ $key_ref ] -> copy );
 531               push( @included_keys, $key_ref );
 532               push( @incl_individuals, $individuals -> [ $key_ref ] -> idnumber );
 533               push( @bs_id_ids, $id_ids[ $key_ref ] );
 534             }
 535
 536             # MUST FIX: If a file already exists with the same name,
 537             # the created bs data set will be appended to this. IT
 538             # MUST BE OVERWRITTEN!
 539             $boot = data -> new( header      => \@header,
 540                                  idcolumn    => $self -> {'idcolumn'},
 541                                  ignoresign  => $self -> {'ignoresign'},
 542                                  individuals => \@bs_inds,
 543                                  filename    => $new_name,
 544                                  ignore_missing_files => 1,
 545                                  target      => 'mem' );
 546             $boot -> renumber_ascending;
 547             $boot -> _write;
 548             $boot -> target( $target );
 549           } else {
 550             # If we are resuming, we still need to generate the
 551             # pseudo-random sequence and initiate a data object
 552             for ( my $i = 1; $i <= $size; $i++ ) {
 553               random_uniform_integer(1,0,scalar @{$individuals}-1)
 554             }
 555             $boot = data -> new( idcolumn    => $self -> {'idcolumn'},
 556                                  ignoresign  => $self -> {'ignoresign'},
 557                                  filename    => $new_name,
 558                                  ignore_missing_files => 1,
 559                                  target      => $target );
 560
 561             $boot -> _write;
 562             $boot -> flush;
 563           }
 564           if( $target eq 'disk'){
 565             $boot -> flush;
 566           }
 567         }
 568         $boot -> register_in_database( individual_ids => \@bs_id_ids,
 569                                        resampled      => 1,
 570                                        model_id       => $model_id );
 571       }
 572 end resample
 573
 574 # }}} resample
 575
 576 # {{{ case_deletion
 577
 578 start case_deletion
 579       {
 580         # case_deletion creates subsets of the data. The number of
 581         # subsets is specified by the bins argument. The individuals
 582         # of each subset is selected randomly or in ascending
 583         # numerical order depending on the selection argument that can
 584         # be either 'consecutive' or 'random'. case_column must be
 585         # specified to give the method something to base the selection
 586         # on. Valid case_column values are either the column number
 587         # (pure digits) or the name of the column in the (optional)
 588         # header row.
 589         $self -> synchronize;
 590         my @header    = @{$self -> {'header'}};
 591         if ( not defined $case_column ) {
 592           debug -> die( message => "case_column must be specified" );
 593         } else {
 594           if ( not $case_column =~ /^\d/ ) {
 595             for ( my $i = 0; $i <= $#header; $i++ ) {
 596               $case_column = $i+1 if ( $header[$i] eq $case_column );
 597             }
 598           }
 599         }
 600         $bins = defined $bins ? $bins :
 601           scalar keys %{$self -> factors( column => $case_column)};
 602         my %factors   = %{$self -> factors( column => $case_column )};
 603         if ( $factors{'Non-unique values found'} eq '1' ) {
 604           debug -> die( message => "Individuals were found to have multiple values in column number $case_column. ".
 605                         "Column $case_column cannot be used for case deletion." );
 606         }
 607
 608         my $maxbins   = scalar keys %factors;
 609         my @ftrs      = sort { $a <=> $b } keys %factors;
 610         my $individuals = $self -> {'individuals'};
 611         my $maxkey    = scalar @{$individuals} - 1;
 612
 613         my ( @tmp_ftrs, @binsize ) =
 614             ((),());
 615         my ( $k, $j, $i ) = ( 0, 0, 0 );
 616         # Create the binsizes
 617         for ( $j = 0; $j < $maxbins; $j++ ) {
 618           $binsize[ $k++ ]++;
 619           $k = 0 if( $k >= $bins );
 620         }
 621         $self -> _fisher_yates_shuffle( array => \@ftrs ) if( $selection eq 'random' );
 622         for ( $k = 0; $k < $bins; $k++ ) {
 623           for ( $j = 0; $j < $binsize[ $k ]; $j++ ) {
 624 #           print "SK: ",$skipped_keys[ $k ]," F: ",$factors{ $ftrs[ $i ] },"\n";
 625             push( @{$skipped_keys[ $k ]}, @{$factors{ $ftrs[ $i ] }} );
 626             push( @{$skipped_values[ $k ]}, $ftrs[ $i++ ] );
 627           }
 628         }
 629
 630         for ( $k = 0; $k < $bins; $k++ ) {
 631           my @cd_inds = ();
 632           my @del_inds = ();
 633         SELKEYS: foreach my $key ( 0..$maxkey ) {
 634           foreach my $skipped ( @{$skipped_keys[ $k ]} ) {
 635             if ( $key == $skipped ) {
 636               push( @{$skipped_ids[ $k ]}, $individuals ->
 637                     [ $skipped ] -> idnumber );
 638               push( @del_inds, $individuals -> [ $key ] -> copy );
 639               next SELKEYS;
 640             }
 641           }
 642           push( @cd_inds, $individuals -> [ $key ] -> copy );
 643         }
 644           # Set ignore_missing_files = 1 to make it possible to get the result
 645           # in memory only
 646           my $newdata = data ->
 647               new ( header      => \@header,
 648                     ignoresign  => $self -> {'ignoresign'},
 649                     idcolumn    => $self -> {'idcolumn'},
 650                     individuals => \@cd_inds,
 651                     target      => $target,
 652                     filename    => $directory.'/cdd_'.($k+1).'.dta',
 653                     ignore_missing_files => 1 );
 654           my $deldata = data ->
 655               new ( header      => \@header,
 656                     ignoresign  => $self -> {'ignoresign'},
 657                     idcolumn    => $self -> {'idcolumn'},
 658                     individuals => \@del_inds,
 659                     target      => $target,
 660                     filename    => $directory.'/rem_'.($k+1).'.dta',
 661                     ignore_missing_files => 1 );
 662           push( @subsets, $newdata );
 663           push( @remainders, $deldata );
 664           $newdata -> _write;
 665           $newdata -> flush;
 666           $deldata -> _write;
 667           $deldata -> flush;
 668         }
 669       }
 670 end case_deletion
 671
 672 # }}} case_deletion
 673
 674 # {{{ copy
 675 start copy
 676       {
 677         # filename: new data file name.
 678         #
 679         # target: keep the copy in memory ('mem') or write it to disk and flush the memory ('disk').
 680
 681         ($directory, $filename) = OSspecific::absolute_path( $directory, $filename );
 682
 683         # Clone self into new data object. Why don't the individuals get cloned too?
 684         # strange. need to set synced to 0 AND set the {'individuals'} to undef.
 685         cp($self -> full_name, $directory.$filename );
 686         $new_data = Storable::dclone( $self );
 687         $new_data -> {'synced'} = 0;
 688         $new_data -> {'individuals'} = undef;
 689         $new_data -> synchronize;
 690
 691         # Set the new file name for the copy
 692         $new_data -> directory( $directory );
 693         $new_data -> filename( $filename );
 694       }
 695 end copy
 696
 697 # }}} copy
 698
 699 # {{{ column_to_array
 700 start column_to_array
 701 {
 702   $self -> synchronize;
 703
 704   if ( not $column =~ /^\d/ ) {
 705     $column = $self -> {'column_head_indices'} -> {$column} - 1;
 706   }
 707
 708   if( $column < 0 or $column > $#{$self -> {'header'}} ){
 709     return [];
 710   }
 711
 712   foreach my $individual ( @{$self -> individuals} ){
 713     foreach my $individual_row( @{$individual -> subject_data} ){
 714       my @row = split(/,/ , $individual_row);
 715       push( @array, $row[$column] );
 716     }
 717   }
 718 }
 719 end column_to_array
 720 # }}}
 721
 722 # {{{ count_ind
 723
 724 start count_ind
 725       {
 726         # Returns the number of individuals in the data set.
 727         $self -> synchronize;
 728         if( defined $self -> individuals() ) {
 729           $num = scalar @{$self -> individuals()};
 730         } else {
 731           debug -> die( message => "No individuals found in file ".
 732                         $self -> filename() );
 733         }
 734       }
 735 end count_ind
 736
 737 # }}} count_ind
 738
 739 # {{{ diff
 740 start diff
 741 {
 742   $self -> synchronize;
 743
 744   my $first_id = $self -> {'individuals'}[0];
 745
 746   debug -> die( message => "No individuals defined in data object based on ".
 747                 $self -> full_name ) unless ( defined $first_id );
 748
 749   # Check if $column(-index) is defined and valid, else try to find index
 750   # using column_head
 751
 752   my @data_row = split( /,/, $first_id -> subject_data -> [0] );
 753   if( $#columns >= 0 ) {
 754     foreach my $column ( @columns ) {
 755       unless ( defined $column && defined( $data_row[$column-1] ) ) {
 756         debug -> die( message => "Error in data -> factors: ".
 757                       "invalid column number: \"$column\"\n".
 758                       "Valid column numbers are 1 to ".
 759                       scalar @{$first_id -> subject_data ->[0]}."\n" );
 760       }
 761     }
 762   } elsif ( $#column_heads >= 0 ) {
 763     foreach my $column_head ( @column_heads ) {
 764       unless (defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})) {
 765         debug -> die( message => "Error in data -> factors: unknown column: \"$column_head\" ".
 766                       "Valid column headers are (in no particular order):\n".
 767                       join(', ',keys(%{$self -> {'column_head_indices'}})) );
 768       } else {
 769         my $column = $self -> {'column_head_indices'}{$column_head};
 770         push( @columns, $column );
 771         debug -> warn( level   => 2,
 772                        message => "$column_head is in column number $column" );
 773       }
 774     }
 775   } else {
 776     debug -> die( message => "No column or column_head defined" );
 777   }
 778
 779   if( $global_largest or $global_smallest or
 780       $largest_per_individual or $smallest_per_individual ) {
 781     if( not scalar @{$self -> {'individuals'}} == scalar @{$against_data -> individuals} ) {
 782       debug -> die( message => "Both data object must hold the same number of individuals ".
 783                     "and observations when calling data -> diff" );
 784     }
 785     for( my $i = 0; $i < scalar @{$self -> {'individuals'}}; $i++ ) {
 786       my %id_diffs = %{$self -> {'individuals'}[$i] ->
 787                            diff( against_individual => $against_data -> individuals -> [$i],
 788                                  columns            => \@columns,
 789                                  absolute_diff      => $absolute_diff,
 790                                  diff_as_fraction   => $diff_as_fraction,
 791                                  largest            => ( $global_largest or $largest_per_individual ),
 792                                  smallest           => ( $global_smallest or $smallest_per_individual ) )};
 793       if( $global_largest ) {
 794         for( my $j = 0; $j <= $#columns; $j++ ) {
 795           my $label = defined $column_heads[$j] ? $column_heads[$j] : $columns[$j];
 796           if( not defined $diff_results{$label} or not defined $diff_results{$label}{'diff'} or
 797               $id_diffs{$columns[$j]}{'diff'} > $diff_results{$label}{'diff'} ) {
 798             $diff_results{$label}{'diff'} = $id_diffs{$columns[$j]}{'diff'};
 799             $diff_results{$label}{'self'} = $id_diffs{$columns[$j]}{'self'};
 800             $diff_results{$label}{'test'} = $id_diffs{$columns[$j]}{'test'};
 801           }
 802         }
 803       }
 804     }
 805   } else {
 806     die "data -> diff is only implemented for finding the largest difference at any observation at this point\n";
 807   }
 808 }
 809 end diff
 810 # }}} diff
 811
 812 # {{{ filename
 813 start filename
 814       {
 815         if ( defined $parm and $parm ne $self -> {'filename'} ) {
 816           $self -> {'filename'} = $parm;
 817           $self -> {'data_id'} = undef;
 818 #         $self -> _write;
 819         }
 820       }
 821 end filename
 822 # }}} filename
 823
 824 # {{{ fractions
 825
 826 start fractions
 827       {
 828         my %factors = $self -> factors( 'return_occurences' => 1,
 829                                         'unique_in_individual' => $unique_in_individual,
 830                                         'column_head' => $column_head,
 831                                         'column' => $column);
 832
 833         my $sum = 0;
 834         while (my ($factor, $amount) = each %factors) {
 835           if ( $factor == $self -> {'missing_data'} && $ignore_missing ) {
 836             next;
 837           } else {
 838             $sum += $amount;
 839           }
 840         }
 841         while (my ($factor, $amount) = each %factors) {
 842           if ( $factor == $self -> {'missing_data'} && $ignore_missing ) {
 843             next;
 844           } else {
 845             $fractions{$factor} = $amount/$sum;
 846           }
 847         }
 848       }
 849 end fractions
 850
 851 # }}} fractions
 852
 853 # {{{ factors
 854
 855 start factors
 856       {
 857         # Either column (number, starting at 1) or column_head must be specified.
 858         #
 859         # The default behaviour is to return a hash with the factors as keys
 860         # and as values references to arrays with the order numbers (not the ID numbers)
 861         # of the individuals that contain this factor
 862         #
 863         # If unique_in_individual is true (1), the returned hash will contain
 864         # an element with key 'Non-unique values found' and value 1 if any
 865         # individual contain more than one value in the specified column.
 866         #
 867         # Return occurences will calculate the occurence of each
 868         # factor value. Several occurences in one individual counts as
 869         # one occurence. The elements of the returned hash will have the factors
 870         # as keys and the number of occurences as values.
 871         #
 872
 873         $self -> synchronize;
 874
 875         # Check if $column(-index) is defined and valid, else try to find index
 876         # using column_head
 877         my $first_id = $self -> {'individuals'}[0];
 878
 879         debug -> die( message => "No individuals defined in data object based on ".
 880                       $self -> full_name ) unless ( defined $first_id );
 881
 882         my @data_row = split( /,/, $first_id -> subject_data -> [0] );
 883         unless ( defined $column && defined( $data_row[$column-1] ) ) {
 884           unless (defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})) {
 885             debug -> die( message => "Error in data -> factors: unknown column: \"$column_head\" ".
 886                           "or invalid column number: \"$column\".\n".
 887                           "Valid column numbers are 1 to ".scalar @data_row ."\n".
 888                           "Valid column headers are (in no particular order):\n".
 889                           join(', ',keys(%{$self -> {'column_head_indices'}})) );
 890           } else {
 891             $column = $self -> {'column_head_indices'}{$column_head};
 892             debug -> warn( level   => 2,
 893                            message => "$column_head is in column number $column" );
 894           }
 895         }
 896
 897         my $key = 0;
 898         foreach my $individual ( @{$self -> {'individuals'}} ) {
 899           my @ifactors = keys %{$individual -> factors( column => $column )};
 900           if ( scalar @ifactors > 1 and $unique_in_individual ) {
 901             %factors = ( 'Non-unique values found' => 1 );
 902             last;
 903           }
 904           debug -> die( message => "No value found in column $column in individual ".
 905                         $individual -> idnumber ) if ( scalar @ifactors == 0 );
 906
 907           # Return occurences will calculate the occurence of each
 908           # factor value. Several occurences in one individual counts as
 909           # one occurence.
 910
 911           if ( $return_occurences ) {
 912             foreach my $ifactor ( @ifactors ) {
 913               $factors{$ifactor}++;
 914             }
 915           } else {
 916             foreach my $ifactor ( @ifactors ) {
 917               push( @{$factors{$ifactor}}, $key );
 918             }
 919           }
 920           $key++;
 921         }
 922       }
 923 end factors
 924
 925 # }}} factors
 926
 927 # {{{ find_individual
 928
 929 # start find_individual
 930 #         foreach my $tmp_ind ( @{$self -> individuals} ) {
 931 #         if ( $tmp_ind -> key == $key ) {
 932 #           $individual = $tmp_ind;
 933 #           last;
 934 #         }
 935 #       }
 936 #         if ( defined $individual ) {
 937 #         if ( $copy ) {
 938 #           $individual = $individual -> copy;
 939 #         }
 940 #       } else {
 941 #         print "No individual with key $key found in call to ".
 942 #           "data -> find_individual\n" if ( $self -> debug );
 943 #         }
 944 # end find_individual
 945
 946 # }}}
 947
 948 # {{{ format_data
 949
 950 start format_data
 951       {
 952         my $header = $self -> {'header'};
 953
 954         # format the data for NONMEM (simple comma-separated layout)
 955         if ( defined $self -> {'comment'} ) {
 956           my @comment   = @{$self -> {'comment'}};
 957           for ( @comment ) {
 958             push( @form_data );
 959           }
 960         }
 961
 962         my $wrap = ( defined $self -> {'wrap_column'} and
 963                      defined $self -> {'cont_column'} );
 964
 965         my @primary_columns = defined $self -> {'primary_columns'} ?
 966           @{$self -> {'primary_columns'}} : ();
 967         my @secondary_columns = defined $self -> {'secondary_columns'} ?
 968           @{$self -> {'secondary_columns'}} : ();
 969         if ( defined $header and defined $self -> {'ignoresign'} ) {
 970           my $istr;
 971           if ( $self -> {'ignoresign'} ne '@' ) {
 972             $istr = $self -> {'ignoresign'};
 973           }
 974           if ( $wrap ) {
 975             my @h_data;
 976             for ( my $i = 0; $i <= $#secondary_columns ; $i++ ) {
 977               my $sstr = $istr;
 978               for ( my $j = 0; $j < scalar @{$secondary_columns[$i]} ; $j++ ) {
 979                 my $jstr = $j == 0 ? '' : ',';
 980                 $sstr = $sstr.$jstr.$secondary_columns[$i][$j][0];
 981               }
 982               push( @h_data, $sstr."\n" );
 983             }
 984             push( @form_data, @h_data );
 985             my $pstr = $istr;
 986             for ( my $i = 0; $i <= $#primary_columns ; $i++ ) {
 987               my $jstr = $i == 0 ? '' : ',';
 988               $pstr = $pstr.$jstr.$primary_columns[$i][0];
 989             }
 990             push( @form_data, $pstr."\n" );
 991           } else {
 992             push( @form_data, $istr.join(',',@{$self -> {'header'}})."\n" );
 993           }
 994         }
 995         if ( $wrap ) {
 996           foreach my $individual ( @{$self -> {'individuals'}} ) {
 997             foreach my $row ( @{$individual -> subject_data} ) {
 998               my @r_data;
 999               for ( my $i = 0; $i <= $#secondary_columns ; $i++ ) {
1000                 my $sstr = '';
1001                 for ( my $j = 0; $j < scalar @{$secondary_columns[$i]} ; $j++ ) {
1002                   my $jstr = $j == 0 ? '' : ',';
1003                   if ( $secondary_columns[$i][$j][0] eq 'CONT' ) {
1004                     $sstr = $sstr.$jstr.'1';
1005                   } else {
1006                     my @data_row = split( /,/, $row );
1007                     $sstr = $sstr.$jstr.$data_row[$secondary_columns[$i][$j][1]];
1008                   }
1009                 }
1010                 push( @r_data, $sstr."\n" );
1011               }
1012               push( @form_data, @r_data );
1013               my $pstr = '';
1014               for ( my $i = 0; $i <= $#primary_columns ; $i++ ) {
1015                 my $jstr = $i == 0 ? '' : ',';
1016                 if ( $primary_columns[$i][0] eq 'CONT' ) {
1017                   $pstr = $pstr.$jstr.'0';
1018                 } else {
1019                   my @data_row = split( /,/, $row );
1020                   $pstr = $pstr.$jstr.$data_row[$primary_columns[$i][1]];
1021                 }
1022               }
1023               push( @form_data, $pstr."\n" );
1024             }
1025           }
1026         } else {
1027           foreach my $individual ( @{$self -> {'individuals'}} ) {
1028             foreach my $row ( @{$individual -> subject_data} ) {
1029               push( @form_data, $row ."\n" );
1030             }
1031           }
1032         }
1033       }
1034 end format_data
1035
1036 # }}} format_data
1037
1038 # {{{ drop_dropped
1039
1040 start drop_dropped
1041       {
1042         # This method removes columns that has '=DROP' value in the
1043         # model header as given by $INPUT. The model header must be
1044         # transfered to this method through the model_header
1045         # argument. The model_header argument should be a
1046         # two-dimensional array where each position in the first
1047         # dimension should be a reference to a 1*2 array holding the
1048         # column name and value. Any ignore-sign must be removed.
1049
1050         debug -> die( message => 'model header must be defined' )
1051           if ( $#model_header < 0 );
1052         # Important that the drop_dropped method of the model::problem
1053         # class is in sync with this method.
1054         $self -> synchronize;
1055
1056         $self -> {'header'} = [];
1057         my @drop;
1058         my $counter = 1;
1059         for( my $i = 0; $i <= $#model_header; $i++ ) {
1060           $self -> {'idcolumn'} = $counter if ( $model_header[$i][0] eq 'ID' );
1061           if( ( $model_header[$i][1] eq 'DROP' or
1062                 $model_header[$i][1] eq 'SKIP' ) and
1063               not $model_header[$i][0] =~ /DAT(E|1|2|3)/ ) {
1064             push( @drop, 1 );
1065           } else {
1066             $counter++;
1067             push( @drop, 0 );
1068             push( @{$self -> {'header'}}, $model_header[$i][0] );
1069           }
1070         }
1071
1072         foreach my $individual ( @{$self -> {'individuals'}} ) {
1073           $individual -> drop_columns( drop => \@drop );
1074         }
1075
1076         $self -> {'synced'} = 0;
1077 #       $Data::Dumper::Maxdepth = 2;
1078 #       die Dumper $self;
1079 #       die Dumper $self -> {'individuals'};
1080       }
1081 end drop_dropped
1082
1083 # }}} drop_dropped
1084
1085 # {{{ wrap
1086 start wrap
1087       {
1088         $self -> synchronize;
1089         $self -> cont_column( $cont_column ) if ( defined $cont_column );
1090         $self -> wrap_column( $wrap_column ) if ( defined $wrap_column );
1091         $self -> prepare_wrap( model_header => \@model_header );
1092         @secondary_columns = @{$self -> {'secondary_columns'}}
1093           if ( defined $self -> {'secondary_columns'} );
1094         @primary_columns = @{$self -> {'primary_columns'}}
1095           if ( defined $self -> {'primary_columns'} );
1096         $self -> synced(0);
1097       }
1098 end wrap
1099 # }}} wrap
1100
1101 # {{{ unwrap
1102 start unwrap
1103       {
1104         $self -> {'cont_column'} = undef;
1105         $self -> {'wrap_column'} = undef;
1106         $self -> {'secondary_columns'} = undef;
1107         $self -> {'primary_columns'} = undef;
1108       }
1109 end unwrap
1110 # }}} unwrap
1111
1112 # {{{ prepare_wrap
1113
1114 start prepare_wrap
1115       {
1116         my $cont_column = $self -> {'cont_column'};
1117         my $wrap_column = $self -> {'wrap_column'};
1118         debug -> die( message => 'cont_column ('.$cont_column.') must be less or equal '.
1119                       'to the requested number of columns in each row ('.
1120                       ($wrap_column).')' )
1121           if ( $cont_column > $wrap_column );
1122         my @header;
1123         if ( scalar @model_header > 0 ) {
1124           @header = @model_header;
1125         } else {
1126           @header = @{$self -> {'header'}};
1127         }
1128
1129         my ( @primary, @secondary, @date_columns );
1130
1131         for ( my $i = 0; $i <= $#header; $i++ ) {
1132           my $name  = ref( $header[$i] ) eq 'ARRAY' ? $header[$i][0] : $header[$i];
1133           my $value = ref( $header[$i] ) eq 'ARRAY' ? $header[$i][1] : undef;
1134           next if ( $name eq 'ID' );
1135           my $found = 0;
1136           foreach my $prim ( @primary_column_names ) {
1137             if ( not $found and
1138                  ( $name eq $prim or $value eq $prim ) ) {
1139               push( @primary, [$name, $i, $value] );
1140               $found = 1;
1141               my $col = ($#primary+2)>= $cont_column ? ($#primary+3) : ($#primary+2);
1142               push( @date_columns, $col ) if ( $name =~ /DAT(E|1|2|3)/ );
1143             }
1144           }
1145           push( @secondary, [$name, $i, $value] ) if ( not $found );
1146         }
1147
1148         my $prim_num = scalar @primary;
1149         debug -> die( message => 'The number of primary columns (that need to '.
1150                       'be part of the row with CONT=0) ('.($prim_num+1).
1151                       ') is larger than the required number of columns (wrap_column='.
1152                       $wrap_column.') - 1' )
1153           if ( scalar $prim_num > ($wrap_column-2) );
1154
1155         my ( $i, $dum ) = ( 0, 1 );
1156         my @tmp;
1157         for ( my $j = 1; $j <= $wrap_column; $j++ ) {
1158           if( $j == 1 ) {
1159             push( @tmp, ['ID', $self -> {'idcolumn'}-1] );
1160           } elsif ( $j == $wrap_column ) {
1161             if ( $j == $cont_column ) {
1162               push( @tmp, ['CONT', undef] );
1163             } else {
1164               my $val;
1165               if ( defined $primary[$i] ) {
1166                 $val = $primary[$i];
1167               } elsif ( defined $secondary[0] ) {
1168                 $val = shift(@secondary);
1169               } else {
1170                 $val = ['XX'.$dum++,$self -> {'idcolumn'}-1];
1171               }
1172               push( @tmp, $val );
1173               $i++;
1174             }
1175             push( @{$self -> {'primary_columns'}}, @tmp );
1176           } else {
1177             if ( $j == $cont_column ) {
1178               push( @tmp, ['CONT', undef] );
1179             } else {
1180               if ( $i <= $#primary ) {
1181                 push( @tmp, $primary[$i] );
1182                 $i++;
1183               } else {
1184                 my $val = defined $secondary[0] ? shift(@secondary) :
1185                   ['XX'.$dum++,$self -> {'idcolumn'}-1];
1186                 push( @tmp, $val );
1187               }
1188             }
1189           }
1190         }
1191
1192         my $i = 0;
1193         while ( $i <= $#secondary ) {
1194           my @tmp;
1195           for ( my $j = 1; $j <= $wrap_column; $j++ ) {
1196             if( $j == 1 ) {
1197               push( @tmp, ['ID', $self -> {'idcolumn'}-1] );
1198             } elsif ( $j == $wrap_column ) {
1199               if ( $j == $cont_column ) {
1200                 push( @tmp, ['CONT', undef] );
1201               } else {
1202                 my $val = defined $secondary[$i] ? $secondary[$i] :
1203                   ['XX'.$dum++,$self -> {'idcolumn'}-1];
1204                 push( @tmp, $val );
1205                 $i++;
1206               }
1207               unshift( @{$self -> {'secondary_columns'}}, \@tmp );
1208             } else {
1209               if ( $j == $cont_column ) {
1210                 push( @tmp, ['CONT', undef] );
1211               } else {
1212                 my $isdate = 0;
1213                 if ( $#date_columns >= 0 ) {
1214                   foreach my $col ( @date_columns ) {
1215                     # This is a date column which may have to be dropped
1216                     # and thus will not appear as a secondary
1217                     # column. Nothing should be pushed. The indexes in
1218                     # model::problem::pk::_format_record will be ok.
1219                     $isdate = 1 if ( $col == $j ) ;
1220                   }
1221                 }
1222                 if ( $isdate ) {
1223                   push( @tmp, ['XX'.$dum++,$self -> {'idcolumn'}-1] );
1224                 } else {
1225                   if ( $i <= $#secondary ) {
1226                     push( @tmp, $secondary[$i] );
1227                     $i++;
1228                   } else {
1229                     push( @tmp, ['XX'.$dum++,$self -> {'idcolumn'}-1] );
1230                   }
1231                 }
1232               }
1233             }
1234           }
1235         }
1236       }
1237 end prepare_wrap
1238
1239 # }}} prepare_wrap
1240
1241 # {{{ have_missing_data
1242 start have_missing_data
1243       {
1244         # Either I<column> or I<column_head> must be specified.
1245         #
1246         # This method looks through the data column with index I<column> or
1247         # (optional) header name I<column_head> and returns O if no missing
1248         # data indicator was found or 1 otherwise.
1249
1250         $self -> synchronize;
1251         my $first_id = $self -> {'individuals'}[0];
1252         debug -> die( message => "No individuals defined in data object based on ".
1253                       $self -> full_name ) unless ( defined $first_id );
1254         my @data_row = split( /,/ , $first_id -> subject_data -> [0] );
1255         unless ( defined $column  && defined( $data_row[$column-1] ) ) {
1256           unless(defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})){
1257             die "Error in data -> have_missing_data: unknown column: \"$column_head\" or invalid column number: \"$column\"\n";
1258           } else {
1259             $column = $self -> {'column_head_indices'}{$column_head};
1260           }
1261         }
1262         $self -> flush if ( $self -> {'target'} eq 'disk' );
1263
1264         # In case anyone wonders, the ternary statment ( bool ? true :
1265         # false ) below will possibly make a minuscle memory
1266         # optimization. But hey, why not :)
1267
1268         $return_value = defined $self -> {'have_missing_data'} ? $self -> {'have_missing_data'} -> {$column} : 0;
1269       }
1270 end have_missing_data
1271 # }}} have_missing_data
1272
1273 # {{{ merge
1274 start merge
1275       {
1276         #$self -> synchronize;
1277         push( @{$self -> {'individuals'}}, @{$mergeobj -> individuals} );
1278       }
1279 end merge
1280 # }}} merge
1281
1282 # {{{ max
1283
1284 start max
1285       {
1286         # Either column or column_head must be specified. Column_head must be a string that
1287         # identifies a column in the (optional ) data file header.
1288
1289 # The if-statement below used to be a cache of allready calculated
1290 # means. But since individuals can be accessed in so many ways, we
1291 # don't know when this cache should be updated. Its easier to
1292 # recalculate the max. Maybe we can include this optimization in the
1293 # future, if it turns out to be a bottleneck
1294 #       my $tmp_column = $self -> {'column_head_indices'}{$column_head};
1295 #       if ( defined $self -> {'max'}[$tmp_column] ) {
1296 #         $return_value = $self -> {'max'}[$tmp_column] ;
1297 #       } else {
1298           $self -> synchronize;
1299           my $first_id = $self -> {'individuals'}[0];
1300           debug -> die( message => "data -> max: No individuals defined in data object based on " .
1301                         $self -> full_name ) unless defined $first_id;
1302
1303           my @data_row = split( /,/ , $first_id -> subject_data ->[0] );
1304
1305           unless ( defined $column  && defined( $data_row[$column-1] ) ) {
1306             unless (defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})) {
1307               die "Error in data -> max: unknown column: \"$column_head\" or invalid column number: \"$column\"\n";
1308             } else {
1309               $column = $self -> {'column_head_indices'}{$column_head};
1310             }
1311           }
1312           foreach my $individual ( @{$self -> {'individuals'}} ) {
1313             my $ifactors = $individual -> factors( 'column' => $column );
1314             foreach ( keys %{$ifactors} ) {
1315               next if ( $_ == $self -> {'missing_data_token'} );
1316               if ( defined ($return_value) ) {
1317                 $return_value = $_ > $return_value ? $_ : $return_value;
1318               } else {
1319                 $return_value = $_;
1320               }
1321             }
1322           }
1323
1324 #         $self -> {'max'}[$column] = $return_value;
1325           $self -> flush if ( $self -> {'target'} eq 'disk' );
1326 #       }
1327       }
1328 end max
1329
1330 # }}} max
1331
1332 # {{{ min
1333
1334 start min
1335       {
1336         # See L</max>.
1337         my $tmp_column = $self -> {'column_head_indices'}{$column_head};
1338
1339 # The if-statement below used to be a cache of allready calculated
1340 # means. But since individuals can be accessed in so many ways, we
1341 # don't know when this cache should be updated. Its easier to
1342 # recalculate the min. Maybe we can include this optimization in the
1343 # future, if it turns out to be a bottleneck
1344 #       if ( defined $self -> {'min'}[$tmp_column] ) {
1345 #         $return_value = $self -> {'min'}[$tmp_column] ;
1346 #       } else {
1347           $self -> synchronize;
1348           my $first_id = $self -> {'individuals'}[0];
1349           die "data -> min: No individuals defined in data object based on ",
1350             $self -> full_name,"\n" unless defined $first_id;
1351
1352           my @data_row = split( /,/ , $first_id -> subject_data ->[0] );
1353
1354           unless ( defined $column  && defined( $data_row[$column-1] ) ) {
1355             unless (defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})) {
1356               die "Error in data -> min: unknown column: \"$column_head\" or invalid column number: \"$column\"\n";
1357             } else {
1358               $column = $self -> {'column_head_indices'}{$column_head};
1359             }
1360           }
1361           foreach my $individual ( @{$self -> {'individuals'}} ) {
1362             my $ifactors = $individual -> factors( 'column' => $column );
1363             foreach ( keys %{$ifactors} ) {
1364               next if ( $_ == $self -> {'missing_data_token'} );
1365               if ( defined ($return_value) ) {
1366                 $return_value = $_ < $return_value ? $_ : $return_value;
1367               } else {
1368                 $return_value = $_;
1369               }
1370             }
1371           }
1372 #         $self -> {'min'}[$column] = $return_value;
1373           $self -> flush if ( $self -> {'target'} eq 'disk' );
1374 #       }
1375       }
1376 end min
1377
1378 # }}} min
1379
1380 # {{{ median
1381
1382 start median
1383       {
1384           # See L</max>.
1385         $self -> synchronize;
1386         my $first_id = $self -> {'individuals'}[0];
1387         die "data -> median: No individuals defined in data object based on ",
1388           $self -> full_name,"\n" unless defined $first_id;
1389
1390         my @data_row = split( /,/ , $first_id -> subject_data ->[0] );
1391
1392         unless ( defined $column  && defined( $data_row[$column-1] ) ) {
1393           unless(defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})){
1394             die "Error in data -> median: unknown column: \"$column_head\" or invalid column number: \"$column\"\n";
1395           } else {
1396             $column = $self -> {'column_head_indices'}{$column_head};
1397           }
1398         }
1399
1400         if( defined $self -> {'median'}[$column] ){
1401           return $self -> {'median'}[$column];
1402         }
1403
1404         my @median_array;
1405
1406         foreach my $individual ( @{$self -> {'individuals'}} ) {
1407           if( $unique_in_individual ){
1408             my $ifactors = $individual -> factors( 'column' => $column );
1409
1410             foreach ( keys %{$ifactors} ) {
1411               next if ( $_ == $self -> {'missing_data_token'} );
1412               push( @median_array, $_ );
1413             }
1414           } else {
1415             my $ifactors = $individual -> subject_data;
1416
1417             for(my $i=0; $i<=$#{$ifactors}; $i++ ) {
1418               my @data_row = split( /,/ , $ifactors -> [$i] );
1419               next if ( $data_row[$column-1] == $self -> {'missing_data_token'} );
1420               push(@median_array, $data_row[$column-1]);
1421             }
1422           }
1423         }
1424         @median_array = sort {$a <=> $b} @median_array ;
1425
1426         if( @median_array % 2 ){
1427           $return_value = $median_array[$#median_array / 2];
1428         } else {
1429           $return_value = ( $median_array[@median_array / 2] +
1430                             $median_array[(@median_array - 2) / 2] ) / 2;
1431         }
1432
1433         $self -> {'median'}[$column] = $return_value;
1434       }
1435 end median
1436
1437 # }}} median
1438
1439 # {{{ mean
1440
1441 start mean
1442   {
1443      # Returns mean value of a column
1444      # If a individual contains more then 1 value (i.e. if an
1445      # individual has different values in different samples a mean
1446      # value of all individuals if calculate first, then the mean
1447      # value of the column If hi_cutoff is defined the mean function
1448      # will cut all value below the cutoff, and set their value to
1449      # 0. It's used to calculate the HI-mean/LOW-mean of a column for
1450      # e.g. Hockey-stick covariates If both hi_cutoff and low_cutoff
1451      # are defined only the hi_cutoff will be used.  See L</max>.
1452      my $tmp_column = $self -> {'column_head_indices'}{$column_head};
1453      $self -> synchronize;
1454      my $first_id = $self -> {'individuals'}[0];
1455        die "data -> mean: No individuals defined in data object based on ",
1456         $self -> full_name,"\n" unless defined $first_id;
1457
1458      my @data_row = split( /,/, $first_id -> subject_data ->[0] );
1459
1460      unless ( defined $column  && defined( $data_row[$column-1] ) ) {
1461        unless (defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})) {
1462          die "Error in data -> mean: unknown column: \"$column_head\" or invalid column number: \"$column\"\n";
1463        } else {
1464               $column = $self -> {'column_head_indices'}{$column_head};
1465          }
1466      }
1467
1468         ## Here the calculation starts
1469         my $num_individuals = 0;
1470         my $sum = 0;
1471
1472      my $all_data_rows=0;
1473         foreach my $individual ( @{$self ->{'individuals'}} ) {
1474
1475           my $ifactors = $individual -> subject_data;
1476           my $individual_sum = 0;
1477           my $data_rows = 0;
1478           for(my $i=0; $i<=$#{$ifactors}; $i++ ) {
1479
1480             # data is stored in strings. We need to split them into an
1481             # array.
1482
1483             my @data_row = split( /,/, $ifactors -> [$i] );
1484             if ( $data_row[$column-1] == $self -> {'missing_data_token'} ) {
1485 #             print "Skipping row with missing data\n";
1486               next;
1487             }
1488
1489             if( defined $subset_column and not eval ( $data_row[$subset_column-1].$subset_syntax ) ) {
1490 #             print "Skipping row outside subset: syntax: ".($subset_column-1)." $subset_syntax\n";
1491               next;
1492             }
1493
1494             if (defined $hi_cutoff) {
1495               if ($data_row[$column-1]>$hi_cutoff) {
1496                 $individual_sum += $data_row[$column-1]-$hi_cutoff;
1497               }
1498             }
1499             else {
1500               if (defined $low_cutoff) {
1501                 if ($data_row[$column-1]<$low_cutoff) {
1502                   $individual_sum += $low_cutoff - $data_row[$column-1];
1503                 }
1504               }
1505               else {
1506                 $individual_sum += $data_row[$column-1];
1507               }
1508             }
1509             $data_rows++;
1510           }
1511           if( $global_mean ) {
1512             $sum += $individual_sum;
1513             $num_individuals += $data_rows;
1514           } else {
1515             if( $data_rows != 0 ) {
1516               $sum += $individual_sum/$data_rows;
1517             }
1518             $num_individuals ++;
1519           }
1520           $all_data_rows += $data_rows;
1521         }
1522      if( $num_individuals != 0 ) {
1523        $return_value = $sum / $num_individuals;
1524      }
1525 #     print "DR: $all_data_rows\n";
1526 #     print "\nNIM: $num_individuals $return_value\n";
1527 }
1528
1529 end mean
1530
1531 # }}} mean
1532
1533 # {{{ sd
1534
1535 start sd
1536   {
1537     # This sub returns standard deviation for a specific column
1538     # If there are more than one sample/individual the value used for that specific
1539     # individual is the mean value of its samples.
1540     # The cut-offs are for hockey stick variables. I.e. If one individual value is
1541     # lower than the hi-cutoff the individual value will be zero.
1542     # HI_cutoff is used to calculate the HI-mean of a column.
1543     # If cut_off is undef it won't be used
1544     # See L</max>.
1545      my $tmp_column = $self -> {'column_head_indices'}{$column_head};
1546      $self -> synchronize;
1547      my $first_id = $self -> {'individuals'}[0];
1548      debug -> die( message => "No individuals defined in data object based on ".
1549                    $self -> full_name ) unless defined $first_id;
1550
1551      my @data_row = split( /,/ , $first_id -> subject_data ->[0] );
1552
1553      unless ( defined $column  && defined( $data_row[$column-1] ) ) {
1554        unless (defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})) {
1555          debug -> die( message => "Unknown column: \"$column_head\" or "
1556                        ."invalid column number: \"$column\"" );
1557        } else {
1558          $column = $self -> {'column_head_indices'}{$column_head};
1559        }
1560      }
1561
1562      ## Here the calculation starts
1563      my $num_individuals = 0;
1564      my $sum = 0;
1565      my $mean;
1566      if (defined $hi_cutoff) {
1567        $mean = $self->mean(column   => $column,
1568                            hi_cutoff => $hi_cutoff,
1569                            global_mean => $global_sd );
1570      } elsif (defined $low_cutoff) {
1571        $mean = $self->mean(column   => $column,
1572                            low_cutoff => $low_cutoff,
1573                            global_mean => $global_sd );
1574      } else {
1575        $mean = $self->mean( column        => $column,
1576                             subset_column => $subset_column,
1577                             subset_syntax => $subset_syntax,
1578                             global_mean => $global_sd );
1579      }
1580
1581      foreach my $individual ( @{$self -> {'individuals'}} ) {
1582        my $ifactors = $individual -> subject_data;
1583        my $individual_sum = 0;
1584        my $data_rows = 0;
1585        for(my $i=0; $i<=$#{$ifactors}; $i++ ) {
1586
1587          # data is stored in strings. We need to split them into an
1588          # array.
1589
1590          my @data_row = split( /,/, $ifactors -> [$i] );
1591
1592          if ( $data_row[$column-1] == $self -> {'missing_data_token'} ) {
1593 #          print "Skipping row with missing data\n";
1594            next;
1595          }
1596
1597          if( defined $subset_column and not eval ( $data_row[$subset_column-1].$subset_syntax ) ) {
1598 #          print "Skipping row outside subset: syntax: ".($subset_column-1)." $subset_syntax\n";
1599            next;
1600          }
1601
1602          if (defined $hi_cutoff) {
1603            if ($data_row[$column-1]>$hi_cutoff) {
1604              if( $global_sd ) {
1605                $individual_sum += ($data_row[$column-1] - $hi_cutoff - $mean) ** 2;
1606              } else {
1607                $individual_sum += $data_row[$column-1]-$hi_cutoff;
1608              }
1609            }
1610          } else {
1611            if (defined $low_cutoff) {
1612              if ($data_row[$column-1]<$low_cutoff) {
1613                if( $global_sd ) {
1614                  $individual_sum += ($low_cutoff - $data_row[$column-1] - $mean) ** 2;
1615                } else {
1616                  $individual_sum += $low_cutoff - $data_row[$column-1];
1617                }
1618              }
1619            } else {
1620              if( $global_sd ) {
1621                $individual_sum += ($data_row[$column-1] - $mean) ** 2;
1622              } else {
1623                $individual_sum += $data_row[$column-1];
1624              }
1625            }
1626          }
1627          $data_rows++;
1628        }
1629        if( $global_sd ) {
1630          $sum += $individual_sum;
1631          $num_individuals += $data_rows;
1632        } else {
1633          if( $data_rows != 0 ) {
1634            $sum += ($individual_sum/$data_rows - $mean) ** 2;
1635          }
1636          $num_individuals++;
1637        }
1638      }
1639      if( $num_individuals < 2 ) {
1640        $return_value = 0;
1641      } else {
1642        if( $num_individuals != 0 ) {
1643          $return_value = (1/($num_individuals-1)*$sum) ** 0.5;
1644        }
1645      }
1646    }
1647
1648 end sd
1649
1650 # }}} sd
1651
1652 # {{{ range
1653 start range
1654       {
1655         # See L</max>.
1656         my $tmp_column = $self -> {'column_head_indices'}{$column_head};
1657         if ( defined $self -> {'range'}[$tmp_column] ) {
1658           $return_value = $self -> {'range'}[$tmp_column];
1659         } else {
1660           my $old_target = $self -> {'target'};
1661           $self -> {'target'} = 'mem';
1662           $self -> synchronize;
1663           $return_value = $self -> max( column      => $column,
1664                                         column_head => $column_head ) -
1665                                           $self -> min( column      => $column,
1666                                                         column_head => $column_head );
1667           $self -> {'range'}[$column] = $return_value;
1668           if ( $old_target eq 'disk' ) {
1669             $self -> flush if ( $self -> {'target'} eq 'disk' );
1670             $self -> {'target'} = 'disk';
1671           }
1672         }
1673       }
1674 end range
1675 # }}} range
1676
1677 # {{{ recalc_column
1678 start recalc_column
1679       {
1680           # Recalculates a column based on expression. Also, see L</max>.
1681         $self -> synchronize;
1682
1683         # Check if $column(-index) is defined and valid, else try to find index using column_head
1684         my $first_id = $self -> {'individuals'}[0];
1685         die "data -> recalc_column: No individuals defined in data object based on ",
1686           $self -> full_name,"\n" unless defined $first_id;
1687
1688         my @data_row = split( /,/ , $first_id -> subject_data ->[0] );
1689
1690         unless ( defined $column  && defined( $data_row[$column-1] ) ) {
1691           if(defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})){
1692             die "Error in data -> recalc_column: unknown column: \"$column_head\" or column number: \"$column\"\n";
1693           } else {
1694             $column = $self -> {'column_head_indices'}{$column_head};
1695           }
1696         }
1697
1698         for my $individual ( @{$self -> {'individuals'}} ) {
1699           $individual -> recalc_column( column     => $column,
1700                                         expression => $expression );
1701         }
1702       }
1703 end recalc_column
1704 # }}} recalc_column
1705
1706 # {{{ renumber_ascending
1707
1708 start renumber_ascending
1709       {
1710 # Renumbers the individuals (changes the subject identifiers) so that
1711 # all have unique integer numbers starting with start_at and
1712 # ascending. The primary use of this
1713 # method is not to order the individuals after their identifiers but to
1714 # ensure that all individuals have unique identifiers.
1715
1716         $self -> synchronize;
1717         foreach my $individual ( @{$self -> {'individuals'}} ) {
1718           $individual -> idnumber ( $start_at++ );
1719         }
1720         $self -> {'synced'} = 0;
1721       }
1722 end renumber_ascending
1723
1724 # }}} renumber_ascending
1725
1726 # {{{ renumber_descending
1727
1728 start renumber_descending
1729       {
1730           # See L</renumber_ascending>.
1731         $self -> synchronize;
1732         foreach my $individual ( @{$self -> {'individuals'}} ) {
1733           $individual -> idnumber ( $start_at-- );
1734         }
1735         $self -> {'synced'} = 0;
1736       }
1737 end renumber_descending
1738
1739 # }}} renumber_descending
1740
1741 # {{{ single_valued_data
1742
1743 start single_valued_data
1744       {
1745         # Usage:
1746         #
1747         # ($single_value_data_set, $remainder, $column_indexes) =
1748         #      $data_object -> single_valued_data( subset_name         => 'subset.dta',
1749         #                                          remainder_name      => 'remainder.dta',
1750         #                                          target              => 'disk',
1751         #                                          do_not_test_columns => [1..18,24,26];
1752         #
1753         # my $single_value_column_indexes = $column_indexes -> [0];
1754         # my $all_other_column_indexes    = $column_indexes -> [1];
1755         #
1756         # Analyses the content of each column, based on the
1757         # ID column, and returns two new data objects: One
1758         # that contains all columns that is has only one value per
1759         # individual and one that contains the
1760         # remainding data. This is useful for creating compact 'extra'
1761         # data sets that can be read in via user-defined sub-routines
1762         # when the number of columns needed exceeds the maximum that
1763         # NONMEM allows (e.g. 20 in NONMEM version V).
1764         #
1765         # The I<do_not_test_columns> argument specifies on which columns
1766         # to skip the single value test
1767
1768         my @multi_value_flags;
1769         my @individuals = @{$self -> {'individuals'}};
1770         # Initiate the flags:
1771         if ( defined $individuals[0] ) {
1772           my @data = @{$individuals[0] -> {'subject_data'}};
1773           my @data_row = split( /,/ , $data[0] );
1774           for ( my $i = 0; $i < scalar @data_row; $i++ ) {
1775             my $dnt_flag = 0;
1776             foreach my $dntc ( @do_not_test_columns ) {
1777               $dnt_flag = 1 if ( $i == $dntc - 1 );
1778             }
1779             $multi_value_flags[$i] = $dnt_flag;
1780           }
1781         } else {
1782           die "data -> single_valued_data: No data in ID number 1\n";
1783         }
1784         # Collect the stats
1785         for ( my $id = 0; $id <= $#individuals; $id++ ) {
1786           my @data = @{$individuals[$id] -> {'subject_data'}};
1787           my @data_row = split( /,/, $data[0] );
1788           for ( my $j = 0; $j < scalar @data_row; $j++ ) {
1789             my %col_unique;
1790             for ( my $i = 0; $i <= $#data; $i++ ) {
1791               my @data_row = split( /,/ , $data[$i] );
1792               $col_unique{$data_row[$j]}++;
1793             }
1794             my $factors = scalar keys %col_unique;
1795             $multi_value_flags[$j]++ if ( $factors > 1 );
1796           }
1797         }
1798         for ( my $i = 0; $i <= $#multi_value_flags; $i++ ) {
1799           if ( $multi_value_flags[$i] ) {
1800             push ( @{$column_indexes[1]}, $i + 1);
1801           } else {
1802             push ( @{$column_indexes[0]}, $i + 1);
1803           }
1804         }
1805         ( $single_value_data_set, $remainder ) =
1806           $self -> subset_vertically( column_indexes      => $column_indexes[0],
1807                                       subset_name         => $subset_name,
1808                                       return_remainder    => 1,
1809                                       remainder_name      => $remainder_name,
1810                                       target              => $target,
1811                                       keep_first_row_only => 1);
1812       }
1813 end single_valued_data
1814
1815 # }}}
1816
1817 # {{{ subset_vertically
1818
1819 start subset_vertically
1820       {
1821         # Usage:
1822         #
1823         # $subset = $data_object -> subset_vertically ( column_indexes => [1,2,6],
1824         #                                               subset_name    => 'subset.dta' );
1825         #
1826         # This basic usage returns a new data object containing
1827         # columns 1,2 and 6 from the original data plus the
1828         # idcolumn. The new data object will be associated with the
1829         # file 'subset.dta'.
1830         #
1831         # You get the remaining data, i.e. the original data minus
1832         # the created subset by specifying
1833         #
1834         # ( $subset, $remainder ) =
1835         #      $data_object -> subset_vertically ( column_indexes   => [1,2,6],
1836         #                                          subset_name      => 'subset.dta',
1837         #                                          return_remainder => 1,
1838         #                                          remainder_name   => 'remainder.dta' );
1839         #
1840         # If you would like to flush the created data sets to disk and
1841         # save memory, set the I<target> argument to 'disk'. The
1842         # default value 'mem' will keep the whole data object in RAM.
1843         #
1844         # The I<keep_first_row_only> argument can be used to reduce
1845         # the size of the subset data obejct by excluding all but the
1846         # first row of data from each individual.
1847         #
1848         my @individuals = @{$self -> {'individuals'}};
1849         # Create remainder index array if necessary
1850         my @remainder_indexes;
1851         if ( defined $individuals[0] ) {
1852           my @data = @{$individuals[0] -> {'subject_data'}};
1853           my $idcolumn = $individuals[0] -> {'idcolumn'};
1854 #         print "IC: $idcolumn\n";
1855           my $id_flag = 0;
1856           foreach my $use_index ( @column_indexes ) {
1857             $id_flag = 1 if ( $use_index == $idcolumn );
1858           }
1859           if ( $return_remainder ) {
1860 #           @remainder_indexes = ( $idcolumn );
1861             for ( my $i = 0; $i < scalar split(/,/,$data[0]); $i++ ) {
1862               my $rem_flag = 1;
1863               foreach my $use_index ( @column_indexes ) {
1864                 $rem_flag = 0 if ( $i == $use_index -1 );
1865 # or
1866 #                                  $i == $idcolumn -1 );
1867               }
1868               push( @remainder_indexes, $i + 1 ) if ( $rem_flag );
1869             }
1870             unshift( @remainder_indexes, $idcolumn ) if ( $id_flag );
1871           }
1872           unshift( @column_indexes, $idcolumn ) unless ( $id_flag );
1873         } else {
1874           die "data -> single_valued_data: No data in ID number 1\n";
1875         }
1876
1877         my @new_ids;
1878         my @new_ids_2;
1879         for ( my $id = 0; $id <= $#individuals; $id++ ) {
1880           my $idnumber = $individuals[$id] -> idnumber;
1881           my $idcolumn = $individuals[$id] -> idcolumn;
1882           my @data = @{$individuals[$id] -> {'subject_data'}};
1883           my @new_data;
1884           my @new_data_2;
1885           my $use_rows = $keep_first_row_only ? 0 : $#data;
1886           for ( my $i = 0; $i <= $use_rows; $i++ ) {
1887             my @new_row;
1888             my @data_row = split( /,/, $data[$i] );
1889             foreach my $use_index ( @column_indexes ) {
1890               push( @new_row, $data_row[$use_index-1] );
1891             }
1892 #           print "@new_row $#new_row\n";
1893             push( @new_data, join( ',', @new_row ) );
1894           }
1895           for ( my $i = 0; $i <= $#data; $i++ ) {
1896             if ( $return_remainder ) {
1897               my @new_row_2;
1898               my @data_row = split( /,/, $data[$i] );
1899               foreach my $use_index ( @remainder_indexes ) {
1900                 push( @new_row_2, $data_row[$use_index-1] );
1901               }
1902 #             print "@new_row_2 $#new_row_2\n";
1903               push( @new_data_2, join( ',' , @new_row_2 ) );
1904             }
1905           }
1906           my $new_id = data::individual -> new( idnumber     => $idnumber,
1907                                                 idcolumn     => $idcolumn,
1908                                                 subject_data => \@new_data );
1909           push( @new_ids, $new_id );
1910           if ( $return_remainder ) {
1911             my $new_id_2;
1912             $new_id_2 = data::individual -> new( idnumber     => $idnumber,
1913                                                  idcolumn     => $idcolumn,
1914                                                  subject_data => \@new_data_2 );
1915           push( @new_ids_2, $new_id_2 );
1916           }
1917         }
1918         my @header = @{$self -> {'header'}};
1919         my @new_header;
1920         foreach my $use_index ( @column_indexes ) {
1921           push( @new_header, @header[$use_index-1] );
1922         }
1923         my $comment;
1924         if( defined $self -> {'comment'} ){
1925           my @comment = @{$self -> {'comment'}};
1926           $comment = \@comment;
1927         }
1928         $subset = data -> new ( filename             => $subset_name,
1929                                 directory            => $self -> {'directory'},
1930                                 ignoresign           => $self -> {'ignoresign'},
1931                                 header               => \@new_header,
1932                                 comment              => $comment,
1933                                 individuals          => \@new_ids,
1934                                 target               => $target,
1935                                 ignore_missing_files => 1 );
1936         if ( $return_remainder ) {
1937           my @new_header_2;
1938           foreach my $use_index ( @remainder_indexes ) {
1939             push( @new_header_2, @header[$use_index-1] );
1940           }
1941           $remainder = data -> new ( filename             => $remainder_name,
1942                                      directory            => $self -> {'directory'},
1943                                      ignoresign           => $self -> {'ignoresign'},
1944                                      header               => \@new_header_2,
1945                                      comment              => $comment,
1946                                      individuals          => \@new_ids_2,
1947                                      target               => $target,
1948                                      ignore_missing_files => 1 );
1949         }
1950       }
1951 end subset_vertically
1952
1953 # }}}
1954
1955 # {{{ subsets
1956
1957 start subsets
1958       {
1959 #       if ( defined $expression and defined $bins ) {
1960 #         die "data -> subset: expression and bins may not both be specified\n";
1961 #       }
1962 #       if ( not ( defined $expression or defined $bins ) ) {
1963 #         die "data -> subset: expression or bins must be specified\n";
1964 #       }
1965         $self -> synchronize;
1966         my @header  = @{$self -> {'header'}};
1967         my @comment = defined $self -> {'comment'} ? @{$self -> {'comment'}} : ();
1968         my @subset_ids= ();
1969         my %rnd_ids;
1970         my $key = 0;
1971         my @ids = @{$self -> {'individuals'}};
1972         if ( defined $stratify_on ) {
1973           my $work_data = $self -> copy( filename => 'work_data.dta',
1974                                          target   => 'mem' );
1975           my %strata = %{$work_data -> factors( column => $stratify_on )};
1976 #         $Data::Dumper::Maxdepth = 1;
1977 #         print Dumper \%strata;
1978
1979           while ( my ( $factor, $keys ) = each %strata ) {
1980               foreach my $key ( @{$keys} ) {
1981                   my $rnd_num = rand;
1982                   while ( defined $rnd_ids{$factor}{$rnd_num} ) {
1983                       $rnd_num = rand;
1984                   }
1985                   $rnd_ids{$factor}{$rnd_num} = $ids[$key];
1986               }
1987           }
1988           my $first = 1;
1989           while ( my ( $factor, $rnd_nums ) = each %rnd_ids ) {
1990               my @sort_rnd_nums = sort { $a <=> $b } keys %{$rnd_nums};
1991               for ( my $i = 0; $i <= $#sort_rnd_nums; $i ) {
1992                   for ( my $j = 0; $j < $bins; $j++ ) {
1993                       if ( $first ) {
1994                           push( @subset_ids, [$rnd_ids{$factor}{$sort_rnd_nums[$i]} -> copy] );
1995                           push( @incl_ids, [$rnd_ids{$factor}{$sort_rnd_nums[$i]} -> idnumber] );
1996                       } else {
1997                           push( @{$subset_ids[$j]}, $rnd_ids{$factor}{$sort_rnd_nums[$i]} -> copy );
1998                           push( @{$incl_ids[$j]}, $rnd_ids{$factor}{$sort_rnd_nums[$i]} -> idnumber );
1999                       }
2000                       $i++;
2001                       last if $i > $#sort_rnd_nums;
2002                   }
2003                   $first = 0;
2004               }
2005           }
2006           for ( my $j = 0; $j < $bins; $j++ ) {
2007             my $sdata = data -> new ( header               => \@header,
2008                                       comment              => \@comment,
2009                                       ignoresign           => $self -> {'ignoresign'},
2010                                       individuals          => $subset_ids[$j],
2011                                       ignore_missing_files => 1,
2012                                       target               => 'disk',
2013                                       idcolumn             => $self -> {'idcolumn'},
2014                                       filename             => "subset_$j.dta" );
2015             #$sdata -> _write;
2016             push( @subsets, $sdata );
2017           }
2018         } else {
2019           for ( my $i = 0; $i <= $#ids; $i++ ) {
2020             my $rnd_num = rand;
2021             while ( defined $rnd_ids{$rnd_num} ) {
2022               $rnd_num = rand;
2023             }
2024             $rnd_ids{$rnd_num} = $ids[$i];
2025           }
2026           my @keys = sort { $a <=> $b } keys %rnd_ids;
2027           my $first = 1;
2028           for ( my $i = 0; $i <= $#keys; $i ) {
2029             for ( my $j = 0; $j < $bins; $j++ ) {
2030               if ( $first ) {
2031                 push( @subset_ids, [$rnd_ids{$keys[$i]} -> copy] );
2032                 push( @incl_ids, [$rnd_ids{$keys[$i]} -> idnumber] );
2033               } else {
2034                 push( @{$subset_ids[$j]}, $rnd_ids{$keys[$i]} -> copy );
2035                 push( @{$incl_ids[$j]}, $rnd_ids{$keys[$i]} -> idnumber );
2036               }
2037               $i++;
2038               last if $i > $#keys;
2039             }
2040             $first = 0;
2041           }
2042           for ( my $j = 0; $j < $bins; $j++ ) {
2043             my $sdata = data -> new ( header               => \@header,
2044                                       comment              => \@comment,
2045                                       ignoresign           => $self -> {'ignoresign'},
2046                                       individuals          => $subset_ids[$j],
2047                                       ignore_missing_files => 1,
2048                                       target               => $target,
2049                                       idcolumn             => $self -> {'idcolumn'},
2050                                       filename             => "subset_$j.dta" );
2051             #$sdata -> _write;
2052             push( @subsets, $sdata );
2053           }
2054         }
2055       }
2056 end subsets
2057
2058 # }}} subsets
2059
2060 # {{{ subset
2061
2062 start subset
2063       {
2064         $self -> synchronize;
2065         my @header  = @{$self -> {'header'}};
2066         my @comment = defined $self -> {'comment'} ? @{$self -> {'comment'}} : ();
2067         my @subset_inds = ();
2068         my $key = 0;
2069         foreach my $individual ( @{$self -> {'individuals'}} ) {
2070           if ( $individual -> evaluate_expression( column     => $based_on,
2071                                                    expression => $expression ) ) {
2072             push( @subset_inds, $individual -> copy );
2073             push( @incl_individuals, $individual -> idnumber );
2074             push( @included_keys, $key );
2075           }
2076           $key++;
2077         }
2078         $subset = data -> new ( header      => \@header,
2079                                 comment     => \@comment,
2080                                 ignoresign  => $self -> {'ignoresign'},
2081                                 individuals => \@subset_inds,
2082                                 idcolumn    => $self -> {'idcolumn'},
2083                                 filename    => "subset.dta" );
2084       }
2085 end subset
2086
2087 # }}} subset
2088
2089 # {{{ target
2090
2091 start target
2092       {
2093         if ( $parm eq 'disk' and $self -> {'target'} eq 'mem' ) {
2094           $self -> {'target'} = 'disk';
2095           $self -> flush;
2096         } elsif ( $parm eq 'mem' and $self -> {'target'} eq 'disk' ) {
2097           $self -> {'target'} = 'mem';
2098           $self -> synchronize;
2099         }
2100       }
2101 end target
2102
2103 # }}}
2104
2105 # {{{ _write
2106
2107 start _write
2108     {
2109       die "ERROR: data -> _write: No filename set in data object.\n"
2110           if( $filename eq '' );
2111
2112 #      $Data::Dumper::Maxdepth = 2;
2113 #      die Dumper $self -> {'individuals'};
2114
2115       if( not defined $self -> {'individuals'} ){
2116
2117         # If we don't have any individuals and write to a new
2118         # filename, we must first read individuals from the old
2119         # file. A call to synchronize will do that. There is no risk
2120         # of a infinite loop here since synchronize allways writes to
2121         # "full_name".
2122
2123         unless( $filename eq $self -> full_name ){
2124           $self -> synchronize;
2125         }
2126       }
2127
2128       open(FILE,">$filename") ||
2129           die "Could not create $filename\n";
2130       my $data_ref = $self -> format_data;
2131       my @data = @{$data_ref};
2132       for ( @data ) {
2133         print ( FILE );
2134       }
2135       close(FILE);
2136
2137 #       if ( $PsN::config -> {'_'} -> {'use_database'} and
2138 #          $self -> {'use_data_table'} ) {
2139 #       # Backslashes messes up the sql syntax
2140 #       my $file_str = $self->{'filename'};
2141 #       my $dir_str = $self->{'directory'};
2142 #       $file_str =~ s/\\/\//g;
2143 #       $dir_str =~ s/\\/\//g;
2144
2145 #       # md5sum
2146 #       my $md5sum = md5_hex(OSspecific::slurp_file($self-> full_name ));
2147 #       my ( $date_str, $time_str );
2148 #       if ( $Config{osname} eq 'MSWin32' ) {
2149 #         $date_str = `date /T`;
2150 #         $time_str = ' '.`time /T`;
2151 #       } else {
2152 #         # Assuming UNIX
2153 #         $date_str = `date`;
2154 #       }
2155 #       chomp($date_str);
2156 #       chomp($time_str);
2157 #       my $date_time = $date_str.$time_str;
2158 #       my $dbh = DBI -> connect("DBI:mysql:host=".$PsN::config -> {'_'} -> {'database_server'}.
2159 #                              ";databse=".$PsN::config -> {'_'} -> {'project'},
2160 #                                $PsN::config -> {'_'} -> {'user'},
2161 #                               $PsN::config -> {'_'} -> {'password'},
2162 #                                {
2163 #                                 'RaiseError' => 1});
2164 #       my $sth;
2165 #       if ( defined $self -> {'data_id'} ) {
2166 #         $sth = $dbh -> prepare( "UPDATE ".$PsN::config -> {'_'} -> {'project'}.
2167 #                              ".data ".
2168 #                                 "SET filename='$file_str',date='$date_time',".
2169 #                                 "directory='$dir_str',md5sum='$md5sum' ".
2170 #                                 "WHERE data_id='".$self -> {'data_id'}."'" );
2171 #         $sth -> execute or debug -> die( message => $sth->errstr ) ;
2172 #       } else {
2173 #         $sth = $dbh -> prepare("INSERT INTO ".$PsN::config -> {'_'} -> {'project'}.
2174 #                              ".data (filename,date,directory,md5sum) ".
2175 #                                "VALUES ('$file_str', '$date_time', '$dir_str','".
2176 #                                $md5sum."' )");
2177 #         $sth -> execute;
2178 #         $self -> {'data_id'} = $sth->{'mysql_insertid'};
2179 #       }
2180 #       $sth -> finish;
2181 #       $dbh -> disconnect;
2182 #       }
2183     }
2184 end _write
2185
2186 # }}} _write
2187
2188 # {{{ flush
2189 start flush
2190     {
2191       # synchronizes the object with the file on disk and empties
2192       # most of the objects attributes to save memory.
2193       if( defined $self -> {'individuals'} and
2194           ( !$self -> {'synced'} or $force ) ) {
2195         $self -> _write;
2196       }
2197 #      $self -> {'header'} = undef;
2198       $self -> {'comment'} = undef;
2199       $self -> {'individuals'} = undef;
2200       $self -> {'synced'} = 0;
2201       $self -> {'column_head_indices'} = undef;
2202       $self -> {'have_missing_data'} = undef;
2203     }
2204 end flush
2205 # }}} flush
2206
2207 # {{{ synchronize
2208
2209 start synchronize
2210     {
2211       # synchronizes the object with the file on disk
2212       unless( $self -> {'synced'} ){
2213         if( defined $self -> {'individuals'} and
2214             scalar @{$self -> {'individuals'}} > 0 ){
2215           # We should not read new data from file if we
2216           # have an individuals defined?
2217           # Perhaps there should be an attribute
2218           # 'from_file' that overrides this and reads in
2219           # the data from the file specified in filename
2220           # and overwrites whatever the object already
2221           # contains?
2222 #           if( -e $self -> {'filename'} ){
2223 #             $self -> _read_header;
2224 #             $self -> _read_individuals;
2225 #           }
2226           $self -> _write;
2227         } else {
2228           if( -e $self -> full_name ){
2229             unless( defined $self -> {'header'} and scalar @{$self -> {'header'}} > 0 ){
2230               $self -> _read_header;
2231             }
2232             $self -> _read_individuals;
2233           } else {
2234             debug -> die( message => "Fatal error: datafile: " . $self -> full_name . " does not exist." );
2235             return;
2236           }
2237         }
2238       }
2239       my $i = 1;
2240       foreach my $head ( @{$self -> {'header'}} ){
2241         $self -> {'column_head_indices'} -> {$head} = $i;
2242         $i++;
2243       }
2244       $self -> {'synced'} = 1;
2245     }
2246 end synchronize
2247
2248 # }}} synchronize
2249
2250 # {{{ _fisher_yates_shuffle
2251
2252 start _fisher_yates_shuffle
2253       {
2254         my $arr_ref = $parm{'array'};
2255         debug -> warn( level   => 1,
2256                        message => "Array of zero length received" )
2257           if ( scalar @{$arr_ref} < 1 );
2258         my $i;
2259         for ($i = @$arr_ref; --$i; ) {
2260           my $j = random_uniform_integer(1,0,$i);
2261 #          my $j = int rand ($i+1);
2262 #         print "$j $j_new\n";
2263           @$arr_ref[$i,$j] = @$arr_ref[$j,$i];
2264         }
2265       }
2266 end _fisher_yates_shuffle
2267
2268 # }}} _fisher_yates_shuffle
2269
2270 # {{{ _read_header
2271
2272 start _read_header
2273       {
2274         my $filename   = $self -> full_name;
2275         my $ignoresign = $self -> ignoresign;
2276         my ( @data, @new_record, $row, $tmp_row, @header, $hdrstring );
2277
2278         open(DATAFILE,"$filename") ||
2279           die "Could not open $filename for reading";
2280         my $columns;
2281         while (<DATAFILE>) {
2282           s/\s*\,\s*/\,/g;
2283           $tmp_row    = $_;
2284           #     @new_record = split(/\,|\s+/,$_);
2285           if ( ! (/^\s*\d+|^\s*\./) ) {
2286             $data[$row] = $tmp_row;
2287             $row++;
2288           } else {
2289             # We have reached the first data-row, return.
2290             $columns = scalar split(/\,\s*|\s+/);
2291             last;
2292           }
2293         }
2294         close(DATAFILE);
2295
2296         if ( defined $self -> {'cont_column'} and not $self -> {'table_file'} ) {
2297           my $data_len = $#data;
2298           for ( my $i = $data_len; $i >= 0; $i-- ) {
2299             my @arr = split(/\,\s*|\s+/,$data[$i]);
2300             if ( $arr[$self -> {'cont_column'}-1] eq 'CONT' ) {
2301               my $start = $i == $data_len ? 0 : 1;
2302               for ( my $j = $start; $j <= $#arr; $j++ ) {
2303                 if ( $j != ($self -> {'cont_column'}-1) ) {
2304                   push( @header, $arr[$j] );
2305                 }
2306               }
2307               pop( @data );
2308             }
2309           }
2310           # the \Q and \E here are to escape wierd ignoresigns
2311           $header[0] =~ s/\Q$ignoresign\E//
2312               if ( defined $self->ignoresign );
2313           shift( @header ) if ( $header[0] eq "" );
2314         } else {
2315           chomp( $hdrstring = pop(@data));
2316           @header = split(/\,\s*|\s+/,$hdrstring);
2317           # the \Q and \E here are to escape wierd ignoresigns
2318           $header[0] =~ s/\Q$ignoresign\E//
2319               if ( defined $self->ignoresign );
2320           shift( @header ) if ( $header[0] eq "" );
2321           if( $self -> {'table_file'} ) {
2322             my @new_header;
2323             for( my $i = 1; $i <= scalar @header; $i++ ) {
2324               if( $header[$i-1] eq 'CONT' ) {
2325                 if ( defined $self -> {'cont_column'} and not $i == $self -> {'cont_column'} ) {
2326                   debug -> warn( level   => 1,
2327                                  message => "The supplied columns for the CONT data item (".
2328                                  $self -> {'cont_column'}.") does not match the column where the CONT ".
2329                                  "header was found ($i), using $i" );
2330                 }
2331                 $self -> {'cont_column'} = $i;
2332               } else {
2333                 push( @new_header, $header[$i-1] );
2334               }
2335             }
2336             @header = @new_header;
2337             for( my $i = 1; $i <= scalar @header; $i++ ) {
2338               if( $header[$i-1] eq 'ID' ) {
2339                 if ( defined $self -> {'idcolumn'} and not $i == $self -> {'idcolumn'} ) {
2340                   debug -> warn( level   => 1,
2341                                  message => "The supplied columns for the ID data item (".
2342                                  $self -> {'idcolumn'}.") does not match the column where the CONT ".
2343                                  "header was found ($i), using $i" );
2344                 }
2345                 $self -> {'idcolumn'} = $i;
2346               }
2347             }
2348           }
2349         }
2350
2351 # I'm not certain on how to deal with this conflict. I'm leaving it commented because I believe this code should not be here.
2352 #
2353 #<<<<<<< data_subs.pm
2354 #       $header[0] =~ s/$ignoresign//
2355 #         if ( defined $self->ignoresign );
2356 #       shift( @header ) if ( $header[0] eq "" );
2357 #=======
2358 #>>>>>>> 1.28
2359
2360 # It is ok with data sets without a header.
2361 #       unless( scalar @header > 0 ){ debug -> die( message => 'Datafile ' . $self -> full_name . ' is empty.' ); }
2362
2363         $self -> {'header'} = \@header;
2364         $self -> {'comment'} = \@data;
2365 #       if ( $PsN::config -> {'_'} -> {'use_database'} and
2366 #            $self -> {'use_data_table'} ) {
2367 #         my $dbh = DBI -> connect("DBI:mysql:host=".$PsN::config -> {'_'} -> {'database_server'}.
2368 #                              ";databse=".$PsN::config -> {'_'} -> {'project'},
2369 #                                  $PsN::config -> {'_'} -> {'user'},
2370 #                               $PsN::config -> {'_'} -> {'password'},
2371 #                                  {'RaiseError' => 1});
2372 #         if ( scalar @header < 1 ) {
2373 #           for ( my $i = 1; $i <= $columns; $i++ ) {
2374 #             push( @header, $i );
2375 #           }
2376 #         }
2377 #         for ( my $i = 0; $i <= $#header; $i++ ) {
2378 #           my $sth = $dbh -> prepare("INSERT INTO ".$PsN::config -> {'_'} -> {'project'}.
2379 #                              ".data_column ".
2380 #                                     "(name,number,data_id) ".
2381 #                                     "VALUES ('".$header[$i]."', '".($i+1).
2382 #                                     "', '".$self -> {'data_id'}."' )");
2383 #           $sth -> execute;
2384 #           push( @{$self -> {'data_column_ids'}}, $sth->{'mysql_insertid'} );
2385 #           $sth -> finish;
2386 #         }
2387 #         $dbh -> disconnect;
2388 #       }
2389       }
2390 end _read_header
2391
2392 # }}} _read_header
2393
2394 # {{{ _read_individuals
2395
2396 start _read_individuals
2397       {
2398         my $idcol        = $self -> idcolumn;
2399         my $filename     = $self -> full_name;
2400         #debug -> warn( level   => 1,
2401         #              message => "Building array of individuals from file " . $self -> {'filename'} );
2402         open(DATAFILE,"$filename") ||
2403           die "Could not open $filename for reading";
2404         my ( @new_row, $new_ID, $old_ID, @init_data );
2405         my $buffer;
2406         my $lines = 0;
2407         while (sysread DATAFILE, $buffer, 4096) {
2408           $lines += ($buffer =~ tr/\n//);
2409         }
2410         seek( DATAFILE, 0,0 );
2411
2412         # For status bar:
2413         my $status_bar = status_bar -> new( steps => $lines );
2414
2415         ui -> print( category => 'scm',
2416                      message  => "Reading data file: ".$self -> filename );
2417         ui -> print( category => 'scm',
2418                      message => $status_bar -> print_step(),
2419                      newline => 0);
2420
2421         my ( $sth, $dbh, $first_row_id, $first_value_id );
2422         my $insert = 1;
2423 #       if ( $PsN::config -> {'_'} -> {'use_database'} and
2424 #            $self -> {'use_data_table'} ) {
2425 #         $dbh = DBI -> connect("DBI:mysql:host=".$PsN::config -> {'_'} -> {'database_server'}.
2426 #                              ";databse=".$PsN::config -> {'_'} -> {'project'},
2427 #                               $PsN::config -> {'_'} -> {'user'},
2428 #                               $PsN::config -> {'_'} -> {'password'},
2429 #                               {'RaiseError' => 1});
2430 #         my $sth = $dbh -> prepare( "SELECT data_row_id FROM ".$PsN::config -> {'_'} -> {'project'}.
2431 #                              ".data_row ".
2432 #                                    "WHERE data_id='".$self -> {'data_id'}."'" );
2433 #         $sth -> execute or debug -> die( message => $sth->errstr ) ;
2434 #         my $select_arr = $sth -> fetchall_arrayref;
2435 #         if ( scalar @{$select_arr} > 0 ) {
2436 #           for ( my $i = 0; $i < scalar @{$select_arr}; $i++ ) {
2437 #             push( @{$self -> {'data_row_ids'}}, $select_arr->[$i][0] );
2438 #           }
2439 #           $sth = $dbh -> prepare( "SELECT data_value_id FROM ".$PsN::config -> {'_'} -> {'project'}.
2440 #                              ".data_value ".
2441 #                                   "WHERE data_id='".$self -> {'data_id'}."'" );
2442 #           $sth -> execute or debug -> die( message => $sth->errstr ) ;
2443 #           my $select_val = $sth -> fetchall_arrayref;
2444 #           for ( my $i = 0; $i < scalar @{$select_val}; $i++ ) {
2445 #             push( @{$self -> {'data_value_ids'}}, $select_val->[$i][0] );
2446 #           }
2447 #           $insert = 0;
2448 #           $dbh -> disconnect;
2449 #         } else {
2450 #           $dbh -> do( "LOCK TABLES ".$PsN::config -> {'_'} -> {'project'}.
2451 #                              ".data_row WRITE, ".$PsN::config -> {'_'} -> {'project'}.
2452 #                              ".data_value WRITE" );
2453 #           $sth = $dbh -> prepare( "SELECT MAX(data_row_id) FROM ".$PsN::config -> {'_'} -> {'project'}.
2454 #                              ".data_row" );
2455 #           $sth -> execute or debug -> die( message => $sth->errstr ) ;
2456 #           my $select_arr = $sth -> fetchall_arrayref;
2457 #           $first_row_id = defined $select_arr -> [0][0] ? $select_arr -> [0][0] : 0;
2458 #           $sth = $dbh -> prepare( "SELECT MAX(data_value_id) FROM ".$PsN::config -> {'_'} -> {'project'}.
2459 #                              ".data_value" );
2460 #           $sth -> execute or debug -> die( message => $sth->errstr ) ;
2461 #           my $select_arr = $sth -> fetchall_arrayref;
2462 #           $first_value_id = defined $select_arr -> [0][0] ? $select_arr -> [0][0] : 0;
2463 #         }
2464 #         $sth -> finish;
2465 #       }
2466
2467         my $insert_rows;
2468         my $insert_values;
2469         my $row_counter = 0;
2470         my $full_row;
2471       ROW: while ( <DATAFILE> ) {
2472           s/^ *//;
2473           s/\s*\,\s*/\,/g;
2474           my @new_row   = split(/\,\s*|\s+/);
2475           # This regexp check is not time consuming.
2476           if ( /^\s*\d+|^\s*\./ ) {
2477             if ( defined $self -> {'cont_column'} ) {
2478               if ( $new_row[$self -> {'cont_column'} - 1] == 1 ) {
2479                 if ( not $self -> {'table_file'} ) { # Skip the CONT=1 rows if this is a table file
2480                   for ( my $i = $#new_row; $i > 0; $i-- ) {
2481                     if ( $i != ($self -> {'cont_column'} - 1) ) {
2482                       unshift( @{$full_row}, $new_row[$i] );
2483                     }
2484                   }
2485                 }
2486                 next ROW;
2487               } else {
2488                 for ( my $i = $#new_row; $i >= 0; $i-- ) {
2489 #                 if ( $i != ($self -> {'cont_column'} - 1) or $self -> {'table_file'} ) {
2490                   if ( $i != ($self -> {'cont_column'} - 1) ) {
2491                     unshift( @{$full_row}, $new_row[$i] );
2492                   }
2493                 }
2494               }
2495             } else {
2496               @{$full_row} = @new_row;
2497             }
2498             $new_ID = $full_row -> [$idcol-1]; # index starts at 0
2499             $old_ID = $new_ID if ( not defined $old_ID );
2500
2501             # Check if column miss data at some row (This adds about 30% of init time)
2502             my $mdt = $self -> {'missing_data_token'};
2503             for( my $i = 0; $i <= $#{$full_row}; $i++ ){
2504                 $self -> {'have_missing_data'} -> {$i+1} = 1
2505                   if( $full_row -> [$i] == $mdt ); # == is slower but safer than eq
2506             }
2507 #           if ( $PsN::config -> {'_'} -> {'use_database'} and
2508 #                $self -> {'use_data_table'} and $insert ) {
2509 #             $row_counter++;
2510 #             $insert_rows = $insert_rows."," if ( defined $insert_rows );
2511 #             $insert_rows = $insert_rows.
2512 #               "('$row_counter', '".$self -> {'data_id'}."' )";
2513 #             for ( my $j = 0; $j <= $#{$full_row}; $j++ ) {
2514 #               $insert_values = $insert_values."," if ( defined $insert_values );
2515 #               $insert_values = $insert_values.
2516 #                 "('".$full_row -> [$j]."', '".
2517 #                   ($first_row_id+$row_counter)."', '".
2518 #                     $self -> {'data_column_ids'}->[$j].
2519 #                       "', '".$self -> {'data_id'}."' )";
2520 #             }
2521 #           }
2522
2523             if ( $new_ID != $old_ID ) {
2524               my @subject_data = @init_data;
2525               my $id = data::individual -> new ( idcolumn     => $idcol,
2526                                                  subject_data => \@subject_data,
2527                                                  data_id      => $self -> {'data_id'} );
2528               push( @{$self -> {'individuals'}}, $id );
2529               @init_data =(join( ",", @{$full_row}));
2530             } else {
2531               push( @init_data, join( ",", @{$full_row}) );
2532             }
2533             $old_ID = $new_ID;
2534             $full_row = undef;
2535           }
2536           if ( $status_bar -> tick() ) {
2537             ui -> print( category => 'scm',
2538                          message  => $status_bar -> print_step(),
2539                          wrap     => 0,
2540                          newline  => 0 );
2541           }
2542         }
2543
2544 #       if ( $PsN::config -> {'_'} -> {'use_database'} and
2545 #            $self -> {'use_data_table'} and $insert ) {
2546 #         $dbh -> do("INSERT INTO ".$PsN::config -> {'_'} -> {'project'}.
2547 #                    ".data_row ".
2548 #                    "(number,data_id) ".
2549 #                    "VALUES ".$insert_rows);
2550 #         push( @{$self -> {'data_row_ids'}}, ($first_row_id..$first_row_id+$row_counter) );
2551 #         $dbh -> do( "INSERT INTO ".$PsN::config -> {'_'} -> {'project'}.
2552 #                     ".data_value ".
2553 #                     "(value,data_row_id,data_column_id,data_id) ".
2554 #                     "VALUES ".$insert_values );
2555 #         push( @{$self -> {'data_value_ids'}},
2556 #               ($first_value_id..$first_value_id+($row_counter*
2557 #                                                  scalar @{$self->{'data_column_ids'}})));
2558 #         $dbh -> do( "UNLOCK TABLES" );
2559 #         $dbh -> disconnect;
2560 #       }
2561
2562         if ( $#init_data >= 0 ) {
2563           push( @{$self -> {'individuals'}},
2564                 data::individual -> new ( idcolumn     => $idcol,
2565                                           subject_data => \@init_data ) );
2566         }
2567         ui -> print( category => 'scm',
2568                      message  => " ... done" );
2569         close(DATAFILE);
2570 #       $self -> _write( filename => 'test.dta' );
2571       }
2572 end _read_individuals
2573
2574 # }}} _read_individuals
2575