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         $num = scalar @{$self -> {'individuals'}};
 729       }
 730 end count_ind
 731
 732 # }}} count_ind
 733
 734 # {{{ diff
 735 start diff
 736 {
 737   $self -> synchronize;
 738
 739   my $first_id = $self -> {'individuals'}[0];
 740
 741   debug -> die( message => "No individuals defined in data object based on ".
 742                 $self -> full_name ) unless ( defined $first_id );
 743
 744   # Check if $column(-index) is defined and valid, else try to find index
 745   # using column_head
 746
 747   my @data_row = split( /,/, $first_id -> subject_data -> [0] );
 748   if( $#columns >= 0 ) {
 749     foreach my $column ( @columns ) {
 750       unless ( defined $column && defined( $data_row[$column-1] ) ) {
 751         debug -> die( message => "Error in data -> factors: ".
 752                       "invalid column number: \"$column\"\n".
 753                       "Valid column numbers are 1 to ".
 754                       scalar @{$first_id -> subject_data ->[0]}."\n" );
 755       }
 756     }
 757   } elsif ( $#column_heads >= 0 ) {
 758     foreach my $column_head ( @column_heads ) {
 759       unless (defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})) {
 760         debug -> die( message => "Error in data -> factors: unknown column: \"$column_head\" ".
 761                       "Valid column headers are (in no particular order):\n".
 762                       join(', ',keys(%{$self -> {'column_head_indices'}})) );
 763       } else {
 764         my $column = $self -> {'column_head_indices'}{$column_head};
 765         push( @columns, $column );
 766         debug -> warn( level   => 2,
 767                        message => "$column_head is in column number $column" );
 768       }
 769     }
 770   } else {
 771     debug -> die( message => "No column or column_head defined" );
 772   }
 773
 774   if( $global_largest or $global_smallest or
 775       $largest_per_individual or $smallest_per_individual ) {
 776     if( not scalar @{$self -> {'individuals'}} == scalar @{$against_data -> individuals} ) {
 777       debug -> die( message => "Both data object must hold the same number of individuals ".
 778                     "and observations when calling data -> diff" );
 779     }
 780     for( my $i = 0; $i < scalar @{$self -> {'individuals'}}; $i++ ) {
 781       my %id_diffs = %{$self -> {'individuals'}[$i] ->
 782                            diff( against_individual => $against_data -> individuals -> [$i],
 783                                  columns            => \@columns,
 784                                  absolute_diff      => $absolute_diff,
 785                                  diff_as_fraction   => $diff_as_fraction,
 786                                  largest            => ( $global_largest or $largest_per_individual ),
 787                                  smallest           => ( $global_smallest or $smallest_per_individual ) )};
 788       if( $global_largest ) {
 789         for( my $j = 0; $j <= $#columns; $j++ ) {
 790           my $label = defined $column_heads[$j] ? $column_heads[$j] : $columns[$j];
 791           if( not defined $diff_results{$label} or not defined $diff_results{$label}{'diff'} or
 792               $id_diffs{$columns[$j]}{'diff'} > $diff_results{$label}{'diff'} ) {
 793             $diff_results{$label}{'diff'} = $id_diffs{$columns[$j]}{'diff'};
 794             $diff_results{$label}{'self'} = $id_diffs{$columns[$j]}{'self'};
 795             $diff_results{$label}{'test'} = $id_diffs{$columns[$j]}{'test'};
 796           }
 797         }
 798       }
 799     }
 800   } else {
 801     die "data -> diff is only implemented for finding the largest difference at any observation at this point\n";
 802   }
 803 }
 804 end diff
 805 # }}} diff
 806
 807 # {{{ filename
 808 start filename
 809       {
 810         if ( defined $parm and $parm ne $self -> {'filename'} ) {
 811           $self -> {'filename'} = $parm;
 812           $self -> {'data_id'} = undef;
 813 #         $self -> _write;
 814         }
 815       }
 816 end filename
 817 # }}} filename
 818
 819 # {{{ fractions
 820
 821 start fractions
 822       {
 823         my %factors = $self -> factors( 'return_occurences' => 1,
 824                                         'unique_in_individual' => $unique_in_individual,
 825                                         'column_head' => $column_head,
 826                                         'column' => $column);
 827
 828         my $sum = 0;
 829         while (my ($factor, $amount) = each %factors) {
 830           if ( $factor == $self -> {'missing_data'} && $ignore_missing ) {
 831             next;
 832           } else {
 833             $sum += $amount;
 834           }
 835         }
 836         while (my ($factor, $amount) = each %factors) {
 837           if ( $factor == $self -> {'missing_data'} && $ignore_missing ) {
 838             next;
 839           } else {
 840             $fractions{$factor} = $amount/$sum;
 841           }
 842         }
 843       }
 844 end fractions
 845
 846 # }}} fractions
 847
 848 # {{{ factors
 849
 850 start factors
 851       {
 852         # Either column (number, starting at 1) or column_head must be specified.
 853         #
 854         # The default behaviour is to return a hash with the factors as keys
 855         # and as values references to arrays with the order numbers (not the ID numbers)
 856         # of the individuals that contain this factor
 857         #
 858         # If unique_in_individual is true (1), the returned hash will contain
 859         # an element with key 'Non-unique values found' and value 1 if any
 860         # individual contain more than one value in the specified column.
 861         #
 862         # Return occurences will calculate the occurence of each
 863         # factor value. Several occurences in one individual counts as
 864         # one occurence. The elements of the returned hash will have the factors
 865         # as keys and the number of occurences as values.
 866         #
 867
 868         $self -> synchronize;
 869
 870         # Check if $column(-index) is defined and valid, else try to find index
 871         # using column_head
 872         my $first_id = $self -> {'individuals'}[0];
 873
 874         debug -> die( message => "No individuals defined in data object based on ".
 875                       $self -> full_name ) unless ( defined $first_id );
 876
 877         my @data_row = split( /,/, $first_id -> subject_data -> [0] );
 878         unless ( defined $column && defined( $data_row[$column-1] ) ) {
 879           unless (defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})) {
 880             debug -> die( message => "Error in data -> factors: unknown column: \"$column_head\" ".
 881                           "or invalid column number: \"$column\".\n".
 882                           "Valid column numbers are 1 to ".scalar @data_row ."\n".
 883                           "Valid column headers are (in no particular order):\n".
 884                           join(', ',keys(%{$self -> {'column_head_indices'}})) );
 885           } else {
 886             $column = $self -> {'column_head_indices'}{$column_head};
 887             debug -> warn( level   => 2,
 888                            message => "$column_head is in column number $column" );
 889           }
 890         }
 891
 892         my $key = 0;
 893         foreach my $individual ( @{$self -> {'individuals'}} ) {
 894           my @ifactors = keys %{$individual -> factors( column => $column )};
 895           if ( scalar @ifactors > 1 and $unique_in_individual ) {
 896             %factors = ( 'Non-unique values found' => 1 );
 897             last;
 898           }
 899           debug -> die( message => "No value found in column $column in individual ".
 900                         $individual -> idnumber ) if ( scalar @ifactors == 0 );
 901
 902           # Return occurences will calculate the occurence of each
 903           # factor value. Several occurences in one individual counts as
 904           # one occurence.
 905
 906           if ( $return_occurences ) {
 907             foreach my $ifactor ( @ifactors ) {
 908               $factors{$ifactor}++;
 909             }
 910           } else {
 911             foreach my $ifactor ( @ifactors ) {
 912               push( @{$factors{$ifactor}}, $key );
 913             }
 914           }
 915           $key++;
 916         }
 917       }
 918 end factors
 919
 920 # }}} factors
 921
 922 # {{{ find_individual
 923
 924 # start find_individual
 925 #         foreach my $tmp_ind ( @{$self -> individuals} ) {
 926 #         if ( $tmp_ind -> key == $key ) {
 927 #           $individual = $tmp_ind;
 928 #           last;
 929 #         }
 930 #       }
 931 #         if ( defined $individual ) {
 932 #         if ( $copy ) {
 933 #           $individual = $individual -> copy;
 934 #         }
 935 #       } else {
 936 #         print "No individual with key $key found in call to ".
 937 #           "data -> find_individual\n" if ( $self -> debug );
 938 #         }
 939 # end find_individual
 940
 941 # }}}
 942
 943 # {{{ format_data
 944
 945 start format_data
 946       {
 947         my $header = $self -> {'header'};
 948
 949         # format the data for NONMEM (simple comma-separated layout)
 950         if ( defined $self -> {'comment'} ) {
 951           my @comment   = @{$self -> {'comment'}};
 952           for ( @comment ) {
 953             push( @form_data );
 954           }
 955         }
 956
 957         my $wrap = ( defined $self -> {'wrap_column'} and
 958                      defined $self -> {'cont_column'} );
 959
 960         my @primary_columns = defined $self -> {'primary_columns'} ?
 961           @{$self -> {'primary_columns'}} : ();
 962         my @secondary_columns = defined $self -> {'secondary_columns'} ?
 963           @{$self -> {'secondary_columns'}} : ();
 964         if ( defined $header and defined $self -> {'ignoresign'} ) {
 965           my $istr;
 966           if ( $self -> {'ignoresign'} ne '@' ) {
 967             $istr = $self -> {'ignoresign'};
 968           }
 969           if ( $wrap ) {
 970             my @h_data;
 971             for ( my $i = 0; $i <= $#secondary_columns ; $i++ ) {
 972               my $sstr = $istr;
 973               for ( my $j = 0; $j < scalar @{$secondary_columns[$i]} ; $j++ ) {
 974                 my $jstr = $j == 0 ? '' : ',';
 975                 $sstr = $sstr.$jstr.$secondary_columns[$i][$j][0];
 976               }
 977               push( @h_data, $sstr."\n" );
 978             }
 979             push( @form_data, @h_data );
 980             my $pstr = $istr;
 981             for ( my $i = 0; $i <= $#primary_columns ; $i++ ) {
 982               my $jstr = $i == 0 ? '' : ',';
 983               $pstr = $pstr.$jstr.$primary_columns[$i][0];
 984             }
 985             push( @form_data, $pstr."\n" );
 986           } else {
 987             push( @form_data, $istr.join(',',@{$self -> {'header'}})."\n" );
 988           }
 989         }
 990         if ( $wrap ) {
 991           foreach my $individual ( @{$self -> {'individuals'}} ) {
 992             foreach my $row ( @{$individual -> subject_data} ) {
 993               my @r_data;
 994               for ( my $i = 0; $i <= $#secondary_columns ; $i++ ) {
 995                 my $sstr = '';
 996                 for ( my $j = 0; $j < scalar @{$secondary_columns[$i]} ; $j++ ) {
 997                   my $jstr = $j == 0 ? '' : ',';
 998                   if ( $secondary_columns[$i][$j][0] eq 'CONT' ) {
 999                     $sstr = $sstr.$jstr.'1';
1000                   } else {
1001                     my @data_row = split( /,/, $row );
1002                     $sstr = $sstr.$jstr.$data_row[$secondary_columns[$i][$j][1]];
1003                   }
1004                 }
1005                 push( @r_data, $sstr."\n" );
1006               }
1007               push( @form_data, @r_data );
1008               my $pstr = '';
1009               for ( my $i = 0; $i <= $#primary_columns ; $i++ ) {
1010                 my $jstr = $i == 0 ? '' : ',';
1011                 if ( $primary_columns[$i][0] eq 'CONT' ) {
1012                   $pstr = $pstr.$jstr.'0';
1013                 } else {
1014                   my @data_row = split( /,/, $row );
1015                   $pstr = $pstr.$jstr.$data_row[$primary_columns[$i][1]];
1016                 }
1017               }
1018               push( @form_data, $pstr."\n" );
1019             }
1020           }
1021         } else {
1022           foreach my $individual ( @{$self -> {'individuals'}} ) {
1023             foreach my $row ( @{$individual -> subject_data} ) {
1024               push( @form_data, $row ."\n" );
1025             }
1026           }
1027         }
1028       }
1029 end format_data
1030
1031 # }}} format_data
1032
1033 # {{{ drop_dropped
1034
1035 start drop_dropped
1036       {
1037         # This method removes columns that has '=DROP' value in the
1038         # model header as given by $INPUT. The model header must be
1039         # transfered to this method through the model_header
1040         # argument. The model_header argument should be a
1041         # two-dimensional array where each position in the first
1042         # dimension should be a reference to a 1*2 array holding the
1043         # column name and value. Any ignore-sign must be removed.
1044
1045         debug -> die( message => 'model header must be defined' )
1046           if ( $#model_header < 0 );
1047         # Important that the drop_dropped method of the model::problem
1048         # class is in sync with this method.
1049         $self -> synchronize;
1050
1051         $self -> {'header'} = [];
1052         my @drop;
1053         my $counter = 1;
1054         for( my $i = 0; $i <= $#model_header; $i++ ) {
1055           $self -> {'idcolumn'} = $counter if ( $model_header[$i][0] eq 'ID' );
1056           if( ( $model_header[$i][1] eq 'DROP' or
1057                 $model_header[$i][1] eq 'SKIP' ) and
1058               not $model_header[$i][0] =~ /DAT(E|1|2|3)/ ) {
1059             push( @drop, 1 );
1060           } else {
1061             $counter++;
1062             push( @drop, 0 );
1063             push( @{$self -> {'header'}}, $model_header[$i][0] );
1064           }
1065         }
1066
1067         foreach my $individual ( @{$self -> {'individuals'}} ) {
1068           $individual -> drop_columns( drop => \@drop );
1069         }
1070
1071         $self -> {'synced'} = 0;
1072 #       $Data::Dumper::Maxdepth = 2;
1073 #       die Dumper $self;
1074 #       die Dumper $self -> {'individuals'};
1075       }
1076 end drop_dropped
1077
1078 # }}} drop_dropped
1079
1080 # {{{ wrap
1081 start wrap
1082       {
1083         $self -> synchronize;
1084         $self -> cont_column( $cont_column ) if ( defined $cont_column );
1085         $self -> wrap_column( $wrap_column ) if ( defined $wrap_column );
1086         $self -> prepare_wrap( model_header => \@model_header );
1087         @secondary_columns = @{$self -> {'secondary_columns'}}
1088           if ( defined $self -> {'secondary_columns'} );
1089         @primary_columns = @{$self -> {'primary_columns'}}
1090           if ( defined $self -> {'primary_columns'} );
1091       }
1092 end wrap
1093 # }}} wrap
1094
1095 # {{{ unwrap
1096 start unwrap
1097       {
1098         $self -> {'cont_column'} = undef;
1099         $self -> {'wrap_column'} = undef;
1100         $self -> {'secondary_columns'} = undef;
1101         $self -> {'primary_columns'} = undef;
1102       }
1103 end unwrap
1104 # }}} unwrap
1105
1106 # {{{ prepare_wrap
1107
1108 start prepare_wrap
1109       {
1110         my $cont_column = $self -> {'cont_column'};
1111         my $wrap_column = $self -> {'wrap_column'};
1112         debug -> die( message => 'cont_column ('.$cont_column.') must be less or equal '.
1113                       'to the requested number of columns in each row ('.
1114                       ($wrap_column).')' )
1115           if ( $cont_column > $wrap_column );
1116         my @header;
1117         if ( scalar @model_header > 0 ) {
1118           @header = @model_header;
1119         } else {
1120           @header = @{$self -> {'header'}};
1121         }
1122
1123         my ( @primary, @secondary, @date_columns );
1124
1125         for ( my $i = 0; $i <= $#header; $i++ ) {
1126           my $name  = ref( $header[$i] ) eq 'ARRAY' ? $header[$i][0] : $header[$i];
1127           my $value = ref( $header[$i] ) eq 'ARRAY' ? $header[$i][1] : undef;
1128           next if ( $name eq 'ID' );
1129           my $found = 0;
1130           foreach my $prim ( @primary_column_names ) {
1131             if ( not $found and
1132                  ( $name eq $prim or $value eq $prim ) ) {
1133               push( @primary, [$name, $i, $value] );
1134               $found = 1;
1135               my $col = ($#primary+2)>= $cont_column ? ($#primary+3) : ($#primary+2);
1136               push( @date_columns, $col ) if ( $name =~ /DAT(E|1|2|3)/ );
1137             }
1138           }
1139           push( @secondary, [$name, $i, $value] ) if ( not $found );
1140         }
1141
1142         my $prim_num = scalar @primary;
1143         debug -> die( message => 'The number of primary columns (that need to '.
1144                       'be part of the row with CONT=0) ('.($prim_num+1).
1145                       ') is larger than the required number of columns (wrap_column='.
1146                       $wrap_column.') - 1' )
1147           if ( scalar $prim_num > ($wrap_column-2) );
1148
1149         my ( $i, $dum ) = ( 0, 1 );
1150         my @tmp;
1151         for ( my $j = 1; $j <= $wrap_column; $j++ ) {
1152           if( $j == 1 ) {
1153             push( @tmp, ['ID', $self -> {'idcolumn'}-1] );
1154           } elsif ( $j == $wrap_column ) {
1155             if ( $j == $cont_column ) {
1156               push( @tmp, ['CONT', undef] );
1157             } else {
1158               my $val;
1159               if ( defined $primary[$i] ) {
1160                 $val = $primary[$i];
1161               } elsif ( defined $secondary[0] ) {
1162                 $val = shift(@secondary);
1163               } else {
1164                 $val = ['XX'.$dum++,$self -> {'idcolumn'}-1];
1165               }
1166               push( @tmp, $val );
1167               $i++;
1168             }
1169             push( @{$self -> {'primary_columns'}}, @tmp );
1170           } else {
1171             if ( $j == $cont_column ) {
1172               push( @tmp, ['CONT', undef] );
1173             } else {
1174               if ( $i <= $#primary ) {
1175                 push( @tmp, $primary[$i] );
1176                 $i++;
1177               } else {
1178                 my $val = defined $secondary[0] ? shift(@secondary) :
1179                   ['XX'.$dum++,$self -> {'idcolumn'}-1];
1180                 push( @tmp, $val );
1181               }
1182             }
1183           }
1184         }
1185
1186         my $i = 0;
1187         while ( $i <= $#secondary ) {
1188           my @tmp;
1189           for ( my $j = 1; $j <= $wrap_column; $j++ ) {
1190             if( $j == 1 ) {
1191               push( @tmp, ['ID', $self -> {'idcolumn'}-1] );
1192             } elsif ( $j == $wrap_column ) {
1193               if ( $j == $cont_column ) {
1194                 push( @tmp, ['CONT', undef] );
1195               } else {
1196                 my $val = defined $secondary[$i] ? $secondary[$i] :
1197                   ['XX'.$dum++,$self -> {'idcolumn'}-1];
1198                 push( @tmp, $val );
1199                 $i++;
1200               }
1201               unshift( @{$self -> {'secondary_columns'}}, \@tmp );
1202             } else {
1203               if ( $j == $cont_column ) {
1204                 push( @tmp, ['CONT', undef] );
1205               } else {
1206                 my $isdate = 0;
1207                 if ( $#date_columns >= 0 ) {
1208                   foreach my $col ( @date_columns ) {
1209                     # This is a date column which may have to be dropped
1210                     # and thus will not appear as a secondary
1211                     # column. Nothing should be pushed. The indexes in
1212                     # model::problem::pk::_format_record will be ok.
1213                     $isdate = 1 if ( $col == $j ) ;
1214                   }
1215                 }
1216                 if ( $isdate ) {
1217                   push( @tmp, ['XX'.$dum++,$self -> {'idcolumn'}-1] );
1218                 } else {
1219                   if ( $i <= $#secondary ) {
1220                     push( @tmp, $secondary[$i] );
1221                     $i++;
1222                   } else {
1223                     push( @tmp, ['XX'.$dum++,$self -> {'idcolumn'}-1] );
1224                   }
1225                 }
1226               }
1227             }
1228           }
1229         }
1230       }
1231 end prepare_wrap
1232
1233 # }}} prepare_wrap
1234
1235 # {{{ have_missing_data
1236 start have_missing_data
1237       {
1238         # Either I<column> or I<column_head> must be specified.
1239         #
1240         # This method looks through the data column with index I<column> or
1241         # (optional) header name I<column_head> and returns O if no missing
1242         # data indicator was found or 1 otherwise.
1243
1244         $self -> synchronize;
1245         my $first_id = $self -> {'individuals'}[0];
1246         debug -> die( message => "No individuals defined in data object based on ".
1247                       $self -> full_name ) unless ( defined $first_id );
1248         my @data_row = split( /,/ , $first_id -> subject_data -> [0] );
1249         unless ( defined $column  && defined( $data_row[$column-1] ) ) {
1250           unless(defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})){
1251             die "Error in data -> have_missing_data: unknown column: \"$column_head\" or invalid column number: \"$column\"\n";
1252           } else {
1253             $column = $self -> {'column_head_indices'}{$column_head};
1254           }
1255         }
1256         $self -> flush if ( $self -> {'target'} eq 'disk' );
1257
1258         # In case anyone wonders, the ternary statment ( bool ? true :
1259         # false ) below will possibly make a minuscle memory
1260         # optimization. But hey, why not :)
1261
1262         $return_value = defined $self -> {'have_missing_data'} ? $self -> {'have_missing_data'} -> {$column} : 0;
1263       }
1264 end have_missing_data
1265 # }}} have_missing_data
1266
1267 # {{{ merge
1268 start merge
1269       {
1270         #$self -> synchronize;
1271         push( @{$self -> {'individuals'}}, @{$mergeobj -> individuals} );
1272       }
1273 end merge
1274 # }}} merge
1275
1276 # {{{ max
1277
1278 start max
1279       {
1280         # Either column or column_head must be specified. Column_head must be a string that
1281         # identifies a column in the (optional ) data file header.
1282
1283 # The if-statement below used to be a cache of allready calculated
1284 # means. But since individuals can be accessed in so many ways, we
1285 # don't know when this cache should be updated. Its easier to
1286 # recalculate the max. Maybe we can include this optimization in the
1287 # future, if it turns out to be a bottleneck
1288 #       my $tmp_column = $self -> {'column_head_indices'}{$column_head};
1289 #       if ( defined $self -> {'max'}[$tmp_column] ) {
1290 #         $return_value = $self -> {'max'}[$tmp_column] ;
1291 #       } else {
1292           $self -> synchronize;
1293           my $first_id = $self -> {'individuals'}[0];
1294           debug -> die( message => "data -> max: No individuals defined in data object based on " .
1295                         $self -> full_name ) unless defined $first_id;
1296
1297           my @data_row = split( /,/ , $first_id -> subject_data ->[0] );
1298
1299           unless ( defined $column  && defined( $data_row[$column-1] ) ) {
1300             unless (defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})) {
1301               die "Error in data -> max: unknown column: \"$column_head\" or invalid column number: \"$column\"\n";
1302             } else {
1303               $column = $self -> {'column_head_indices'}{$column_head};
1304             }
1305           }
1306           foreach my $individual ( @{$self -> {'individuals'}} ) {
1307             my $ifactors = $individual -> factors( 'column' => $column );
1308             foreach ( keys %{$ifactors} ) {
1309               next if ( $_ == $self -> {'missing_data_token'} );
1310               if ( defined ($return_value) ) {
1311                 $return_value = $_ > $return_value ? $_ : $return_value;
1312               } else {
1313                 $return_value = $_;
1314               }
1315             }
1316           }
1317
1318 #         $self -> {'max'}[$column] = $return_value;
1319           $self -> flush if ( $self -> {'target'} eq 'disk' );
1320 #       }
1321       }
1322 end max
1323
1324 # }}} max
1325
1326 # {{{ min
1327
1328 start min
1329       {
1330         # See L</max>.
1331         my $tmp_column = $self -> {'column_head_indices'}{$column_head};
1332
1333 # The if-statement below used to be a cache of allready calculated
1334 # means. But since individuals can be accessed in so many ways, we
1335 # don't know when this cache should be updated. Its easier to
1336 # recalculate the min. Maybe we can include this optimization in the
1337 # future, if it turns out to be a bottleneck
1338 #       if ( defined $self -> {'min'}[$tmp_column] ) {
1339 #         $return_value = $self -> {'min'}[$tmp_column] ;
1340 #       } else {
1341           $self -> synchronize;
1342           my $first_id = $self -> {'individuals'}[0];
1343           die "data -> min: No individuals defined in data object based on ",
1344             $self -> full_name,"\n" unless defined $first_id;
1345
1346           my @data_row = split( /,/ , $first_id -> subject_data ->[0] );
1347
1348           unless ( defined $column  && defined( $data_row[$column-1] ) ) {
1349             unless (defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})) {
1350               die "Error in data -> min: unknown column: \"$column_head\" or invalid column number: \"$column\"\n";
1351             } else {
1352               $column = $self -> {'column_head_indices'}{$column_head};
1353             }
1354           }
1355           foreach my $individual ( @{$self -> {'individuals'}} ) {
1356             my $ifactors = $individual -> factors( 'column' => $column );
1357             foreach ( keys %{$ifactors} ) {
1358               next if ( $_ == $self -> {'missing_data_token'} );
1359               if ( defined ($return_value) ) {
1360                 $return_value = $_ < $return_value ? $_ : $return_value;
1361               } else {
1362                 $return_value = $_;
1363               }
1364             }
1365           }
1366 #         $self -> {'min'}[$column] = $return_value;
1367           $self -> flush if ( $self -> {'target'} eq 'disk' );
1368 #       }
1369       }
1370 end min
1371
1372 # }}} min
1373
1374 # {{{ median
1375
1376 start median
1377       {
1378           # See L</max>.
1379         $self -> synchronize;
1380         my $first_id = $self -> {'individuals'}[0];
1381         die "data -> median: No individuals defined in data object based on ",
1382           $self -> full_name,"\n" unless defined $first_id;
1383
1384         my @data_row = split( /,/ , $first_id -> subject_data ->[0] );
1385
1386         unless ( defined $column  && defined( $data_row[$column-1] ) ) {
1387           unless(defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})){
1388             die "Error in data -> median: unknown column: \"$column_head\" or invalid column number: \"$column\"\n";
1389           } else {
1390             $column = $self -> {'column_head_indices'}{$column_head};
1391           }
1392         }
1393
1394         if( defined $self -> {'median'}[$column] ){
1395           return $self -> {'median'}[$column];
1396         }
1397
1398         my @median_array;
1399
1400         foreach my $individual ( @{$self -> {'individuals'}} ) {
1401           if( $unique_in_individual ){
1402             my $ifactors = $individual -> factors( 'column' => $column );
1403
1404             foreach ( keys %{$ifactors} ) {
1405               next if ( $_ == $self -> {'missing_data_token'} );
1406               push( @median_array, $_ );
1407             }
1408           } else {
1409             my $ifactors = $individual -> subject_data;
1410
1411             for(my $i=0; $i<=$#{$ifactors}; $i++ ) {
1412               my @data_row = split( /,/ , $ifactors -> [$i] );
1413               next if ( $data_row[$column-1] == $self -> {'missing_data_token'} );
1414               push(@median_array, $data_row[$column-1]);
1415             }
1416           }
1417         }
1418         @median_array = sort {$a <=> $b} @median_array ;
1419
1420         if( @median_array % 2 ){
1421           $return_value = $median_array[$#median_array / 2];
1422         } else {
1423           $return_value = ( $median_array[@median_array / 2] +
1424                             $median_array[(@median_array - 2) / 2] ) / 2;
1425         }
1426
1427         $self -> {'median'}[$column] = $return_value;
1428       }
1429 end median
1430
1431 # }}} median
1432
1433 # {{{ mean
1434
1435 start mean
1436   {
1437      # Returns mean value of a column
1438      # If a individual contains more then 1 value (i.e. if an
1439      # individual has different values in different samples a mean
1440      # value of all individuals if calculate first, then the mean
1441      # value of the column If hi_cutoff is defined the mean function
1442      # will cut all value below the cutoff, and set their value to
1443      # 0. It's used to calculate the HI-mean/LOW-mean of a column for
1444      # e.g. Hockey-stick covariates If both hi_cutoff and low_cutoff
1445      # are defined only the hi_cutoff will be used.  See L</max>.
1446      my $tmp_column = $self -> {'column_head_indices'}{$column_head};
1447      $self -> synchronize;
1448      my $first_id = $self -> {'individuals'}[0];
1449        die "data -> mean: No individuals defined in data object based on ",
1450         $self -> full_name,"\n" unless defined $first_id;
1451
1452      my @data_row = split( /,/, $first_id -> subject_data ->[0] );
1453
1454      unless ( defined $column  && defined( $data_row[$column-1] ) ) {
1455        unless (defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})) {
1456          die "Error in data -> mean: unknown column: \"$column_head\" or invalid column number: \"$column\"\n";
1457        } else {
1458               $column = $self -> {'column_head_indices'}{$column_head};
1459          }
1460      }
1461
1462         ## Here the calculation starts
1463         my $num_individuals = 0;
1464         my $sum = 0;
1465
1466      my $all_data_rows=0;
1467         foreach my $individual ( @{$self ->{'individuals'}} ) {
1468
1469           my $ifactors = $individual -> subject_data;
1470           my $individual_sum = 0;
1471           my $data_rows = 0;
1472           for(my $i=0; $i<=$#{$ifactors}; $i++ ) {
1473
1474             # data is stored in strings. We need to split them into an
1475             # array.
1476
1477             my @data_row = split( /,/, $ifactors -> [$i] );
1478             if ( $data_row[$column-1] == $self -> {'missing_data_token'} ) {
1479 #             print "Skipping row with missing data\n";
1480               next;
1481             }
1482
1483             if( defined $subset_column and not eval ( $data_row[$subset_column-1].$subset_syntax ) ) {
1484 #             print "Skipping row outside subset: syntax: ".($subset_column-1)." $subset_syntax\n";
1485               next;
1486             }
1487
1488             if (defined $hi_cutoff) {
1489               if ($data_row[$column-1]>$hi_cutoff) {
1490                 $individual_sum += $data_row[$column-1]-$hi_cutoff;
1491               }
1492             }
1493             else {
1494               if (defined $low_cutoff) {
1495                 if ($data_row[$column-1]<$low_cutoff) {
1496                   $individual_sum += $low_cutoff - $data_row[$column-1];
1497                 }
1498               }
1499               else {
1500                 $individual_sum += $data_row[$column-1];
1501               }
1502             }
1503             $data_rows++;
1504           }
1505           if( $global_mean ) {
1506             $sum += $individual_sum;
1507             $num_individuals += $data_rows;
1508           } else {
1509             if( $data_rows != 0 ) {
1510               $sum += $individual_sum/$data_rows;
1511             }
1512             $num_individuals ++;
1513           }
1514           $all_data_rows += $data_rows;
1515         }
1516      if( $num_individuals != 0 ) {
1517        $return_value = $sum / $num_individuals;
1518      }
1519 #     print "DR: $all_data_rows\n";
1520 #     print "\nNIM: $num_individuals $return_value\n";
1521 }
1522
1523 end mean
1524
1525 # }}} mean
1526
1527 # {{{ sd
1528
1529 start sd
1530   {
1531     # This sub returns standard deviation for a specific column
1532     # If there are more than one sample/individual the value used for that specific
1533     # individual is the mean value of its samples.
1534     # The cut-offs are for hockey stick variables. I.e. If one individual value is
1535     # lower than the hi-cutoff the individual value will be zero.
1536     # HI_cutoff is used to calculate the HI-mean of a column.
1537     # If cut_off is undef it won't be used
1538     # See L</max>.
1539      my $tmp_column = $self -> {'column_head_indices'}{$column_head};
1540      $self -> synchronize;
1541      my $first_id = $self -> {'individuals'}[0];
1542      debug -> die( message => "No individuals defined in data object based on ".
1543                    $self -> full_name ) unless defined $first_id;
1544
1545      my @data_row = split( /,/ , $first_id -> subject_data ->[0] );
1546
1547      unless ( defined $column  && defined( $data_row[$column-1] ) ) {
1548        unless (defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})) {
1549          debug -> die( message => "Unknown column: \"$column_head\" or "
1550                        ."invalid column number: \"$column\"" );
1551        } else {
1552          $column = $self -> {'column_head_indices'}{$column_head};
1553        }
1554      }
1555
1556      ## Here the calculation starts
1557      my $num_individuals = 0;
1558      my $sum = 0;
1559      my $mean;
1560      if (defined $hi_cutoff) {
1561        $mean = $self->mean(column   => $column,
1562                            hi_cutoff => $hi_cutoff,
1563                            global_mean => $global_sd );
1564      } elsif (defined $low_cutoff) {
1565        $mean = $self->mean(column   => $column,
1566                            low_cutoff => $low_cutoff,
1567                            global_mean => $global_sd );
1568      } else {
1569        $mean = $self->mean( column        => $column,
1570                             subset_column => $subset_column,
1571                             subset_syntax => $subset_syntax,
1572                             global_mean => $global_sd );
1573      }
1574
1575      foreach my $individual ( @{$self -> {'individuals'}} ) {
1576        my $ifactors = $individual -> subject_data;
1577        my $individual_sum = 0;
1578        my $data_rows = 0;
1579        for(my $i=0; $i<=$#{$ifactors}; $i++ ) {
1580
1581          # data is stored in strings. We need to split them into an
1582          # array.
1583
1584          my @data_row = split( /,/, $ifactors -> [$i] );
1585
1586          if ( $data_row[$column-1] == $self -> {'missing_data_token'} ) {
1587 #          print "Skipping row with missing data\n";
1588            next;
1589          }
1590
1591          if( defined $subset_column and not eval ( $data_row[$subset_column-1].$subset_syntax ) ) {
1592 #          print "Skipping row outside subset: syntax: ".($subset_column-1)." $subset_syntax\n";
1593            next;
1594          }
1595
1596          if (defined $hi_cutoff) {
1597            if ($data_row[$column-1]>$hi_cutoff) {
1598              if( $global_sd ) {
1599                $individual_sum += ($data_row[$column-1] - $hi_cutoff - $mean) ** 2;
1600              } else {
1601                $individual_sum += $data_row[$column-1]-$hi_cutoff;
1602              }
1603            }
1604          } else {
1605            if (defined $low_cutoff) {
1606              if ($data_row[$column-1]<$low_cutoff) {
1607                if( $global_sd ) {
1608                  $individual_sum += ($low_cutoff - $data_row[$column-1] - $mean) ** 2;
1609                } else {
1610                  $individual_sum += $low_cutoff - $data_row[$column-1];
1611                }
1612              }
1613            } else {
1614              if( $global_sd ) {
1615                $individual_sum += ($data_row[$column-1] - $mean) ** 2;
1616              } else {
1617                $individual_sum += $data_row[$column-1];
1618              }
1619            }
1620          }
1621          $data_rows++;
1622        }
1623        if( $global_sd ) {
1624          $sum += $individual_sum;
1625          $num_individuals += $data_rows;
1626        } else {
1627          if( $data_rows != 0 ) {
1628            $sum += ($individual_sum/$data_rows - $mean) ** 2;
1629          }
1630          $num_individuals++;
1631        }
1632      }
1633      if( $num_individuals < 2 ) {
1634        $return_value = 0;
1635      } else {
1636        if( $num_individuals != 0 ) {
1637          $return_value = (1/($num_individuals-1)*$sum) ** 0.5;
1638        }
1639      }
1640    }
1641
1642 end sd
1643
1644 # }}} sd
1645
1646 # {{{ range
1647 start range
1648       {
1649         # See L</max>.
1650         my $tmp_column = $self -> {'column_head_indices'}{$column_head};
1651         if ( defined $self -> {'range'}[$tmp_column] ) {
1652           $return_value = $self -> {'range'}[$tmp_column];
1653         } else {
1654           my $old_target = $self -> {'target'};
1655           $self -> {'target'} = 'mem';
1656           $self -> synchronize;
1657           $return_value = $self -> max( column      => $column,
1658                                         column_head => $column_head ) -
1659                                           $self -> min( column      => $column,
1660                                                         column_head => $column_head );
1661           $self -> {'range'}[$column] = $return_value;
1662           if ( $old_target eq 'disk' ) {
1663             $self -> flush if ( $self -> {'target'} eq 'disk' );
1664             $self -> {'target'} = 'disk';
1665           }
1666         }
1667       }
1668 end range
1669 # }}} range
1670
1671 # {{{ recalc_column
1672 start recalc_column
1673       {
1674           # Recalculates a column based on expression. Also, see L</max>.
1675         $self -> synchronize;
1676
1677         # Check if $column(-index) is defined and valid, else try to find index using column_head
1678         my $first_id = $self -> {'individuals'}[0];
1679         die "data -> recalc_column: No individuals defined in data object based on ",
1680           $self -> full_name,"\n" unless defined $first_id;
1681
1682         my @data_row = split( /,/ , $first_id -> subject_data ->[0] );
1683
1684         unless ( defined $column  && defined( $data_row[$column-1] ) ) {
1685           if(defined($column_head) && defined($self -> {'column_head_indices'}{$column_head})){
1686             die "Error in data -> recalc_column: unknown column: \"$column_head\" or column number: \"$column\"\n";
1687           } else {
1688             $column = $self -> {'column_head_indices'}{$column_head};
1689           }
1690         }
1691
1692         for my $individual ( @{$self -> {'individuals'}} ) {
1693           $individual -> recalc_column( column     => $column,
1694                                         expression => $expression );
1695         }
1696       }
1697 end recalc_column
1698 # }}} recalc_column
1699
1700 # {{{ renumber_ascending
1701
1702 start renumber_ascending
1703       {
1704 # Renumbers the individuals (changes the subject identifiers) so that
1705 # all have unique integer numbers starting with start_at and
1706 # ascending. The primary use of this
1707 # method is not to order the individuals after their identifiers but to
1708 # ensure that all individuals have unique identifiers.
1709
1710         $self -> synchronize;
1711         foreach my $individual ( @{$self -> {'individuals'}} ) {
1712           $individual -> idnumber ( $start_at++ );
1713         }
1714         $self -> {'synced'} = 0;
1715       }
1716 end renumber_ascending
1717
1718 # }}} renumber_ascending
1719
1720 # {{{ renumber_descending
1721
1722 start renumber_descending
1723       {
1724           # See L</renumber_ascending>.
1725         $self -> synchronize;
1726         foreach my $individual ( @{$self -> {'individuals'}} ) {
1727           $individual -> idnumber ( $start_at-- );
1728         }
1729         $self -> {'synced'} = 0;
1730       }
1731 end renumber_descending
1732
1733 # }}} renumber_descending
1734
1735 # {{{ single_valued_data
1736
1737 start single_valued_data
1738       {
1739         # Usage:
1740         #
1741         # ($single_value_data_set, $remainder, $column_indexes) =
1742         #      $data_object -> single_valued_data( subset_name         => 'subset.dta',
1743         #                                          remainder_name      => 'remainder.dta',
1744         #                                          target              => 'disk',
1745         #                                          do_not_test_columns => [1..18,24,26];
1746         #
1747         # my $single_value_column_indexes = $column_indexes -> [0];
1748         # my $all_other_column_indexes    = $column_indexes -> [1];
1749         #
1750         # Analyses the content of each column, based on the
1751         # ID column, and returns two new data objects: One
1752         # that contains all columns that is has only one value per
1753         # individual and one that contains the
1754         # remainding data. This is useful for creating compact 'extra'
1755         # data sets that can be read in via user-defined sub-routines
1756         # when the number of columns needed exceeds the maximum that
1757         # NONMEM allows (e.g. 20 in NONMEM version V).
1758         #
1759         # The I<do_not_test_columns> argument specifies on which columns
1760         # to skip the single value test
1761
1762         my @multi_value_flags;
1763         my @individuals = @{$self -> {'individuals'}};
1764         # Initiate the flags:
1765         if ( defined $individuals[0] ) {
1766           my @data = @{$individuals[0] -> {'subject_data'}};
1767           my @data_row = split( /,/ , $data[0] );
1768           for ( my $i = 0; $i < scalar @data_row; $i++ ) {
1769             my $dnt_flag = 0;
1770             foreach my $dntc ( @do_not_test_columns ) {
1771               $dnt_flag = 1 if ( $i == $dntc - 1 );
1772             }
1773             $multi_value_flags[$i] = $dnt_flag;
1774           }
1775         } else {
1776           die "data -> single_valued_data: No data in ID number 1\n";
1777         }
1778         # Collect the stats
1779         for ( my $id = 0; $id <= $#individuals; $id++ ) {
1780           my @data = @{$individuals[$id] -> {'subject_data'}};
1781           my @data_row = split( /,/, $data[0] );
1782           for ( my $j = 0; $j < scalar @data_row; $j++ ) {
1783             my %col_unique;
1784             for ( my $i = 0; $i <= $#data; $i++ ) {
1785               my @data_row = split( /,/ , $data[$i] );
1786               $col_unique{$data_row[$j]}++;
1787             }
1788             my $factors = scalar keys %col_unique;
1789             $multi_value_flags[$j]++ if ( $factors > 1 );
1790           }
1791         }
1792         for ( my $i = 0; $i <= $#multi_value_flags; $i++ ) {
1793           if ( $multi_value_flags[$i] ) {
1794             push ( @{$column_indexes[1]}, $i + 1);
1795           } else {
1796             push ( @{$column_indexes[0]}, $i + 1);
1797           }
1798         }
1799         ( $single_value_data_set, $remainder ) =
1800           $self -> subset_vertically( column_indexes      => $column_indexes[0],
1801                                       subset_name         => $subset_name,
1802                                       return_remainder    => 1,
1803                                       remainder_name      => $remainder_name,
1804                                       target              => $target,
1805                                       keep_first_row_only => 1);
1806       }
1807 end single_valued_data
1808
1809 # }}}
1810
1811 # {{{ subset_vertically
1812
1813 start subset_vertically
1814       {
1815         # Usage:
1816         #
1817         # $subset = $data_object -> subset_vertically ( column_indexes => [1,2,6],
1818         #                                               subset_name    => 'subset.dta' );
1819         #
1820         # This basic usage returns a new data object containing
1821         # columns 1,2 and 6 from the original data plus the
1822         # idcolumn. The new data object will be associated with the
1823         # file 'subset.dta'.
1824         #
1825         # You get the remaining data, i.e. the original data minus
1826         # the created subset by specifying
1827         #
1828         # ( $subset, $remainder ) =
1829         #      $data_object -> subset_vertically ( column_indexes   => [1,2,6],
1830         #                                          subset_name      => 'subset.dta',
1831         #                                          return_remainder => 1,
1832         #                                          remainder_name   => 'remainder.dta' );
1833         #
1834         # If you would like to flush the created data sets to disk and
1835         # save memory, set the I<target> argument to 'disk'. The
1836         # default value 'mem' will keep the whole data object in RAM.
1837         #
1838         # The I<keep_first_row_only> argument can be used to reduce
1839         # the size of the subset data obejct by excluding all but the
1840         # first row of data from each individual.
1841         #
1842         my @individuals = @{$self -> {'individuals'}};
1843         # Create remainder index array if necessary
1844         my @remainder_indexes;
1845         if ( defined $individuals[0] ) {
1846           my @data = @{$individuals[0] -> {'subject_data'}};
1847           my $idcolumn = $individuals[0] -> {'idcolumn'};
1848 #         print "IC: $idcolumn\n";
1849           my $id_flag = 0;
1850           foreach my $use_index ( @column_indexes ) {
1851             $id_flag = 1 if ( $use_index == $idcolumn );
1852           }
1853           if ( $return_remainder ) {
1854 #           @remainder_indexes = ( $idcolumn );
1855             for ( my $i = 0; $i < scalar split(/,/,$data[0]); $i++ ) {
1856               my $rem_flag = 1;
1857               foreach my $use_index ( @column_indexes ) {
1858                 $rem_flag = 0 if ( $i == $use_index -1 );
1859 # or
1860 #                                  $i == $idcolumn -1 );
1861               }
1862               push( @remainder_indexes, $i + 1 ) if ( $rem_flag );
1863             }
1864             unshift( @remainder_indexes, $idcolumn ) if ( $id_flag );
1865           }
1866           unshift( @column_indexes, $idcolumn ) unless ( $id_flag );
1867         } else {
1868           die "data -> single_valued_data: No data in ID number 1\n";
1869         }
1870
1871         my @new_ids;
1872         my @new_ids_2;
1873         for ( my $id = 0; $id <= $#individuals; $id++ ) {
1874           my $idnumber = $individuals[$id] -> idnumber;
1875           my $idcolumn = $individuals[$id] -> idcolumn;
1876           my @data = @{$individuals[$id] -> {'subject_data'}};
1877           my @new_data;
1878           my @new_data_2;
1879           my $use_rows = $keep_first_row_only ? 0 : $#data;
1880           for ( my $i = 0; $i <= $use_rows; $i++ ) {
1881             my @new_row;
1882             my @data_row = split( /,/, $data[$i] );
1883             foreach my $use_index ( @column_indexes ) {
1884               push( @new_row, $data_row[$use_index-1] );
1885             }
1886 #           print "@new_row $#new_row\n";
1887             push( @new_data, join( ',', @new_row ) );
1888           }
1889           for ( my $i = 0; $i <= $#data; $i++ ) {
1890             if ( $return_remainder ) {
1891               my @new_row_2;
1892               my @data_row = split( /,/, $data[$i] );
1893               foreach my $use_index ( @remainder_indexes ) {
1894                 push( @new_row_2, $data_row[$use_index-1] );
1895               }
1896 #             print "@new_row_2 $#new_row_2\n";
1897               push( @new_data_2, join( ',' , @new_row_2 ) );
1898             }
1899           }
1900           my $new_id = data::individual -> new( idnumber     => $idnumber,
1901                                                 idcolumn     => $idcolumn,
1902                                                 subject_data => \@new_data );
1903           push( @new_ids, $new_id );
1904           if ( $return_remainder ) {
1905             my $new_id_2;
1906             $new_id_2 = data::individual -> new( idnumber     => $idnumber,
1907                                                  idcolumn     => $idcolumn,
1908                                                  subject_data => \@new_data_2 );
1909           push( @new_ids_2, $new_id_2 );
1910           }
1911         }
1912         my @header = @{$self -> {'header'}};
1913         my @new_header;
1914         foreach my $use_index ( @column_indexes ) {
1915           push( @new_header, @header[$use_index-1] );
1916         }
1917         my $comment;
1918         if( defined $self -> {'comment'} ){
1919           my @comment = @{$self -> {'comment'}};
1920           $comment = \@comment;
1921         }
1922         $subset = data -> new ( filename             => $subset_name,
1923                                 directory            => $self -> {'directory'},
1924                                 ignoresign           => $self -> {'ignoresign'},
1925                                 header               => \@new_header,
1926                                 comment              => $comment,
1927                                 individuals          => \@new_ids,
1928                                 target               => $target,
1929                                 ignore_missing_files => 1 );
1930         if ( $return_remainder ) {
1931           my @new_header_2;
1932           foreach my $use_index ( @remainder_indexes ) {
1933             push( @new_header_2, @header[$use_index-1] );
1934           }
1935           $remainder = data -> new ( filename             => $remainder_name,
1936                                      directory            => $self -> {'directory'},
1937                                      ignoresign           => $self -> {'ignoresign'},
1938                                      header               => \@new_header_2,
1939                                      comment              => $comment,
1940                                      individuals          => \@new_ids_2,
1941                                      target               => $target,
1942                                      ignore_missing_files => 1 );
1943         }
1944       }
1945 end subset_vertically
1946
1947 # }}}
1948
1949 # {{{ subsets
1950
1951 start subsets
1952       {
1953 #       if ( defined $expression and defined $bins ) {
1954 #         die "data -> subset: expression and bins may not both be specified\n";
1955 #       }
1956 #       if ( not ( defined $expression or defined $bins ) ) {
1957 #         die "data -> subset: expression or bins must be specified\n";
1958 #       }
1959         $self -> synchronize;
1960         my @header  = @{$self -> {'header'}};
1961         my @comment = defined $self -> {'comment'} ? @{$self -> {'comment'}} : ();
1962         my @subset_ids= ();
1963         my %rnd_ids;
1964         my $key = 0;
1965         my @ids = @{$self -> {'individuals'}};
1966         if ( defined $stratify_on ) {
1967           my $work_data = $self -> copy( filename => 'work_data.dta',
1968                                          target   => 'mem' );
1969           my %strata = %{$work_data -> factors( column => $stratify_on )};
1970 #         $Data::Dumper::Maxdepth = 1;
1971 #         print Dumper \%strata;
1972
1973           while ( my ( $factor, $keys ) = each %strata ) {
1974               foreach my $key ( @{$keys} ) {
1975                   my $rnd_num = rand;
1976                   while ( defined $rnd_ids{$factor}{$rnd_num} ) {
1977                       $rnd_num = rand;
1978                   }
1979                   $rnd_ids{$factor}{$rnd_num} = $ids[$key];
1980               }
1981           }
1982           my $first = 1;
1983           while ( my ( $factor, $rnd_nums ) = each %rnd_ids ) {
1984               my @sort_rnd_nums = sort { $a <=> $b } keys %{$rnd_nums};
1985               for ( my $i = 0; $i <= $#sort_rnd_nums; $i ) {
1986                   for ( my $j = 0; $j < $bins; $j++ ) {
1987                       if ( $first ) {
1988                           push( @subset_ids, [$rnd_ids{$factor}{$sort_rnd_nums[$i]} -> copy] );
1989                           push( @incl_ids, [$rnd_ids{$factor}{$sort_rnd_nums[$i]} -> idnumber] );
1990                       } else {
1991                           push( @{$subset_ids[$j]}, $rnd_ids{$factor}{$sort_rnd_nums[$i]} -> copy );
1992                           push( @{$incl_ids[$j]}, $rnd_ids{$factor}{$sort_rnd_nums[$i]} -> idnumber );
1993                       }
1994                       $i++;
1995                       last if $i > $#sort_rnd_nums;
1996                   }
1997                   $first = 0;
1998               }
1999           }
2000           for ( my $j = 0; $j < $bins; $j++ ) {
2001             my $sdata = data -> new ( header               => \@header,
2002                                       comment              => \@comment,
2003                                       ignoresign           => $self -> {'ignoresign'},
2004                                       individuals          => $subset_ids[$j],
2005                                       ignore_missing_files => 1,
2006                                       target               => 'disk',
2007                                       idcolumn             => $self -> {'idcolumn'},
2008                                       filename             => "subset_$j.dta" );
2009             #$sdata -> _write;
2010             push( @subsets, $sdata );
2011           }
2012         } else {
2013           for ( my $i = 0; $i <= $#ids; $i++ ) {
2014             my $rnd_num = rand;
2015             while ( defined $rnd_ids{$rnd_num} ) {
2016               $rnd_num = rand;
2017             }
2018             $rnd_ids{$rnd_num} = $ids[$i];
2019           }
2020           my @keys = sort { $a <=> $b } keys %rnd_ids;
2021           my $first = 1;
2022           for ( my $i = 0; $i <= $#keys; $i ) {
2023             for ( my $j = 0; $j < $bins; $j++ ) {
2024               if ( $first ) {
2025                 push( @subset_ids, [$rnd_ids{$keys[$i]} -> copy] );
2026                 push( @incl_ids, [$rnd_ids{$keys[$i]} -> idnumber] );
2027               } else {
2028                 push( @{$subset_ids[$j]}, $rnd_ids{$keys[$i]} -> copy );
2029                 push( @{$incl_ids[$j]}, $rnd_ids{$keys[$i]} -> idnumber );
2030               }
2031               $i++;
2032               last if $i > $#keys;
2033             }
2034             $first = 0;
2035           }
2036           for ( my $j = 0; $j < $bins; $j++ ) {
2037             my $sdata = data -> new ( header               => \@header,
2038                                       comment              => \@comment,
2039                                       ignoresign           => $self -> {'ignoresign'},
2040                                       individuals          => $subset_ids[$j],
2041                                       ignore_missing_files => 1,
2042                                       target               => $target,
2043                                       idcolumn             => $self -> {'idcolumn'},
2044                                       filename             => "subset_$j.dta" );
2045             #$sdata -> _write;
2046             push( @subsets, $sdata );
2047           }
2048         }
2049       }
2050 end subsets
2051
2052 # }}} subsets
2053
2054 # {{{ subset
2055
2056 start subset
2057       {
2058         $self -> synchronize;
2059         my @header  = @{$self -> {'header'}};
2060         my @comment = defined $self -> {'comment'} ? @{$self -> {'comment'}} : ();
2061         my @subset_inds = ();
2062         my $key = 0;
2063         foreach my $individual ( @{$self -> {'individuals'}} ) {
2064           if ( $individual -> evaluate_expression( column     => $based_on,
2065                                                    expression => $expression ) ) {
2066             push( @subset_inds, $individual -> copy );
2067             push( @incl_individuals, $individual -> idnumber );
2068             push( @included_keys, $key );
2069           }
2070           $key++;
2071         }
2072         $subset = data -> new ( header      => \@header,
2073                                 comment     => \@comment,
2074                                 ignoresign  => $self -> {'ignoresign'},
2075                                 individuals => \@subset_inds,
2076                                 idcolumn    => $self -> {'idcolumn'},
2077                                 filename    => "subset.dta" );
2078       }
2079 end subset
2080
2081 # }}} subset
2082
2083 # {{{ target
2084
2085 start target
2086       {
2087         if ( $parm eq 'disk' and $self -> {'target'} eq 'mem' ) {
2088           $self -> {'target'} = 'disk';
2089           $self -> flush;
2090         } elsif ( $parm eq 'mem' and $self -> {'target'} eq 'disk' ) {
2091           $self -> {'target'} = 'mem';
2092           $self -> synchronize;
2093         }
2094       }
2095 end target
2096
2097 # }}}
2098
2099 # {{{ _write
2100
2101 start _write
2102     {
2103       die "ERROR: data -> _write: No filename set in data object.\n"
2104           if( $filename eq '' );
2105
2106 #      $Data::Dumper::Maxdepth = 2;
2107 #      die Dumper $self -> {'individuals'};
2108
2109       if( not defined $self -> {'individuals'} ){
2110
2111         # If we don't have any individuals and write to a new
2112         # filename, we must first read individuals from the old
2113         # file. A call to synchronize will do that. There is no risk
2114         # of a infinite loop here since synchronize allways writes to
2115         # "full_name".
2116
2117         unless( $filename eq $self -> full_name ){
2118           $self -> synchronize;
2119         }
2120       }
2121
2122       open(FILE,">$filename") ||
2123           die "Could not create $filename\n";
2124       my $data_ref = $self -> format_data;
2125       my @data = @{$data_ref};
2126       for ( @data ) {
2127         print ( FILE );
2128       }
2129       close(FILE);
2130
2131 #       if ( $PsN::config -> {'_'} -> {'use_database'} and
2132 #          $self -> {'use_data_table'} ) {
2133 #       # Backslashes messes up the sql syntax
2134 #       my $file_str = $self->{'filename'};
2135 #       my $dir_str = $self->{'directory'};
2136 #       $file_str =~ s/\\/\//g;
2137 #       $dir_str =~ s/\\/\//g;
2138
2139 #       # md5sum
2140 #       my $md5sum = md5_hex(OSspecific::slurp_file($self-> full_name ));
2141 #       my ( $date_str, $time_str );
2142 #       if ( $Config{osname} eq 'MSWin32' ) {
2143 #         $date_str = `date /T`;
2144 #         $time_str = ' '.`time /T`;
2145 #       } else {
2146 #         # Assuming UNIX
2147 #         $date_str = `date`;
2148 #       }
2149 #       chomp($date_str);
2150 #       chomp($time_str);
2151 #       my $date_time = $date_str.$time_str;
2152 #       my $dbh = DBI -> connect("DBI:mysql:host=".$PsN::config -> {'_'} -> {'database_server'}.
2153 #                              ";databse=".$PsN::config -> {'_'} -> {'project'},
2154 #                                $PsN::config -> {'_'} -> {'user'},
2155 #                               $PsN::config -> {'_'} -> {'password'},
2156 #                                {
2157 #                                 'RaiseError' => 1});
2158 #       my $sth;
2159 #       if ( defined $self -> {'data_id'} ) {
2160 #         $sth = $dbh -> prepare( "UPDATE ".$PsN::config -> {'_'} -> {'project'}.
2161 #                              ".data ".
2162 #                                 "SET filename='$file_str',date='$date_time',".
2163 #                                 "directory='$dir_str',md5sum='$md5sum' ".
2164 #                                 "WHERE data_id='".$self -> {'data_id'}."'" );
2165 #         $sth -> execute or debug -> die( message => $sth->errstr ) ;
2166 #       } else {
2167 #         $sth = $dbh -> prepare("INSERT INTO ".$PsN::config -> {'_'} -> {'project'}.
2168 #                              ".data (filename,date,directory,md5sum) ".
2169 #                                "VALUES ('$file_str', '$date_time', '$dir_str','".
2170 #                                $md5sum."' )");
2171 #         $sth -> execute;
2172 #         $self -> {'data_id'} = $sth->{'mysql_insertid'};
2173 #       }
2174 #       $sth -> finish;
2175 #       $dbh -> disconnect;
2176 #       }
2177     }
2178 end _write
2179
2180 # }}} _write
2181
2182 # {{{ flush
2183 start flush
2184     {
2185       # synchronizes the object with the file on disk and empties
2186       # most of the objects attributes to save memory.
2187       if( defined $self -> {'individuals'} and
2188           ( !$self -> {'synced'} or $force ) ) {
2189         $self -> _write;
2190       }
2191 #      $self -> {'header'} = undef;
2192       $self -> {'comment'} = undef;
2193       $self -> {'individuals'} = undef;
2194       $self -> {'synced'} = 0;
2195       $self -> {'column_head_indices'} = undef;
2196       $self -> {'have_missing_data'} = undef;
2197     }
2198 end flush
2199 # }}} flush
2200
2201 # {{{ synchronize
2202
2203 start synchronize
2204     {
2205       # synchronizes the object with the file on disk
2206       unless( $self -> {'synced'} ){
2207         if( defined $self -> {'individuals'} and
2208             scalar @{$self -> {'individuals'}} > 0 ){
2209           # We should not read new data from file if we
2210           # have an individuals defined?
2211           # Perhaps there should be an attribute
2212           # 'from_file' that overrides this and reads in
2213           # the data from the file specified in filename
2214           # and overwrites whatever the object already
2215           # contains?
2216 #           if( -e $self -> {'filename'} ){
2217 #             $self -> _read_header;
2218 #             $self -> _read_individuals;
2219 #           }
2220           $self -> _write;
2221         } else {
2222           if( -e $self -> full_name ){
2223             unless( defined $self -> {'header'} and scalar @{$self -> {'header'}} > 0 ){
2224               $self -> _read_header;
2225             }
2226             $self -> _read_individuals;
2227           } else {
2228             debug -> die( message => "Fatal error: datafile: " . $self -> full_name . " does not exist." );
2229             return;
2230           }
2231         }
2232       }
2233       my $i = 1;
2234       foreach my $head ( @{$self -> {'header'}} ){
2235         $self -> {'column_head_indices'} -> {$head} = $i;
2236         $i++;
2237       }
2238       $self -> {'synced'} = 1;
2239     }
2240 end synchronize
2241
2242 # }}} synchronize
2243
2244 # {{{ _fisher_yates_shuffle
2245
2246 start _fisher_yates_shuffle
2247       {
2248         my $arr_ref = $parm{'array'};
2249         debug -> warn( level   => 1,
2250                        message => "Array of zero length received" )
2251           if ( scalar @{$arr_ref} < 1 );
2252         my $i;
2253         for ($i = @$arr_ref; --$i; ) {
2254           my $j = random_uniform_integer(1,0,$i);
2255 #          my $j = int rand ($i+1);
2256 #         print "$j $j_new\n";
2257           @$arr_ref[$i,$j] = @$arr_ref[$j,$i];
2258         }
2259       }
2260 end _fisher_yates_shuffle
2261
2262 # }}} _fisher_yates_shuffle
2263
2264 # {{{ _read_header
2265
2266 start _read_header
2267       {
2268         my $filename   = $self -> full_name;
2269         my $ignoresign = $self -> ignoresign;
2270         my ( @data, @new_record, $row, $tmp_row, @header, $hdrstring );
2271
2272         open(DATAFILE,"$filename") ||
2273           die "Could not open $filename for reading";
2274         my $columns;
2275         while (<DATAFILE>) {
2276           s/\s*\,\s*/\,/g;
2277           $tmp_row    = $_;
2278           #     @new_record = split(/\,|\s+/,$_);
2279           if ( ! (/^\s*\d+|^\s*\./) ) {
2280             $data[$row] = $tmp_row;
2281             $row++;
2282           } else {
2283             # We have reached the first data-row, return.
2284             $columns = scalar split(/\,\s*|\s+/);
2285             last;
2286           }
2287         }
2288         close(DATAFILE);
2289
2290         if ( defined $self -> {'cont_column'} and not $self -> {'table_file'} ) {
2291           my $data_len = $#data;
2292           for ( my $i = $data_len; $i >= 0; $i-- ) {
2293             my @arr = split(/\,\s*|\s+/,$data[$i]);
2294             if ( $arr[$self -> {'cont_column'}-1] eq 'CONT' ) {
2295               my $start = $i == $data_len ? 0 : 1;
2296               for ( my $j = $start; $j <= $#arr; $j++ ) {
2297                 if ( $j != ($self -> {'cont_column'}-1) ) {
2298                   push( @header, $arr[$j] );
2299                 }
2300               }
2301               pop( @data );
2302             }
2303           }
2304           # the \Q and \E here are to escape wierd ignoresigns
2305           $header[0] =~ s/\Q$ignoresign\E//
2306               if ( defined $self->ignoresign );
2307           shift( @header ) if ( $header[0] eq "" );
2308         } else {
2309           chomp( $hdrstring = pop(@data));
2310           @header = split(/\,\s*|\s+/,$hdrstring);
2311           # the \Q and \E here are to escape wierd ignoresigns
2312           $header[0] =~ s/\Q$ignoresign\E//
2313               if ( defined $self->ignoresign );
2314           shift( @header ) if ( $header[0] eq "" );
2315           if( $self -> {'table_file'} ) {
2316             my @new_header;
2317             for( my $i = 1; $i <= scalar @header; $i++ ) {
2318               if( $header[$i-1] eq 'CONT' ) {
2319                 if ( defined $self -> {'cont_column'} and not $i == $self -> {'cont_column'} ) {
2320                   debug -> warn( level   => 1,
2321                                  message => "The supplied columns for the CONT data item (".
2322                                  $self -> {'cont_column'}.") does not match the column where the CONT ".
2323                                  "header was found ($i), using $i" );
2324                 }
2325                 $self -> {'cont_column'} = $i;
2326               } else {
2327                 push( @new_header, $header[$i-1] );
2328               }
2329             }
2330             @header = @new_header;
2331             for( my $i = 1; $i <= scalar @header; $i++ ) {
2332               if( $header[$i-1] eq 'ID' ) {
2333                 if ( defined $self -> {'idcolumn'} and not $i == $self -> {'idcolumn'} ) {
2334                   debug -> warn( level   => 1,
2335                                  message => "The supplied columns for the ID data item (".
2336                                  $self -> {'idcolumn'}.") does not match the column where the CONT ".
2337                                  "header was found ($i), using $i" );
2338                 }
2339                 $self -> {'idcolumn'} = $i;
2340               }
2341             }
2342           }
2343         }
2344
2345 # 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.
2346 #
2347 #<<<<<<< data_subs.pm
2348 #       $header[0] =~ s/$ignoresign//
2349 #         if ( defined $self->ignoresign );
2350 #       shift( @header ) if ( $header[0] eq "" );
2351 #=======
2352 #>>>>>>> 1.28
2353
2354 # It is ok with data sets without a header.
2355 #       unless( scalar @header > 0 ){ debug -> die( message => 'Datafile ' . $self -> full_name . ' is empty.' ); }
2356
2357         $self -> {'header'} = \@header;
2358         $self -> {'comment'} = \@data;
2359 #       if ( $PsN::config -> {'_'} -> {'use_database'} and
2360 #            $self -> {'use_data_table'} ) {
2361 #         my $dbh = DBI -> connect("DBI:mysql:host=".$PsN::config -> {'_'} -> {'database_server'}.
2362 #                              ";databse=".$PsN::config -> {'_'} -> {'project'},
2363 #                                  $PsN::config -> {'_'} -> {'user'},
2364 #                               $PsN::config -> {'_'} -> {'password'},
2365 #                                  {'RaiseError' => 1});
2366 #         if ( scalar @header < 1 ) {
2367 #           for ( my $i = 1; $i <= $columns; $i++ ) {
2368 #             push( @header, $i );
2369 #           }
2370 #         }
2371 #         for ( my $i = 0; $i <= $#header; $i++ ) {
2372 #           my $sth = $dbh -> prepare("INSERT INTO ".$PsN::config -> {'_'} -> {'project'}.
2373 #                              ".data_column ".
2374 #                                     "(name,number,data_id) ".
2375 #                                     "VALUES ('".$header[$i]."', '".($i+1).
2376 #                                     "', '".$self -> {'data_id'}."' )");
2377 #           $sth -> execute;
2378 #           push( @{$self -> {'data_column_ids'}}, $sth->{'mysql_insertid'} );
2379 #           $sth -> finish;
2380 #         }
2381 #         $dbh -> disconnect;
2382 #       }
2383       }
2384 end _read_header
2385
2386 # }}} _read_header
2387
2388 # {{{ _read_individuals
2389
2390 start _read_individuals
2391       {
2392         my $idcol        = $self -> idcolumn;
2393         my $filename     = $self -> full_name;
2394         #debug -> warn( level   => 1,
2395         #              message => "Building array of individuals from file " . $self -> {'filename'} );
2396         open(DATAFILE,"$filename") ||
2397           die "Could not open $filename for reading";
2398         my ( @new_row, $new_ID, $old_ID, @init_data );
2399         my $buffer;
2400         my $lines = 0;
2401         while (sysread DATAFILE, $buffer, 4096) {
2402           $lines += ($buffer =~ tr/\n//);
2403         }
2404         seek( DATAFILE, 0,0 );
2405
2406         # For status bar:
2407         my $status_bar = status_bar -> new( steps => $lines );
2408
2409         ui -> print( category => 'scm',
2410                      message  => "Reading data file: ".$self -> filename );
2411         ui -> print( category => 'scm',
2412                      message => $status_bar -> print_step(),
2413                      newline => 0);
2414
2415         my ( $sth, $dbh, $first_row_id, $first_value_id );
2416         my $insert = 1;
2417 #       if ( $PsN::config -> {'_'} -> {'use_database'} and
2418 #            $self -> {'use_data_table'} ) {
2419 #         $dbh = DBI -> connect("DBI:mysql:host=".$PsN::config -> {'_'} -> {'database_server'}.
2420 #                              ";databse=".$PsN::config -> {'_'} -> {'project'},
2421 #                               $PsN::config -> {'_'} -> {'user'},
2422 #                               $PsN::config -> {'_'} -> {'password'},
2423 #                               {'RaiseError' => 1});
2424 #         my $sth = $dbh -> prepare( "SELECT data_row_id FROM ".$PsN::config -> {'_'} -> {'project'}.
2425 #                              ".data_row ".
2426 #                                    "WHERE data_id='".$self -> {'data_id'}."'" );
2427 #         $sth -> execute or debug -> die( message => $sth->errstr ) ;
2428 #         my $select_arr = $sth -> fetchall_arrayref;
2429 #         if ( scalar @{$select_arr} > 0 ) {
2430 #           for ( my $i = 0; $i < scalar @{$select_arr}; $i++ ) {
2431 #             push( @{$self -> {'data_row_ids'}}, $select_arr->[$i][0] );
2432 #           }
2433 #           $sth = $dbh -> prepare( "SELECT data_value_id FROM ".$PsN::config -> {'_'} -> {'project'}.
2434 #                              ".data_value ".
2435 #                                   "WHERE data_id='".$self -> {'data_id'}."'" );
2436 #           $sth -> execute or debug -> die( message => $sth->errstr ) ;
2437 #           my $select_val = $sth -> fetchall_arrayref;
2438 #           for ( my $i = 0; $i < scalar @{$select_val}; $i++ ) {
2439 #             push( @{$self -> {'data_value_ids'}}, $select_val->[$i][0] );
2440 #           }
2441 #           $insert = 0;
2442 #           $dbh -> disconnect;
2443 #         } else {
2444 #           $dbh -> do( "LOCK TABLES ".$PsN::config -> {'_'} -> {'project'}.
2445 #                              ".data_row WRITE, ".$PsN::config -> {'_'} -> {'project'}.
2446 #                              ".data_value WRITE" );
2447 #           $sth = $dbh -> prepare( "SELECT MAX(data_row_id) FROM ".$PsN::config -> {'_'} -> {'project'}.
2448 #                              ".data_row" );
2449 #           $sth -> execute or debug -> die( message => $sth->errstr ) ;
2450 #           my $select_arr = $sth -> fetchall_arrayref;
2451 #           $first_row_id = defined $select_arr -> [0][0] ? $select_arr -> [0][0] : 0;
2452 #           $sth = $dbh -> prepare( "SELECT MAX(data_value_id) FROM ".$PsN::config -> {'_'} -> {'project'}.
2453 #                              ".data_value" );
2454 #           $sth -> execute or debug -> die( message => $sth->errstr ) ;
2455 #           my $select_arr = $sth -> fetchall_arrayref;
2456 #           $first_value_id = defined $select_arr -> [0][0] ? $select_arr -> [0][0] : 0;
2457 #         }
2458 #         $sth -> finish;
2459 #       }
2460
2461         my $insert_rows;
2462         my $insert_values;
2463         my $row_counter = 0;
2464         my $full_row;
2465       ROW: while ( <DATAFILE> ) {
2466           s/^ *//;
2467           s/\s*\,\s*/\,/g;
2468           my @new_row   = split(/\,\s*|\s+/);
2469           # This regexp check is not time consuming.
2470           if ( /^\s*\d+|^\s*\./ ) {
2471             if ( defined $self -> {'cont_column'} ) {
2472               if ( $new_row[$self -> {'cont_column'} - 1] == 1 ) {
2473                 if ( not $self -> {'table_file'} ) { # Skip the CONT=1 rows if this is a table file
2474                   for ( my $i = $#new_row; $i > 0; $i-- ) {
2475                     if ( $i != ($self -> {'cont_column'} - 1) ) {
2476                       unshift( @{$full_row}, $new_row[$i] );
2477                     }
2478                   }
2479                 }
2480                 next ROW;
2481               } else {
2482                 for ( my $i = $#new_row; $i >= 0; $i-- ) {
2483 #                 if ( $i != ($self -> {'cont_column'} - 1) or $self -> {'table_file'} ) {
2484                   if ( $i != ($self -> {'cont_column'} - 1) ) {
2485                     unshift( @{$full_row}, $new_row[$i] );
2486                   }
2487                 }
2488               }
2489             } else {
2490               @{$full_row} = @new_row;
2491             }
2492             $new_ID = $full_row -> [$idcol-1]; # index starts at 0
2493             $old_ID = $new_ID if ( not defined $old_ID );
2494
2495             # Check if column miss data at some row (This adds about 30% of init time)
2496             my $mdt = $self -> {'missing_data_token'};
2497             for( my $i = 0; $i <= $#{$full_row}; $i++ ){
2498                 $self -> {'have_missing_data'} -> {$i+1} = 1
2499                   if( $full_row -> [$i] == $mdt ); # == is slower but safer than eq
2500             }
2501 #           if ( $PsN::config -> {'_'} -> {'use_database'} and
2502 #                $self -> {'use_data_table'} and $insert ) {
2503 #             $row_counter++;
2504 #             $insert_rows = $insert_rows."," if ( defined $insert_rows );
2505 #             $insert_rows = $insert_rows.
2506 #               "('$row_counter', '".$self -> {'data_id'}."' )";
2507 #             for ( my $j = 0; $j <= $#{$full_row}; $j++ ) {
2508 #               $insert_values = $insert_values."," if ( defined $insert_values );
2509 #               $insert_values = $insert_values.
2510 #                 "('".$full_row -> [$j]."', '".
2511 #                   ($first_row_id+$row_counter)."', '".
2512 #                     $self -> {'data_column_ids'}->[$j].
2513 #                       "', '".$self -> {'data_id'}."' )";
2514 #             }
2515 #           }
2516
2517             if ( $new_ID != $old_ID ) {
2518               my @subject_data = @init_data;
2519               my $id = data::individual -> new ( idcolumn     => $idcol,
2520                                                  subject_data => \@subject_data,
2521                                                  data_id      => $self -> {'data_id'} );
2522               push( @{$self -> {'individuals'}}, $id );
2523               @init_data =(join( ",", @{$full_row}));
2524             } else {
2525               push( @init_data, join( ",", @{$full_row}) );
2526             }
2527             $old_ID = $new_ID;
2528             $full_row = undef;
2529           }
2530           if ( $status_bar -> tick() ) {
2531             ui -> print( category => 'scm',
2532                          message  => $status_bar -> print_step(),
2533                          wrap     => 0,
2534                          newline  => 0 );
2535           }
2536         }
2537
2538 #       if ( $PsN::config -> {'_'} -> {'use_database'} and
2539 #            $self -> {'use_data_table'} and $insert ) {
2540 #         $dbh -> do("INSERT INTO ".$PsN::config -> {'_'} -> {'project'}.
2541 #                    ".data_row ".
2542 #                    "(number,data_id) ".
2543 #                    "VALUES ".$insert_rows);
2544 #         push( @{$self -> {'data_row_ids'}}, ($first_row_id..$first_row_id+$row_counter) );
2545 #         $dbh -> do( "INSERT INTO ".$PsN::config -> {'_'} -> {'project'}.
2546 #                     ".data_value ".
2547 #                     "(value,data_row_id,data_column_id,data_id) ".
2548 #                     "VALUES ".$insert_values );
2549 #         push( @{$self -> {'data_value_ids'}},
2550 #               ($first_value_id..$first_value_id+($row_counter*
2551 #                                                  scalar @{$self->{'data_column_ids'}})));
2552 #         $dbh -> do( "UNLOCK TABLES" );
2553 #         $dbh -> disconnect;
2554 #       }
2555
2556         if ( $#init_data >= 0 ) {
2557           push( @{$self -> {'individuals'}},
2558                 data::individual -> new ( idcolumn     => $idcol,
2559                                           subject_data => \@init_data ) );
2560         }
2561         ui -> print( category => 'scm',
2562                      message  => " ... done" );
2563         close(DATAFILE);
2564 #       $self -> _write( filename => 'test.dta' );
2565       }
2566 end _read_individuals
2567
2568 # }}} _read_individuals
2569