From c973bfff243954e4c967cee0e809cbc8e4b379e2 Mon Sep 17 00:00:00 2001
From: pontus_pih <pontus_pih>
Date: Fri, 1 Jul 2005 08:12:41 +0000
Subject: [PATCH] Multiple changes, see the README

---
 bin/scm               |   5 +-
 bin/sumo              | 201 ++++++++++++++++++++++++++++++++------------------
 devel/pheno.scm       |   3 +
 diagrams/model.dia    | 115 +++++++++++++++++++++--------
 diagrams/modelfit.dia |  38 +++++++++-
 diagrams/scm.dia      |   6 +-
 diagrams/tool.dia     |   2 +-
 7 files changed, 257 insertions(+), 113 deletions(-)

diff --git a/bin/scm b/bin/scm
index a5f3f61..49bd2fb 100755
--- a/bin/scm
+++ b/bin/scm
@@ -242,8 +242,8 @@ my $eval_string = common_options::model_parameters(\%options);
 
 if( defined $config_file and $config_file -> extra_data_files ){
   foreach my $extra_data_file ( keys %{$config_file -> extra_data_files} ){
-    push( @{$options{'extra_data_file'}}, $extra_data_file );
-    push( @{$options{'extra_data_header'}}, $config_file -> extra_data_files -> {$extra_data_file} );
+    push( @{$options{'extra_data_files'}}, $extra_data_file );
+    push( @{$options{'extra_data_headers'}}, $config_file -> extra_data_files -> {$extra_data_file} );
   }
 }
 
@@ -281,7 +281,6 @@ if( $direction eq 'forward' or $direction eq 'both' ){
       new ( eval( $common_options::parameters ),
 	    models	=> $models_array,
 	    config_file => $config_file );
-  
   open(CMD, ">", $scm -> directory . "/command.txt");
   print CMD $cmd_line, "\n";
   close(CMD);
diff --git a/bin/sumo b/bin/sumo
index e612ae7..0b37b1d 100755
--- a/bin/sumo
+++ b/bin/sumo
@@ -12,31 +12,31 @@ use debug;
 use strict;
 use Getopt::Long;
 
-my ($opt_help,
-    $opt_long_help,
-    $opt_debug,
-    $opt_debug_package,
-    $opt_debug_subroutine,
-    $opt_compact_format );
-
-my $opts = { "h|?"                => \$opt_help,
-	     "help"               => \$opt_long_help,
-	     "debug:0"		  => \$opt_debug,
-	     "debug_package:s"	  => \$opt_debug_package,
-	     "debug_subroutine:s" => \$opt_debug_subroutine,
-	     "compact_format:1"   => \$opt_compact_format };
-
-my $res = GetOptions( %{$opts} );
+my %options;
+
+$options{'precision'} = 4;
+
+my $opts = { "h|?"                => $options{'help'},
+	     "help"               => $options{'long_help'},
+	     "debug:0"		  => $options{'debug'},
+	     "debug_package:s"	  => $options{'debug_package'},
+	     "debug_subroutine:s" => $options{'debug_subroutine'},
+	     "compact_format:1"   => $options{'compact_format'},
+	     "csv"                => $options{'csv'},
+	     "precision:4"        => $options{'precision'}};
+
+
+my $res = GetOptions( \%options, %{$opts} );
 
 exit unless $res;
 
-if ( scalar( @ARGV ) < 1 and !($opt_help or $opt_long_help) ){
+if ( scalar( @ARGV ) < 1 and !($options{'help'} or $options{'long_help'}) ){
   print "At least one list file must be specified. Use 'sumo.pl -h' for help.\n";
   exit;
 }
 
 
-if($opt_help or $opt_long_help) {
+if($options{'help'} or $options{'long_help'}) {
   print <<'ENDHELP';
 
   sumo.pl
@@ -53,7 +53,7 @@ if($opt_help or $opt_long_help) {
 
 ENDHELP
 
-  if( $opt_long_help and !$opt_help ){ 
+  if( $options{'long_help'} and !$options{'help'} ){ 
 
     print <<'ENDHELP';
 
@@ -116,76 +116,131 @@ ENDHELP
   exit;
 }
 
-debug -> level( $opt_debug );
-debug -> package( $opt_debug_package );
-debug -> subroutine( $opt_debug_subroutine );
+debug -> level( $options{'debug'} );
+debug -> package( $options{'debug_package'} );
+debug -> subroutine( $options{'debug_subroutine'} );
+
+my $form = '%.' . $options{'precision'} . 'g';
 
 my $outfile = $ARGV[0];
 
 my $outobj = output -> new ('filename'=> $outfile);
 
-my @thetas = defined $outobj -> thetas -> [0][0] ? @{$outobj -> thetas -> [0][0]} : ();
-my @thnam  = defined $outobj -> thetanames -> [0] ? @{$outobj -> thetanames -> [0]} : ();
-my @sethet = defined $outobj -> sethetas -> [0][0] ? @{$outobj -> sethetas -> [0][0]} : ();
-
-#my @omegas = defined $outobj -> omegas -> [0][0] ? @{$outobj -> omegas -> [0][0]} : ();
-my @omegas = defined $outobj -> comegas -> [0][0] ? @{$outobj -> comegas -> [0][0]} : ();
-my @omnam  = defined $outobj -> omeganames -> [0] ? @{$outobj -> omeganames -> [0]} : ();
-
-my @sigmas = defined $outobj -> csigmas -> [0][0] ? @{$outobj -> csigmas -> [0][0]} : ();
-my @signam = defined $outobj -> sigmanames -> [0] ? @{$outobj -> sigmanames -> [0]} : ();
+my @output_matrix;
+my @output_matrix_sizes;
 
-my $ofv    = $outobj -> ofv -> [0][0];
-my $termess= $outobj -> minimization_message -> [0][0];
+#use Data::Dumper;
+#print Dumper( $outobj );
 
 print "$outfile\n\n";
 
-print join( "",@{$termess} ), "\n";
-
-if ( defined $ofv ) {
-  print "Objective function value: ",$ofv,"\n\n";
-} else {
-  print "Objective function value: UNDEFINED\n\n";
-}
-
-my @seomeg;
-my @sesigm;
-
-if(@sethet) {
-  
-  @sethet = @{$outobj -> cvsethetas -> [0][0]};
-  @seomeg = @{$outobj -> cvseomegas -> [0][0]};
-  @sesigm = @{$outobj -> cvsesigmas -> [0][0]};
-
-}
-  
-printf "%-4s %-29s %-29s %-18s\n"," ","THETA","OMEGA","SIGMA";
-
-my $max_par = $#thetas;
-$max_par = $#omegas if ( $#omegas > $max_par );
-$max_par = $#sigmas if ( $#sigmas > $max_par );
-
-for ( my $i = 0; $i <= $max_par; $i++ ) {
-  if ( defined $thetas[$i] ) {
-    my $se_str = sprintf( "(%.3g)", $sethet[$i] );
-    printf( "%-4s %-10.4g %-12s ", $thnam[$i], $thetas[$i], $se_str );
-  } else {
-    printf( "%29s", " " );
-  }
-  if ( defined $omegas[$i] ) {
-    my $se_str = sprintf( "(%.3g)", $seomeg[$i] );
-    printf( "%-5s %-10.4g %-12s ", $omnam[$i], $omegas[$i], $se_str );
-  } else {
-    printf( "%30s", " " );
+for( my $problems = 0; $problems <= $#{$outobj -> problems}; $problems++){
+  my $row_counter = 0;
+  for( my $sub_problems = 0; $sub_problems <= $#{$outobj -> problems -> [$problems] -> subproblems}; $sub_problems++){
+    
+    my @thetas = defined $outobj -> thetas -> [$problems][$sub_problems] ? @{$outobj -> thetas -> [$problems][$sub_problems]} : ();
+    my @thnam  = defined $outobj -> thetanames -> [$problems] ? @{$outobj -> thetanames -> [$problems]} : ();
+    my @sethet = defined $outobj -> sethetas -> [$problems][$sub_problems] ? @{$outobj -> sethetas -> [$problems][$sub_problems]} : ();
+    
+    my @omegas = defined $outobj -> comegas -> [$problems][$sub_problems] ? @{$outobj -> comegas -> [$problems][$sub_problems]} : ();
+    my @omnam  = defined $outobj -> omeganames -> [$problems] ? @{$outobj -> omeganames -> [$problems]} : ();
+    
+    my @sigmas = defined $outobj -> csigmas -> [$problems][$sub_problems] ? @{$outobj -> csigmas -> [$problems][$sub_problems]} : ();
+    my @signam = defined $outobj -> sigmanames -> [$problems] ? @{$outobj -> sigmanames -> [$problems]} : ();
+    
+    my $ofv    = $outobj -> ofv -> [$problems][$sub_problems];
+    my $termess= $outobj -> minimization_message -> [$problems][$sub_problems];
+    
+    if( $termess ){
+      print join( "",@{$termess} ), "\n";
+    }
+    
+    if ( defined $ofv ) {
+      print "Objective function value: ",$ofv,"\n\n";
+    } else {
+      print "Objective function value: UNDEFINED\n\n";
+    }
+
+    my @seomeg;
+    my @sesigm;
+
+    if(@sethet) {
+      
+      @sethet = @{$outobj -> cvsethetas -> [$problems][$sub_problems]};
+      @seomeg = @{$outobj -> cvseomegas -> [$problems][$sub_problems]};
+      @sesigm = @{$outobj -> cvsesigmas -> [$problems][$sub_problems]};
+      
+    }
+    
+    push( @{$output_matrix[$row_counter]}, "","THETA","","","OMEGA","","","SIGMA", "" );
+    for( my $i = 0; $i <= $#{$output_matrix[$row_counter]}; $i++ ){
+      if( $output_matrix_sizes[$i] < length( $output_matrix[$row_counter][$i] ) ){
+	$output_matrix_sizes[$i] = length( $output_matrix[$row_counter][$i] );
+      }
+    }
+    $row_counter++;
+
+#printf "%-4s %-29s %-29s %-18s\n"," ","THETA","OMEGA","SIGMA";
+
+    my $max_par = $#thetas;
+    $max_par = $#omegas if ( $#omegas > $max_par );
+    $max_par = $#sigmas if ( $#sigmas > $max_par );
+    
+    for ( my $i = 0; $i <= $max_par; $i++ ) {
+      my @row;
+      if ( defined $thetas[$i] ) {
+	push( @row, $thnam[$i], sprintf( $form, $thetas[$i] ), 
+	      $sethet[$i] ? sprintf( "($form)", $sethet[$i] ) : '' );
+      } else {
+	push( @row, '','','' ); 
+      }
+      if ( defined $omegas[$i] ) {
+	push( @row, $omnam[$i], sprintf( $form, $omegas[$i] ), 
+	      $seomeg[$i] ? sprintf( "($form)", $seomeg[$i] ) : '' );
+      } else {
+	push( @row, '','',''); 
+      }
+      if ( defined $sigmas[$i] ) {
+	push( @row, $signam[$i], sprintf( $form, $sigmas[$i] ), 
+	      $sesigm[$i] ? sprintf( "($form)", $sesigm[$i] ) : '' );
+      } else {
+	push( @row, '','',''); 
+      }
+
+      push(@{$output_matrix[$row_counter]}, @row);
+      for( my $i = 0; $i <= $#{$output_matrix[$row_counter]}; $i++ ){
+	if( $output_matrix_sizes[$i] < length( $output_matrix[$row_counter][$i] ) ){
+	  $output_matrix_sizes[$i] = length( $output_matrix[$row_counter][$i] );
+	}
+      }
+      $row_counter++;
+
+    }
   }
-  if ( defined $sigmas[$i] ) {
-    my $se_str = sprintf( "(%.3g)", $sesigm[$i] );
-    printf( "%-5s %-10.4g %-12s ", $signam[$i], $sigmas[$i], $se_str );
+}
+    
+#for( my $j = 0; $j <= $#output_matrix; $j++ ){
+#  for( my $i = 0; $i <= $#{$output_matrix[$j]}; $i++ ){
+#    if( $output_matrix_sizes[$i] < length( $output_matrix[$j][$i] ) ){
+#      $output_matrix_sizes[$i] = length( $output_matrix[$j][$i] );
+#    }
+#  }  
+#}
+
+foreach my $row ( @output_matrix ){
+  for( my $i = 0; $i <= $#{$row}; $i++ ){
+    my $spaces = $output_matrix_sizes[$i] - length($row -> [$i]);
+    if( $options{'csv'} ){
+      print $row -> [$i], ",";
+    } else {
+      print " " x $spaces, $row -> [$i], "  ";
+    }
   }
   print "\n";
 }
 
 
+
 # my $pl = 1;
 # my @plist;
 # while($pl) {
diff --git a/devel/pheno.scm b/devel/pheno.scm
index 6a3267b..347833c 100644
--- a/devel/pheno.scm
+++ b/devel/pheno.scm
@@ -10,6 +10,9 @@ nm_version=6
 continuous_covariates=WGT
 categorical_covariates=APGR
 
+[extra_data_files]
+pheno_extra.dta=ID,WGT,APGR
+
 [test_relations]
 CL=WGT,APGR
 V=WGT,APGR
diff --git a/diagrams/model.dia b/diagrams/model.dia
index 493aa91..f6f1d49 100644
--- a/diagrams/model.dia
+++ b/diagrams/model.dia
@@ -155,13 +155,13 @@
         <dia:point val="-0.3,7.5"/>
       </dia:attribute>
       <dia:attribute name="obj_bb">
-        <dia:rectangle val="-0.35,7.45;92.65,31.75"/>
+        <dia:rectangle val="-0.35,7.45;93.1,31.75"/>
       </dia:attribute>
       <dia:attribute name="elem_corner">
         <dia:point val="-0.3,7.5"/>
       </dia:attribute>
       <dia:attribute name="elem_width">
-        <dia:real val="92.899999999999991"/>
+        <dia:real val="93.349999999999994"/>
       </dia:attribute>
       <dia:attribute name="elem_height">
         <dia:real val="24.200000000000003"/>
@@ -1648,13 +1648,13 @@
         <dia:point val="4,61"/>
       </dia:attribute>
       <dia:attribute name="obj_bb">
-        <dia:rectangle val="3.95,60.95;23.8,68.45"/>
+        <dia:rectangle val="3.95,60.95;23.9,68.45"/>
       </dia:attribute>
       <dia:attribute name="elem_corner">
         <dia:point val="4,61"/>
       </dia:attribute>
       <dia:attribute name="elem_width">
-        <dia:real val="19.75"/>
+        <dia:real val="19.850000000000001"/>
       </dia:attribute>
       <dia:attribute name="elem_height">
         <dia:real val="7.4000000000000004"/>
@@ -1969,14 +1969,14 @@
         <dia:point val="-0.3,7.5"/>
       </dia:attribute>
       <dia:attribute name="obj_bb">
-        <dia:rectangle val="-0.35,-16.9;101.05,10.1"/>
+        <dia:rectangle val="-0.35,-18.05;101.05,10.1"/>
       </dia:attribute>
       <dia:attribute name="orth_points">
         <dia:point val="-0.3,7.5"/>
         <dia:point val="-0.3,10"/>
         <dia:point val="101,10"/>
-        <dia:point val="101,-16.15"/>
-        <dia:point val="97,-16.15"/>
+        <dia:point val="101,-17.3"/>
+        <dia:point val="96.85,-17.3"/>
       </dia:attribute>
       <dia:attribute name="orth_orient">
         <dia:enum val="1"/>
@@ -2025,7 +2025,7 @@
       </dia:attribute>
       <dia:connections>
         <dia:connection handle="0" to="O3" connection="0"/>
-        <dia:connection handle="1" to="O22" connection="109"/>
+        <dia:connection handle="1" to="O22" connection="113"/>
       </dia:connections>
     </dia:object>
     <dia:object type="UML - Association" version="0" id="O6">
@@ -3415,13 +3415,13 @@
         <dia:point val="5,86"/>
       </dia:attribute>
       <dia:attribute name="obj_bb">
-        <dia:rectangle val="4.95,85.95;24.8,90.45"/>
+        <dia:rectangle val="4.95,85.95;24.9,90.45"/>
       </dia:attribute>
       <dia:attribute name="elem_corner">
         <dia:point val="5,86"/>
       </dia:attribute>
       <dia:attribute name="elem_width">
-        <dia:real val="19.75"/>
+        <dia:real val="19.850000000000001"/>
       </dia:attribute>
       <dia:attribute name="elem_height">
         <dia:real val="4.4000000000000004"/>
@@ -3675,19 +3675,19 @@
     </dia:object>
     <dia:object type="UML - Class" version="0" id="O22">
       <dia:attribute name="obj_pos">
-        <dia:point val="-0.85,-58.25"/>
+        <dia:point val="-1,-61"/>
       </dia:attribute>
       <dia:attribute name="obj_bb">
-        <dia:rectangle val="-0.9,-58.3;97.05,5.2"/>
+        <dia:rectangle val="-1.05,-61.05;96.9,3.25"/>
       </dia:attribute>
       <dia:attribute name="elem_corner">
-        <dia:point val="-0.85,-58.25"/>
+        <dia:point val="-1,-61"/>
       </dia:attribute>
       <dia:attribute name="elem_width">
         <dia:real val="97.849999999999994"/>
       </dia:attribute>
       <dia:attribute name="elem_height">
-        <dia:real val="63.399999999999963"/>
+        <dia:real val="64.19999999999996"/>
       </dia:attribute>
       <dia:attribute name="name">
         <dia:string>#model#</dia:string>
@@ -4136,6 +4136,29 @@
             <dia:boolean val="false"/>
           </dia:attribute>
         </dia:composite>
+        <dia:composite type="umlattribute">
+          <dia:attribute name="name">
+            <dia:string>#reference_object#</dia:string>
+          </dia:attribute>
+          <dia:attribute name="type">
+            <dia:string>##</dia:string>
+          </dia:attribute>
+          <dia:attribute name="value">
+            <dia:string>##</dia:string>
+          </dia:attribute>
+          <dia:attribute name="comment">
+            <dia:string>##</dia:string>
+          </dia:attribute>
+          <dia:attribute name="visibility">
+            <dia:enum val="0"/>
+          </dia:attribute>
+          <dia:attribute name="abstract">
+            <dia:boolean val="false"/>
+          </dia:attribute>
+          <dia:attribute name="class_scope">
+            <dia:boolean val="false"/>
+          </dia:attribute>
+        </dia:composite>
       </dia:attribute>
       <dia:attribute name="operations">
         <dia:composite type="umloperation">
@@ -4222,6 +4245,36 @@
         </dia:composite>
         <dia:composite type="umloperation">
           <dia:attribute name="name">
+            <dia:string>#clean_extra_data_code#</dia:string>
+          </dia:attribute>
+          <dia:attribute name="stereotype">
+            <dia:string>##</dia:string>
+          </dia:attribute>
+          <dia:attribute name="type">
+            <dia:string>##</dia:string>
+          </dia:attribute>
+          <dia:attribute name="visibility">
+            <dia:enum val="0"/>
+          </dia:attribute>
+          <dia:attribute name="comment">
+            <dia:string>##</dia:string>
+          </dia:attribute>
+          <dia:attribute name="abstract">
+            <dia:boolean val="false"/>
+          </dia:attribute>
+          <dia:attribute name="inheritance_type">
+            <dia:enum val="2"/>
+          </dia:attribute>
+          <dia:attribute name="query">
+            <dia:boolean val="false"/>
+          </dia:attribute>
+          <dia:attribute name="class_scope">
+            <dia:boolean val="false"/>
+          </dia:attribute>
+          <dia:attribute name="parameters"/>
+        </dia:composite>
+        <dia:composite type="umloperation">
+          <dia:attribute name="name">
             <dia:string>#copy#</dia:string>
           </dia:attribute>
           <dia:attribute name="stereotype">
@@ -9331,14 +9384,14 @@
         <dia:point val="109,-35"/>
       </dia:attribute>
       <dia:attribute name="obj_bb">
-        <dia:rectangle val="96.25,-36.7;109.35,-12.95"/>
+        <dia:rectangle val="96.1,-36.7;109.35,-14.1"/>
       </dia:attribute>
       <dia:attribute name="orth_points">
         <dia:point val="109,-35"/>
         <dia:point val="109,-36"/>
         <dia:point val="104,-36"/>
-        <dia:point val="104,-14.55"/>
-        <dia:point val="97,-14.55"/>
+        <dia:point val="104,-15.7"/>
+        <dia:point val="96.85,-15.7"/>
       </dia:attribute>
       <dia:attribute name="orth_orient">
         <dia:enum val="1"/>
@@ -9387,7 +9440,7 @@
       </dia:attribute>
       <dia:connections>
         <dia:connection handle="0" to="O23" connection="0"/>
-        <dia:connection handle="1" to="O22" connection="113"/>
+        <dia:connection handle="1" to="O22" connection="117"/>
       </dia:connections>
     </dia:object>
     <dia:object type="UML - Class" version="0" id="O25">
@@ -9496,13 +9549,13 @@
         <dia:point val="103,-36"/>
       </dia:attribute>
       <dia:attribute name="obj_bb">
-        <dia:rectangle val="96.25,-36.05;103.05,-12.15"/>
+        <dia:rectangle val="96.1,-36.05;103.05,-13.3"/>
       </dia:attribute>
       <dia:attribute name="orth_points">
         <dia:point val="103,-36"/>
-        <dia:point val="100,-36"/>
-        <dia:point val="100,-13.75"/>
-        <dia:point val="97,-13.75"/>
+        <dia:point val="99.925,-36"/>
+        <dia:point val="99.925,-14.9"/>
+        <dia:point val="96.85,-14.9"/>
       </dia:attribute>
       <dia:attribute name="orth_orient">
         <dia:enum val="0"/>
@@ -9547,7 +9600,7 @@
       </dia:attribute>
       <dia:connections>
         <dia:connection handle="0" to="O25" connection="0"/>
-        <dia:connection handle="1" to="O22" connection="115"/>
+        <dia:connection handle="1" to="O22" connection="119"/>
       </dia:connections>
     </dia:object>
     <dia:object type="UML - Class" version="0" id="O27">
@@ -12920,13 +12973,13 @@
         <dia:point val="4,45"/>
       </dia:attribute>
       <dia:attribute name="obj_bb">
-        <dia:rectangle val="3.95,44.95;24.85,49.25"/>
+        <dia:rectangle val="3.95,44.95;24.95,49.25"/>
       </dia:attribute>
       <dia:attribute name="elem_corner">
         <dia:point val="4,45"/>
       </dia:attribute>
       <dia:attribute name="elem_width">
-        <dia:real val="20.800000000000001"/>
+        <dia:real val="20.900000000000002"/>
       </dia:attribute>
       <dia:attribute name="elem_height">
         <dia:real val="4.2000000000000002"/>
@@ -13831,13 +13884,13 @@
         <dia:point val="2,34"/>
       </dia:attribute>
       <dia:attribute name="obj_bb">
-        <dia:rectangle val="1.95,33.95;22.85,40.65"/>
+        <dia:rectangle val="1.95,33.95;22.95,40.65"/>
       </dia:attribute>
       <dia:attribute name="elem_corner">
         <dia:point val="2,34"/>
       </dia:attribute>
       <dia:attribute name="elem_width">
-        <dia:real val="20.800000000000001"/>
+        <dia:real val="20.900000000000002"/>
       </dia:attribute>
       <dia:attribute name="elem_height">
         <dia:real val="6.5999999999999996"/>
@@ -14645,13 +14698,13 @@
         <dia:point val="152,25"/>
       </dia:attribute>
       <dia:attribute name="obj_bb">
-        <dia:rectangle val="151.95,24.95;171.1,27.85"/>
+        <dia:rectangle val="151.95,24.95;171.2,27.85"/>
       </dia:attribute>
       <dia:attribute name="elem_corner">
         <dia:point val="152,25"/>
       </dia:attribute>
       <dia:attribute name="elem_width">
-        <dia:real val="19.050000000000001"/>
+        <dia:real val="19.150000000000002"/>
       </dia:attribute>
       <dia:attribute name="elem_height">
         <dia:real val="2.7999999999999998"/>
@@ -14890,13 +14943,13 @@
         <dia:point val="96,45"/>
       </dia:attribute>
       <dia:attribute name="obj_bb">
-        <dia:rectangle val="95.95,44.95;142.4,54.85"/>
+        <dia:rectangle val="95.95,44.95;142.5,54.85"/>
       </dia:attribute>
       <dia:attribute name="elem_corner">
         <dia:point val="96,45"/>
       </dia:attribute>
       <dia:attribute name="elem_width">
-        <dia:real val="46.350000000000001"/>
+        <dia:real val="46.450000000000003"/>
       </dia:attribute>
       <dia:attribute name="elem_height">
         <dia:real val="9.8000000000000007"/>
diff --git a/diagrams/modelfit.dia b/diagrams/modelfit.dia
index 64f6d75..6f47028 100644
--- a/diagrams/modelfit.dia
+++ b/diagrams/modelfit.dia
@@ -233,7 +233,7 @@
         <dia:point val="2.55,2.05"/>
       </dia:attribute>
       <dia:attribute name="obj_bb">
-        <dia:rectangle val="2.5,2;195.35,30.3"/>
+        <dia:rectangle val="2.5,2;195.35,29.5"/>
       </dia:attribute>
       <dia:attribute name="elem_corner">
         <dia:point val="2.55,2.05"/>
@@ -242,7 +242,7 @@
         <dia:real val="192.75"/>
       </dia:attribute>
       <dia:attribute name="elem_height">
-        <dia:real val="28.20000000000001"/>
+        <dia:real val="27.400000000000006"/>
       </dia:attribute>
       <dia:attribute name="name">
         <dia:string>#modelfit#</dia:string>
@@ -1549,6 +1549,40 @@
           <dia:attribute name="parameters">
             <dia:composite type="umlparameter">
               <dia:attribute name="name">
+                <dia:string>#model#</dia:string>
+              </dia:attribute>
+              <dia:attribute name="type">
+                <dia:string>#mandatory object model#</dia:string>
+              </dia:attribute>
+              <dia:attribute name="value">
+                <dia:string>##</dia:string>
+              </dia:attribute>
+              <dia:attribute name="comment">
+                <dia:string>##</dia:string>
+              </dia:attribute>
+              <dia:attribute name="kind">
+                <dia:enum val="1"/>
+              </dia:attribute>
+            </dia:composite>
+            <dia:composite type="umlparameter">
+              <dia:attribute name="name">
+                <dia:string>#run#</dia:string>
+              </dia:attribute>
+              <dia:attribute name="type">
+                <dia:string>#mandatory scalar integer#</dia:string>
+              </dia:attribute>
+              <dia:attribute name="value">
+                <dia:string>##</dia:string>
+              </dia:attribute>
+              <dia:attribute name="comment">
+                <dia:string>##</dia:string>
+              </dia:attribute>
+              <dia:attribute name="kind">
+                <dia:enum val="1"/>
+              </dia:attribute>
+            </dia:composite>
+            <dia:composite type="umlparameter">
+              <dia:attribute name="name">
                 <dia:string>#batchSize#</dia:string>
               </dia:attribute>
               <dia:attribute name="type">
diff --git a/diagrams/scm.dia b/diagrams/scm.dia
index 2f433b2..49b76bf 100644
--- a/diagrams/scm.dia
+++ b/diagrams/scm.dia
@@ -4000,7 +4000,7 @@
         </dia:composite>
         <dia:composite type="umlattribute">
           <dia:attribute name="name">
-            <dia:string>#rm_temp_files#</dia:string>
+            <dia:string>#remove_temp_files#</dia:string>
           </dia:attribute>
           <dia:attribute name="type">
             <dia:string>#scalar boolean#</dia:string>
@@ -4563,7 +4563,7 @@
         <dia:point val="159.55,98.7"/>
       </dia:attribute>
       <dia:attribute name="obj_bb">
-        <dia:rectangle val="136.7,97.85;159.9,130.2"/>
+        <dia:rectangle val="136.7,98;159.9,130.2"/>
       </dia:attribute>
       <dia:attribute name="orth_points">
         <dia:point val="159.55,98.7"/>
@@ -4726,7 +4726,7 @@
         <dia:point val="209.45,101.7"/>
       </dia:attribute>
       <dia:attribute name="obj_bb">
-        <dia:rectangle val="196.7,97.95;209.8,102.45"/>
+        <dia:rectangle val="196.7,97.95;209.8,102.6"/>
       </dia:attribute>
       <dia:attribute name="orth_points">
         <dia:point val="209.45,101.7"/>
diff --git a/diagrams/tool.dia b/diagrams/tool.dia
index 2b4d3b7..5330231 100644
--- a/diagrams/tool.dia
+++ b/diagrams/tool.dia
@@ -896,7 +896,7 @@
         </dia:composite>
         <dia:composite type="umlattribute">
           <dia:attribute name="name">
-            <dia:string>#rm_temp_files#</dia:string>
+            <dia:string>#remove_temp_files#</dia:string>
           </dia:attribute>
           <dia:attribute name="type">
             <dia:string>#scalar boolean#</dia:string>
-- 
2.11.4.GIT