vpc: add option refcorr_table

UUPharmacometrics · Mar 7, 2024 · 99e3939 · 99e3939
1 parent 836d8e1
commit 99e3939
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Showing 2 changed files with 23 additions and 5 deletions.
diff --git a/bin/vpc b/bin/vpc
@@ -69,6 +69,7 @@ my %optional_options = ( 'idv:s' => undef,
     'so!' => undef,
     'mix!' => undef,
     'refcorr:s' => undef,
+    'refcorr_table:s' => undef,
 );
 
 my $res = GetOptions( \%options,
@@ -511,6 +512,13 @@ $help_text{-refcorr} = <<'EOF';
     Cannot be used together with -predcorr or -varcorr.
 EOF
 
+$help_text{-refcorr_table} = <<'EOF';
+    -refcorr_table=filename
+
+    Perform reference correction on dependent variable. Same as the refcorr option, but instead
+    of letting PsN create the reference simulations the user will provide them in a separate file. 
+EOF
+
 $help_text{-refstrat} = <<'EOF';
     -refstrat=number
 
@@ -740,6 +748,7 @@ my $vpc =
       directory_name_prefix => 'vpc',
       mix                  => $options{'mix'},
       refcorr => \%refcorr,
+      refcorr_table => $options{'refcorr_table'},
       );
 
 $vpc-> print_options (cmd_line => $cmd_line,

diff --git a/lib/tool/npc.pm b/lib/tool/npc.pm
@@ -109,6 +109,7 @@ has 'results_file' => ( is => 'rw', isa => 'Str', default => 'npc_results.csv' )
 has 'nca' => ( is => 'rw', isa => 'Bool', default => 0 );
 has 'mix' => ( is => 'rw', isa => 'Bool', default => 0 );
 has 'refcorr' => ( is => 'rw', isa => 'Maybe[HashRef]' );
+has 'refcorr_table' => ( is => 'rw', isa => 'Maybe[Str]' );
 
 sub BUILD
 {
@@ -117,6 +118,9 @@ sub BUILD
     if (defined $self->refcorr and not keys %{$self->refcorr}) {
         $self->refcorr(undef);
     }
+    if (defined $self->refcorr_table) {
+        $self->refcorr({});
+    }
     if (defined $self->auto_bin_mode) {
         unless ($self->auto_bin_mode eq 'auto' or $self->auto_bin_mode eq 'minmax' or $self->auto_bin_mode eq 'auto_equal_count') {
             croak("There are only three possible auto_bin modes: auto, minmax and auto_equal_count\n");
@@ -1599,7 +1603,7 @@ sub modelfit_setup
                                        problem_numbers => [$self->simprobnum()]);
         $model_sims[$i] -> _write(relative_data_path => $self->copy_data);
 
-        if (defined $self->refcorr) { 
+        if (defined $self->refcorr and not defined $self->refcorr_table) { 
             my %refcorr = %{$self->refcorr};
             if (%refcorr) {
                 my $num = $i + 1;
@@ -3473,10 +3477,15 @@ sub create_mirror_and_plot_data
 
     if (defined $self->refcorr) {
         # Read in reference predictions from the first sample of the refcorr simulation data
-        my $reftab_path = $self->original_model->directory() . 'vpc_simulation_refcorr.1.' .
-            $self->original_model->get_option_value(record_name => 'table',
-                                                    option_name => 'FILE',
-                                                    problem_index => ($self->origprobnum()-1));
+        my $reftab_path;
+        if (not defined $self->refcorr_table) {
+            $reftab_path = $self->original_model->directory() . 'vpc_simulation_refcorr.1.' .
+                $self->original_model->get_option_value(record_name => 'table',
+                                                        option_name => 'FILE',
+                                                        problem_index => ($self->origprobnum()-1));
+        } else {
+            $reftab_path = $self->directory . '../' . $self->refcorr_table; 
+        }
         my $reftab = data->new(filename => $reftab_path, ignoresign => '@', idcolumn => 1);
         my $pred_ref = $reftab->column_to_array('column'=>'PRED', 'filter'=>$filter);
         my $npreds = scalar(@$pred_ref);