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Add refcorr_data option to vpc
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@rikardn
rikardn committed Apr 21, 2024
1 parent 6dddc2d commit bbf56aa
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Showing 3 changed files with 73 additions and 18 deletions.
17 changes: 15 additions & 2 deletions bin/vpc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,7 @@ my %optional_options = ( 'idv:s' => undef,
'so!' => undef,
'mix!' => undef,
'refcorr:s' => undef,
'refcorr_data:s' => undef,
'refcorr_table:s' => undef,
);

Expand Down Expand Up @@ -512,6 +513,15 @@ $help_text{-refcorr} = <<'EOF';
Cannot be used together with -predcorr or -varcorr.
EOF

$help_text{-refcorr_data} = <<'EOF';
-refcorr_data
Option to specify a custom reference dataset to be used for reference simulations
when doing reference correction. The dataset needs to have a REF column containing the
row number (starting with 1) of the original dataset. Can only be used together with the -refcorr
options.
EOF

$help_text{-refcorr_table} = <<'EOF';
-refcorr_table=filename
Expand Down Expand Up @@ -686,13 +696,15 @@ if ($dummymodel){

}

my %refcorr;
my $refcorr;
if (defined $options{'refcorr'}) {
my %refcorr;
my @a = split ',', $options{'refcorr'};
for my $e (@a) {
my @pair = split '=', $e;
$refcorr{$pair[0]} = $pair[1];
}
$refcorr = \%refcorr;
}

input_checking::check_options(tool => 'vpc', options => \%options, model => $model);
Expand Down Expand Up @@ -747,7 +759,8 @@ my $vpc =
min_points_in_bin => $options{'min_points_in_bin'},
directory_name_prefix => 'vpc',
mix => $options{'mix'},
refcorr => \%refcorr,
refcorr => $refcorr,
refcorr_data => $options{'refcorr_data'},
refcorr_table => $options{'refcorr_table'},
);

Expand Down
72 changes: 57 additions & 15 deletions lib/tool/npc.pm
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@ package tool::npc;
use include_modules;
use random;
use strict;
use PsN;
use tool::modelfit;
use model;
use ui;
Expand Down Expand Up @@ -109,15 +110,13 @@ 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_data' => ( is => 'rw', isa => 'Maybe[Str]' );
has 'refcorr_table' => ( is => 'rw', isa => 'Maybe[Str]' );

sub BUILD
{
my $self = shift;

if (defined $self->refcorr and not keys %{$self->refcorr}) {
$self->refcorr(undef);
}
if (defined $self->refcorr_table) {
$self->refcorr({});
}
Expand Down Expand Up @@ -1181,13 +1180,22 @@ sub modelfit_setup
}
@rec_strings = @rec_strings2;

my @ref_strings;
if (defined $self->refcorr) {
@ref_strings = @sim_strings;
push @ref_strings, "REF";
}

my @trailing = ('ONEHEADER', 'NOPRINT', 'NOAPPEND');
if (($PsN::nm_major_version == 7 and $PsN::nm_minor_version >= 5) or $PsN::nm_major_version > 7) {
push @trailing, 'IDFORMAT=I';
}
push @trailing, 'FILE=npctab.dta';
push (@rec_strings,@trailing);
push (@sim_strings,@trailing);
if (defined $self->refcorr) {
push @ref_strings, @trailing;
}

$model_orig -> set_records(type => 'table',
record_strings => \@rec_strings,
Expand Down Expand Up @@ -1605,10 +1613,11 @@ sub modelfit_setup

if (defined $self->refcorr and not defined $self->refcorr_table) {
my %refcorr = %{$self->refcorr};
my $num = $i + 1;
my $path = "m1/" . $model_sims[$i]->filename;
my $destname = "${type}_simulation_refcorr.$num.mod";
my $destpath = "m1/$destname";
if (%refcorr) {
my $num = $i + 1;
my $path = "m1/" . $model_sims[$i]->filename;
my $destpath = "m1/${type}_simulation_refcorr.$num.mod";
my @refstrs;
for my $k (keys %refcorr) {
push @refstrs, "$k=" . $refcorr{$k};
Expand All @@ -1617,6 +1626,21 @@ sub modelfit_setup
PsN::call_pharmpy("data reference $path -o $destpath $refstr");
my $refmodel = model->new(filename => $destpath);
push @refcorr_models, $refmodel;
} elsif (defined $self->refcorr_data) {
my $refmodel = $model_sims[$i]->copy(
filename => $destname,
directory => 'm1',
copy_datafile => 0,
write_copy => 0,
output_same_directory => 1,
copy_output => 0);
$refmodel->datafiles(new_names => [$self->refcorr_data]);
$refmodel->remove_records(type => 'table');
$refmodel->set_records(type => 'table',
record_strings => \@ref_strings,
problem_numbers => [($self->origprobnum())]);
$refmodel->_write();
push @refcorr_models, $refmodel;
}
}
}
Expand Down Expand Up @@ -2392,7 +2416,17 @@ sub get_data_matrix
croak("File $orig_file \nwith table output for original data does not exist. ".
"It is recommended to check lst-file $file_to_check for NONMEM error messages.");
}
my $d = data -> new(filename => $orig_file, ignoresign => '@', idcolumn => 1); #we made this table file, ID is 1

my $origfile_name;
if (defined $self->refcorr and defined $self->refcorr_data) {
my $code = "from pharmpy.tools.vpc.psn_vpc import reference_correction_from_psn_vpc; reference_correction_from_psn_vpc(" . PsN::path_literal($self->directory) . ")";
PsN::call_pharmpy_wrapper($code);

$origfile_name = $orig_file . ".refcorr";
} else {
$origfile_name = $orig_file;
}
my $d = data->new(filename => $origfile_name, ignoresign => '@', idcolumn => 1); #we made this table file, ID is 1

unless (defined $d->individuals()){
croak("File $orig_file \nexists but PsN failed to read any individuals from it.");
Expand Down Expand Up @@ -2478,7 +2512,13 @@ sub get_data_matrix
"It is recommended to check lst-file\n$file_to_check \nfor NONMEM error messages.");
}

open (FILE, "$sim_file") or croak("Could not open $sim_file for reading");
my $simfile_name;
if (defined $self->refcorr and defined $self->refcorr_data) {
$simfile_name = "$sim_file" . ".refcorr";
} else {
$simfile_name = "$sim_file";
}
open (FILE, $simfile_name) or croak("Could not open $sim_file for reading");
my $prev_irep;
while (1){
my $line = readline(FILE);
Expand Down Expand Up @@ -2943,6 +2983,8 @@ sub create_binned_data
}
}

my $do_refcorr = (defined($self->refcorr) and not defined($self->refcorr_data));

for (my $strat_ind = 0; $strat_ind < $no_of_strata; $strat_ind++) {
my @bin_array;
my @pred_array;
Expand All @@ -2953,11 +2995,11 @@ sub create_binned_data
my @strt_array;
foreach my $index (@{$self->strata_matrix->[$strat_ind]}) {
push (@bin_array, $self->idv_array->[$index]);
push (@pred_array, $self->pred_array->[$index]) if ($self->predcorr || $self->varcorr || defined $self->refcorr);
push (@predref_array, $self->predref_array->[$index]) if (defined $self->refcorr);
push (@sdref_array, $self->sdref_array->[$index]) if (defined $self->refcorr);
push (@pred_array, $self->pred_array->[$index]) if ($self->predcorr || $self->varcorr || $do_refcorr);
push (@predref_array, $self->predref_array->[$index]) if (defined $do_refcorr);
push (@sdref_array, $self->sdref_array->[$index]) if (defined $do_refcorr);
push (@bound_array, $self->bound_array->[$index]) if ($self->predcorr and
(defined $self->bound_variable) or defined $self->refcorr );
(defined $self->bound_variable) or defined $do_refcorr);
push (@id_array,$self->id_array->[$index]);
push (@strt_array,$self->strata_variable_vector->[$index]) if (defined $self->stratify_on);
}
Expand Down Expand Up @@ -3114,7 +3156,7 @@ sub create_binned_data
my $censorstring = $self->censor_stratified_data->[$strat_ind]->[$index];
push (@bin_data_censor,$censorstring);
}
if ($self->predcorr || $self->varcorr || defined $self->refcorr) {
if ($self->predcorr || $self->varcorr || $do_refcorr) {
my $val = $pred_array[$index];
if ($self->lnDV == 3){
croak("cannot log non-positive PRED value ".$val) unless ($val>0);
Expand Down Expand Up @@ -3152,7 +3194,7 @@ sub create_binned_data
push (@strt_values,$strt_array[$index]) if (defined $self->stratify_on);
}

if (($self->predcorr and (scalar(@pred_values) > 0)) or defined $self->refcorr) {
if (($self->predcorr and (scalar(@pred_values) > 0)) or $do_refcorr) {
my $new_data = do_predcorr_and_varcorr(pred_array=>\@pred_values,
predref_array => \@predref_values,
sdref_array => \@sdref_values,
Expand Down Expand Up @@ -3475,7 +3517,7 @@ sub create_mirror_and_plot_data
}
}

if (defined $self->refcorr) {
if (defined $self->refcorr and not defined $self->refcorr_data) {
# Read in reference predictions from the first sample of the refcorr simulation data
my $reftab_path;
if (not defined $self->refcorr_table) {
Expand Down
2 changes: 1 addition & 1 deletion pharmpy
Submodule pharmpy updated 168 files

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