:orphan:

.. The content of this file was generated
.. automatically by the popy.conf.fio.rstdoc_writer module
.. at 19 Mar 2026, 01:37:10


.. _vpc_spec:



.. _vpc-x-method-options-x-spec:

METHOD_OPTIONS
**************

Type: :term:`dict_record <dict_record>`

method options for plt_vpc

Example:-

.. code-block:: pyml

    METHOD_OPTIONS:
        py_module: vpc


.. _vpc-x-method-options-x-py-module-x-spec:

py_module
=========

Type: :term:`one_of(vpc) <one_of>`

Python module required to process this script file

Example:-

.. code-block:: pyml

    py_module: vpc


.. _vpc-x-parallel-x-spec:

PARALLEL
********

Type: :term:`one_of_record <one_of_record>`

one of many possible servers

Example:-

.. code-block:: pyml

    PARALLEL:
        SINGLE: {progress_bar_length: 0}


.. _vpc-x-parallel-x-single-x-spec:

SINGLE
======

Type: :term:`dict_record <dict_record>`

single process server spec.

Example:-

.. code-block:: pyml

    SINGLE:
        progress_bar_length: 0


.. _vpc-x-parallel-x-single-x-progress-bar-length-x-spec:

progress_bar_length
-------------------

Type: :term:`int <int>`

Length of progress bar on screen (default=0, off)

Example:-

.. code-block:: pyml

    progress_bar_length: 0


.. _vpc-x-parallel-x-mpi-workers-x-spec:

MPI_WORKERS
===========

Type: :term:`dict_record <dict_record>`

MPI local server spec.

Example:-

.. code-block:: pyml

    MPI_WORKERS:
        n_workers: auto
        cpu_load: 1.0
        progress_bar_length: 0


.. _vpc-x-parallel-x-mpi-workers-x-n-workers-x-spec:

n_workers
---------

Type: :term:`int <int>` / :term:`auto <auto>`

Number of workers to use on this machine, defaults to number of processors, but could be more or fewer.

Example:-

.. code-block:: pyml

    n_workers: auto


.. _vpc-x-parallel-x-mpi-workers-x-cpu-load-x-spec:

cpu_load
--------

Type: :term:`float <float>`

Desired load on CPU as a decimal greater than 0.0 (0%) and less than or equal to 1.0 (100%)

Example:-

.. code-block:: pyml

    cpu_load: 1.0


.. _vpc-x-parallel-x-mpi-workers-x-progress-bar-length-x-spec:

progress_bar_length
-------------------

Type: :term:`int <int>`

Length of progress bar on screen (default=0, off)

Example:-

.. code-block:: pyml

    progress_bar_length: 0


.. _vpc-x-file-paths-x-spec:

FILE_PATHS
**********

Type: :term:`dict_record <dict_record>`

file paths

Example:-

.. code-block:: pyml

    FILE_PATHS:
        output_folder: auto
        temp_folder: auto
        log_folder: auto
        output_file_ext: ['svg']
        solutions:
            fit_obs: ../input_observations_soln.pyml
            msim_obs: msim_obs/msim_observations_soln.pyml
            pred_pop: predicted_mean_population_solution.pyml


.. _vpc-x-file-paths-x-output-folder-x-spec:

output_folder
=============

Type: :term:`output_folder <output_folder>` / :term:`auto <auto>`

Output folder - results of computation stored here

Example:-

.. code-block:: pyml

    output_folder: auto


.. _vpc-x-file-paths-x-temp-folder-x-spec:

temp_folder
===========

Type: :term:`output_folder <output_folder>` / :term:`auto <auto>`

Temp folder - temporary files stored here

Example:-

.. code-block:: pyml

    temp_folder: auto


.. _vpc-x-file-paths-x-log-folder-x-spec:

log_folder
==========

Type: :term:`output_folder <output_folder>` / :term:`auto <auto>`

Log folder - log files stored here

Example:-

.. code-block:: pyml

    log_folder: auto


.. _vpc-x-file-paths-x-output-file-ext-x-spec:

output_file_ext
===============

Type: :term:`list_of(pdf,png,svg) <list_of>`

Output file extension - determines graphical output file format.

Example:-

.. code-block:: pyml

    output_file_ext: ['svg']


.. _vpc-x-file-paths-x-solutions-x-spec:

solutions
=========

Type: :term:`dict <dict>`

Solutions to compare

Example:-

.. code-block:: pyml

    solutions:
        fit_obs: ../input_observations_soln.pyml
        msim_obs: msim_obs/msim_observations_soln.pyml
        pred_pop: predicted_mean_population_solution.pyml


.. _vpc-x-preprocess-x-spec:

PREPROCESS
**********

Type: :term:`verbatim <verbatim>`

Code that preprocesses the input data.
Use this to filter rows and create derived covariates.

Example:-

.. code-block:: pyml

    PREPROCESS: |


.. _vpc-x-data-fields-x-spec:

DATA_FIELDS
***********

Type: :term:`dict_record <dict_record>`

data fields for popy.dat.fields object

Example:-

.. code-block:: pyml

    DATA_FIELDS:
        type_field: TYPE
        id_field: ID
        time_field: TIME


.. _vpc-x-data-fields-x-type-field-x-spec:

type_field
==========

Type: :term:`str <str>`

Field name in data file that contains row type info, e.g. obs/dose etc

Example:-

.. code-block:: pyml

    type_field: TYPE


.. _vpc-x-data-fields-x-id-field-x-spec:

id_field
========

Type: :term:`str <str>`

Field name in data file that contains identity string for each data row e.g. obs/dose etc

Example:-

.. code-block:: pyml

    id_field: ID


.. _vpc-x-data-fields-x-time-field-x-spec:

time_field
==========

Type: :term:`str <str>`

Field name in data file that contains time or event for each data row

Example:-

.. code-block:: pyml

    time_field: TIME


.. _vpc-x-output-graphs-x-spec:

OUTPUT_GRAPHS
*************

Type: :term:`list_record <list_record>`

List of graphs to output.

Example:-

.. code-block:: pyml

    OUTPUT_GRAPHS:
        - COMB_QUANT_SIM_VPC:
            output_subdir: none
            graph_title: My rather excellent graph
            x_axis_label: TIME
            x_var: TIME
            x_scale: linear
            y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
            y_var_src_list: ['observed_data', 'final_fit_ppred', 'final_fit_ipred']
            y_var_list: ['DV_CENTRAL', 'DV_CENTRAL', 'DV_CENTRAL']
            y_var_label_list: ['Drug conc. (units)', 'Drug conc. (units)', 'Drug conc. (units)']
            y_var_colour_list: ['b', 'g']
            y_scale_list: ['linear', 'log']
            bin_indexer: {EQUAL_SPACE: {n_bins: auto}}
            quantile_list: [0.05, 0.5, 0.95]
            min_bin_count: 3
            options_list: ['legend_above', 'grid', 'plot_orig_points']
            conf_interval_prop: 0.9
            y_var_norm_list: ['DV_CENTRAL_pred', 'DV_CENTRAL_pred', 'DV_CENTRAL_pred']
            norm_method: none
            split_field: none
            export_stats: False


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-spec:

COMB_QUANT_SIM_VPC
==================

Type: :term:`dict_record <dict_record>`

Plot vpc data using histograms of each simulation one graph.

Example:-

.. code-block:: pyml

    COMB_QUANT_SIM_VPC:
        output_subdir: none
        graph_title: My rather excellent graph
        x_axis_label: TIME
        x_var: TIME
        x_scale: linear
        y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
        y_var_src_list: ['observed_data', 'final_fit_ppred', 'final_fit_ipred']
        y_var_list: ['DV_CENTRAL', 'DV_CENTRAL', 'DV_CENTRAL']
        y_var_label_list: ['Drug conc. (units)', 'Drug conc. (units)', 'Drug conc. (units)']
        y_var_colour_list: ['b', 'g']
        y_scale_list: ['linear', 'log']
        bin_indexer: {EQUAL_SPACE: {n_bins: auto}}
        quantile_list: [0.05, 0.5, 0.95]
        min_bin_count: 3
        options_list: ['legend_above', 'grid', 'plot_orig_points']
        conf_interval_prop: 0.9
        y_var_norm_list: ['DV_CENTRAL_pred', 'DV_CENTRAL_pred', 'DV_CENTRAL_pred']
        norm_method: none
        split_field: none
        export_stats: False


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-output-subdir-x-spec:

output_subdir
-------------

Type: :term:`output_folder <output_folder>`

Destination subdirectory for these plots.

Example:-

.. code-block:: pyml

    output_subdir: none


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-graph-title-x-spec:

graph_title
-----------

Type: :term:`str <str>`

Title of graph.

Example:-

.. code-block:: pyml

    graph_title: My rather excellent graph


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-x-axis-label-x-spec:

x_axis_label
------------

Type: :term:`str <str>`

x axis label text

Example:-

.. code-block:: pyml

    x_axis_label: TIME


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-x-var-x-spec:

x_var
-----

Type: :term:`str <str>`

x axis variable name.

Example:-

.. code-block:: pyml

    x_var: TIME


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-x-scale-x-spec:

x_scale
-------

Type: :term:`one_of(linear,log) <one_of>`

x axis scale - can be either 'linear' or 'log'.

Example:-

.. code-block:: pyml

    x_scale: linear


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-y-axis-label-list-x-spec:

y_axis_label_list
-----------------

Type: :term:`list(str) <list>`

List of labels for y variables that appear on axes.

Example:-

.. code-block:: pyml

    y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-y-var-src-list-x-spec:

y_var_src_list
--------------

Type: :term:`list(str) <list>`

Names of the solution folders that contain the predictions to be plotted

Example:-

.. code-block:: pyml

    y_var_src_list: ['observed_data', 'final_fit_ppred', 'final_fit_ipred']


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-y-var-list-x-spec:

y_var_list
----------

Type: :term:`list(str) <list>`

List of y variable names (i.e. columns in the predictions table) to be plotted on graph.

Example:-

.. code-block:: pyml

    y_var_list: ['DV_CENTRAL', 'DV_CENTRAL', 'DV_CENTRAL']


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-y-var-label-list-x-spec:

y_var_label_list
----------------

Type: :term:`list(str) <list>`

List of y variable labels which will appear in the legend as <y_var_label> (<y_var_src>).

Example:-

.. code-block:: pyml

    y_var_label_list: ['Drug conc. (units)', 'Drug conc. (units)', 'Drug conc. (units)']


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-y-var-colour-list-x-spec:

y_var_colour_list
-----------------

Type: :term:`list(str) <list>`

List of colours for y variable plot lines.

Example:-

.. code-block:: pyml

    y_var_colour_list: ['b', 'g']


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-y-scale-list-x-spec:

y_scale_list
------------

Type: :term:`list(str) <list>`

List of scales (linear or log) for multiple y axes.

Example:-

.. code-block:: pyml

    y_scale_list: ['linear', 'log']


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-bin-indexer-x-spec:

bin_indexer
-----------

Type: :term:`one_of_record <one_of_record>`

Possible bin indexing methods.

Example:-

.. code-block:: pyml

    bin_indexer:
        EQUAL_SPACE: {n_bins: auto}


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-bin-indexer-x-equal-space-x-spec:

EQUAL_SPACE
^^^^^^^^^^^

Type: :term:`dict_record <dict_record>`

Equally spaced index builder.

Example:-

.. code-block:: pyml

    EQUAL_SPACE:
        n_bins: auto


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-bin-indexer-x-equal-space-x-n-bins-x-spec:

n_bins
""""""

Type: :term:`int <int>` / :term:`auto <auto>`

Number of equally spaced bins in index.

Example:-

.. code-block:: pyml

    n_bins: auto


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-bin-indexer-x-unequal-space-x-spec:

UNEQUAL_SPACE
^^^^^^^^^^^^^

Type: :term:`dict_record <dict_record>`

fixed, irregularly spaced user defined bin edges.

Example:-

.. code-block:: pyml

    UNEQUAL_SPACE:
        bin_edge_list: [2.0, 4.0, 8.0]


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-bin-indexer-x-unequal-space-x-bin-edge-list-x-spec:

bin_edge_list
"""""""""""""

Type: :term:`list(float) <list>`

List of user-defined bin edges.

Example:-

.. code-block:: pyml

    bin_edge_list: [2.0, 4.0, 8.0]


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-bin-indexer-x-k-means-x-spec:

K_MEANS
^^^^^^^

Type: :term:`dict_record <dict_record>`

Deduce bin centres automatically using k-means algorithm for a pre-determined number of bins.

Example:-

.. code-block:: pyml

    K_MEANS:
        n_bins: 10
        init_method: random


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-bin-indexer-x-k-means-x-n-bins-x-spec:

n_bins
""""""

Type: :term:`int <int>`

Number of bins.

Example:-

.. code-block:: pyml

    n_bins: 10


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-bin-indexer-x-k-means-x-init-method-x-spec:

init_method
"""""""""""

Type: :term:`one_of(random) <one_of>`

Initialisation method for k-means algorithm.

Example:-

.. code-block:: pyml

    init_method: random


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-bin-indexer-x-pop-index-x-spec:

POP_INDEX
^^^^^^^^^

Type: :term:`dict_record <dict_record>`

Take unique values from first individual as bin centres.

Example:-

.. code-block:: pyml

    POP_INDEX: {}


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-quantile-list-x-spec:

quantile_list
-------------

Type: :term:`list(float) <list>`

List of quantiles to plot for each bin of the histogram.

Example:-

.. code-block:: pyml

    quantile_list: [0.05, 0.5, 0.95]


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-min-bin-count-x-spec:

min_bin_count
-------------

Type: :term:`int <int>`

Number of data points required to plot an individual bin.

Example:-

.. code-block:: pyml

    min_bin_count: 3


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-options-list-x-spec:

options_list
------------

Type: :term:`list_of(legend,legend_above,grid,contour_conf_intervals,plot_orig_points) <list_of>`

List of visual options to apply to individual plots.

Example:-

.. code-block:: pyml

    options_list: ['legend_above', 'grid', 'plot_orig_points']


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-conf-interval-prop-x-spec:

conf_interval_prop
------------------

Type: :term:`float <float>`

Confidence interval proportion to display for each quantile.

Example:-

.. code-block:: pyml

    conf_interval_prop: 0.9


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-y-var-norm-list-x-spec:

y_var_norm_list
---------------

Type: :term:`list(str) <list>`

List of y variable names (i.e. columns in the predictions table) to normalise y_var_list.

Example:-

.. code-block:: pyml

    y_var_norm_list: ['DV_CENTRAL_pred', 'DV_CENTRAL_pred', 'DV_CENTRAL_pred']


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-norm-method-x-spec:

norm_method
-----------

Type: :term:`one_of(none,pred_corr,predvar_corr) <one_of>`

Normalisation method applied to predictions in each bin.

Example:-

.. code-block:: pyml

    norm_method: none


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-split-field-x-spec:

split_field
-----------

Type: :term:`str <str>`

field in c[X] data use each value to split data.

Example:-

.. code-block:: pyml

    split_field: none


.. _vpc-x-output-graphs-x-comb-quant-sim-vpc-x-export-stats-x-spec:

export_stats
------------

Type: :term:`bool <bool>`

Export any computed statistics to a .csv file

Example:-

.. code-block:: pyml

    export_stats: False



