:orphan:

.. The content of this file was generated
.. automatically by the popy.conf.fio.rstdoc_writer module


.. _grph_spec:



.. _grph-method_options_spec:

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

Type: :term:`dict_record <dict_record>`

method options for plt_grph

Example:-

.. code-block:: pyml

    METHOD_OPTIONS:
        py_module: grph


.. _grph-method_options-py_module_spec:

py_module
=========

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

Python module required to process this script file

Example:-

.. code-block:: pyml

    py_module: grph


.. _grph-parallel_spec:

PARALLEL
********

Type: :term:`one_of_record <one_of_record>`

one of many possible servers

Example:-

.. code-block:: pyml

    PARALLEL:
        SINGLE: {}


.. _grph-parallel-single_spec:

SINGLE
======

Type: :term:`dict_record <dict_record>`

single process server spec.

Example:-

.. code-block:: pyml

    SINGLE: {}


.. _grph-parallel-mpi_workers_spec:

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

Type: :term:`dict_record <dict_record>`

MPI local server spec.

Example:-

.. code-block:: pyml

    MPI_WORKERS:
        n_workers: auto


.. _grph-parallel-mpi_workers-n_workers_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


.. _grph-file_paths_spec:

FILE_PATHS
**********

Type: :term:`dict_record <dict_record>`

file paths

Example:-

.. code-block:: pyml

    FILE_PATHS:
        output_folder: auto
        log_folder: auto
        output_file_ext: ['svg']
        delete_old_files_flag: False
        solutions:
            pop: ./path_to_final_pop_solution.pyml
            indiv: ./path_to_final_indiv_solution.pyml


.. _grph-file_paths-output_folder_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


.. _grph-file_paths-log_folder_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


.. _grph-file_paths-output_file_ext_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']


.. _grph-file_paths-delete_old_files_flag_spec:

delete_old_files_flag
=====================

Type: :term:`bool <bool>`

Option to delete any existing files before running.

Example:-

.. code-block:: pyml

    delete_old_files_flag: False


.. _grph-file_paths-solutions_spec:

solutions
=========

Type: :term:`dict <dict>`

Solutions to compare

Example:-

.. code-block:: pyml

    solutions:
        pop: ./path_to_final_pop_solution.pyml
        indiv: ./path_to_final_indiv_solution.pyml


.. _grph-data_fields_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


.. _grph-data_fields-type_field_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


.. _grph-data_fields-id_field_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


.. _grph-data_fields-time_field_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


.. _grph-output_graphs_spec:

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

Type: :term:`list_record <list_record>`

List of graphs to output.

Example:-

.. code-block:: pyml

    OUTPUT_GRAPHS:
        - SPAG_GRPH:
            graph_title: My rather excellent graph
            y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
            y_var_src_list: ['orig', 'sim']
            y_var_label_list: ['drug in plasma', 'bio marker in plasma']
            y_var_colour_list: ['b', 'g']
            y_var_symbol_list: ['-', '-']
            x_var: TIME
            x_axis_label: Time (hours)
            x_scale: linear
            y_var_list: ['CONC_DRUG', 'CONC_DRUG_sim']
            y_scale_list: ['linear', 'log']
            options_list: ['legend', 'grid', 'dose_lines']

        - COMB_SPAG_GRPH:
            graph_title: My rather excellent graph
            y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
            y_var_src_list: ['orig', 'sim']
            y_var_label_list: ['drug in plasma', 'bio marker in plasma']
            y_var_colour_list: ['b', 'g']
            y_var_symbol_list: ['-', '-']
            x_var: TIME
            x_axis_label: Time (hours)
            x_scale: linear
            y_var_list: ['CONC_DRUG', 'CONC_DRUG_sim']
            y_scale_list: ['linear', 'log']
            options_list: ['legend', 'grid', 'dose_lines']


.. _grph-output_graphs-spag_grph_spec:

SPAG_GRPH
=========

Type: :term:`dict_record <dict_record>`

Plot data for all individuals on separate graphs.

Example:-

.. code-block:: pyml

    SPAG_GRPH:
        graph_title: My rather excellent graph
        y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
        y_var_src_list: ['orig', 'sim']
        y_var_label_list: ['drug in plasma', 'bio marker in plasma']
        y_var_colour_list: ['b', 'g']
        y_var_symbol_list: ['-', '-']
        x_var: TIME
        x_axis_label: Time (hours)
        x_scale: linear
        y_var_list: ['CONC_DRUG', 'CONC_DRUG_sim']
        y_scale_list: ['linear', 'log']
        options_list: ['legend', 'grid', 'dose_lines']


.. _grph-output_graphs-spag_grph-graph_title_spec:

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

Type: :term:`str <str>`

Title of graph.

Example:-

.. code-block:: pyml

    graph_title: My rather excellent graph


.. _grph-output_graphs-spag_grph-y_axis_label_list_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']


.. _grph-output_graphs-spag_grph-y_var_src_list_spec:

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

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

List of y variable types, orig = original data set 
sim = simulated data

Example:-

.. code-block:: pyml

    y_var_src_list: ['orig', 'sim']


.. _grph-output_graphs-spag_grph-y_var_label_list_spec:

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

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

List of y variable labels, which appear in the legend.

Example:-

.. code-block:: pyml

    y_var_label_list: ['drug in plasma', 'bio marker in plasma']


.. _grph-output_graphs-spag_grph-y_var_colour_list_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']


.. _grph-output_graphs-spag_grph-y_var_symbol_list_spec:

y_var_symbol_list
-----------------

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

List of plot line styles for y variable plot lines.

Example:-

.. code-block:: pyml

    y_var_symbol_list: ['-', '-']


.. _grph-output_graphs-spag_grph-x_var_spec:

x_var
-----

Type: :term:`str <str>`

x axis variable name.

Example:-

.. code-block:: pyml

    x_var: TIME


.. _grph-output_graphs-spag_grph-x_axis_label_spec:

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

Type: :term:`str <str>`

x axis label text.

Example:-

.. code-block:: pyml

    x_axis_label: Time (hours)


.. _grph-output_graphs-spag_grph-x_scale_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


.. _grph-output_graphs-spag_grph-y_var_list_spec:

y_var_list
----------

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

List of y variable names to be plotted on graph.

Example:-

.. code-block:: pyml

    y_var_list: ['CONC_DRUG', 'CONC_DRUG_sim']


.. _grph-output_graphs-spag_grph-y_scale_list_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']


.. _grph-output_graphs-spag_grph-options_list_spec:

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

Type: :term:`list_of(legend,legend_above,grid,dose_lines,share_axes,45degree_line,sim_xy) <list_of>`

List of visual options to apply to individual plots.

Example:-

.. code-block:: pyml

    options_list: ['legend', 'grid', 'dose_lines']


.. _grph-output_graphs-comb_spag_grph_spec:

COMB_SPAG_GRPH
==============

Type: :term:`dict_record <dict_record>`

Plot data for all individuals one one graph.

Example:-

.. code-block:: pyml

    COMB_SPAG_GRPH:
        graph_title: My rather excellent graph
        y_axis_label_list: ['Drug concentration in plasma', 'Bio-marker concentration in plasma']
        y_var_src_list: ['orig', 'sim']
        y_var_label_list: ['drug in plasma', 'bio marker in plasma']
        y_var_colour_list: ['b', 'g']
        y_var_symbol_list: ['-', '-']
        x_var: TIME
        x_axis_label: Time (hours)
        x_scale: linear
        y_var_list: ['CONC_DRUG', 'CONC_DRUG_sim']
        y_scale_list: ['linear', 'log']
        options_list: ['legend', 'grid', 'dose_lines']


.. _grph-output_graphs-comb_spag_grph-graph_title_spec:

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

Type: :term:`str <str>`

Title of graph.

Example:-

.. code-block:: pyml

    graph_title: My rather excellent graph


.. _grph-output_graphs-comb_spag_grph-y_axis_label_list_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']


.. _grph-output_graphs-comb_spag_grph-y_var_src_list_spec:

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

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

List of y variable types, orig = original data set 
sim = simulated data

Example:-

.. code-block:: pyml

    y_var_src_list: ['orig', 'sim']


.. _grph-output_graphs-comb_spag_grph-y_var_label_list_spec:

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

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

List of y variable labels, which appear in the legend.

Example:-

.. code-block:: pyml

    y_var_label_list: ['drug in plasma', 'bio marker in plasma']


.. _grph-output_graphs-comb_spag_grph-y_var_colour_list_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']


.. _grph-output_graphs-comb_spag_grph-y_var_symbol_list_spec:

y_var_symbol_list
-----------------

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

List of plot line styles for y variable plot lines.

Example:-

.. code-block:: pyml

    y_var_symbol_list: ['-', '-']


.. _grph-output_graphs-comb_spag_grph-x_var_spec:

x_var
-----

Type: :term:`str <str>`

x axis variable name.

Example:-

.. code-block:: pyml

    x_var: TIME


.. _grph-output_graphs-comb_spag_grph-x_axis_label_spec:

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

Type: :term:`str <str>`

x axis label text.

Example:-

.. code-block:: pyml

    x_axis_label: Time (hours)


.. _grph-output_graphs-comb_spag_grph-x_scale_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


.. _grph-output_graphs-comb_spag_grph-y_var_list_spec:

y_var_list
----------

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

List of y variable names to be plotted on graph.

Example:-

.. code-block:: pyml

    y_var_list: ['CONC_DRUG', 'CONC_DRUG_sim']


.. _grph-output_graphs-comb_spag_grph-y_scale_list_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']


.. _grph-output_graphs-comb_spag_grph-options_list_spec:

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

Type: :term:`list_of(legend,legend_above,grid,dose_lines,share_axes,45degree_line,sim_xy) <list_of>`

List of visual options to apply to individual plots.

Example:-

.. code-block:: pyml

    options_list: ['legend', 'grid', 'dose_lines']



