:orphan:

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


.. _vpc_spec:



.. _vpc-method_options_spec:

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

Type: :term:`dict_record <dict_record>`

method options for plt_vpc

Example:-

.. code-block:: pyml

    METHOD_OPTIONS:
        py_module: vpc


.. _vpc-method_options-py_module_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-parallel_spec:

PARALLEL
********

Type: :term:`one_of_record <one_of_record>`

one of many possible servers

Example:-

.. code-block:: pyml

    PARALLEL:
        SINGLE: {}


.. _vpc-parallel-single_spec:

SINGLE
======

Type: :term:`dict_record <dict_record>`

single process server spec.

Example:-

.. code-block:: pyml

    SINGLE: {}


.. _vpc-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


.. _vpc-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


.. _vpc-file_paths_spec:

FILE_PATHS
**********

Type: :term:`dict_record <dict_record>`

file paths

Example:-

.. code-block:: pyml

    FILE_PATHS:
        input_data_file: input.csv
        msim_file_glob: msol/sim_*_pop.csv
        rx_zero_data_file: sim_rx_zero_pop.csv
        output_folder: auto
        temp_folder: auto
        log_folder: auto
        output_file_ext: ['svg']


.. _vpc-file_paths-input_data_file_spec:

input_data_file
===============

Type: :term:`input_file <input_file>`

path to input comma separated value file in popy data format

Example:-

.. code-block:: pyml

    input_data_file: input.csv


.. _vpc-file_paths-msim_file_glob_spec:

msim_file_glob
==============

Type: :term:`str <str>`

File path glob for simulated pops in msim folder

Example:-

.. code-block:: pyml

    msim_file_glob: msol/sim_*_pop.csv


.. _vpc-file_paths-rx_zero_data_file_spec:

rx_zero_data_file
=================

Type: :term:`input_file <input_file>`

Path to r[X]=0 zero noise population predictions.

Example:-

.. code-block:: pyml

    rx_zero_data_file: sim_rx_zero_pop.csv


.. _vpc-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


.. _vpc-file_paths-temp_folder_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-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


.. _vpc-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']


.. _vpc-preprocess_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-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


.. _vpc-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


.. _vpc-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


.. _vpc-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


.. _vpc-output_graphs_spec:

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

Type: :term:`list_record <list_record>`

List of graphs to output.

Example:-

.. code-block:: pyml

    OUTPUT_GRAPHS:
        - COMB_QUANT_SIM_VPC:
            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']
            x_var: TIME
            x_axis_label: Time (hours)
            x_scale: linear
            y_var_list: ['CONC_DRUG', 'CONC_DRUG_sim']
            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: ['CONC_DRUG_pred', 'CONC_DRUG_pred']
            norm_method: none
            split_field: none


.. _vpc-output_graphs-comb_quant_sim_vpc_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:
        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']
        x_var: TIME
        x_axis_label: Time (hours)
        x_scale: linear
        y_var_list: ['CONC_DRUG', 'CONC_DRUG_sim']
        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: ['CONC_DRUG_pred', 'CONC_DRUG_pred']
        norm_method: none
        split_field: none


.. _vpc-output_graphs-comb_quant_sim_vpc-graph_title_spec:

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

Type: :term:`str <str>`

Title of graph.

Example:-

.. code-block:: pyml

    graph_title: My rather excellent graph


.. _vpc-output_graphs-comb_quant_sim_vpc-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']


.. _vpc-output_graphs-comb_quant_sim_vpc-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']


.. _vpc-output_graphs-comb_quant_sim_vpc-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']


.. _vpc-output_graphs-comb_quant_sim_vpc-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']


.. _vpc-output_graphs-comb_quant_sim_vpc-x_var_spec:

x_var
-----

Type: :term:`str <str>`

x axis variable name.

Example:-

.. code-block:: pyml

    x_var: TIME


.. _vpc-output_graphs-comb_quant_sim_vpc-x_axis_label_spec:

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

Type: :term:`str <str>`

x axis label text.

Example:-

.. code-block:: pyml

    x_axis_label: Time (hours)


.. _vpc-output_graphs-comb_quant_sim_vpc-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


.. _vpc-output_graphs-comb_quant_sim_vpc-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']


.. _vpc-output_graphs-comb_quant_sim_vpc-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']


.. _vpc-output_graphs-comb_quant_sim_vpc-bin_indexer_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-output_graphs-comb_quant_sim_vpc-bin_indexer-equal_space_spec:

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

Type: :term:`dict_record <dict_record>`

Equally spaced index builder.

Example:-

.. code-block:: pyml

    EQUAL_SPACE:
        n_bins: auto


.. _vpc-output_graphs-comb_quant_sim_vpc-bin_indexer-equal_space-n_bins_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-output_graphs-comb_quant_sim_vpc-bin_indexer-unequal_space_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-output_graphs-comb_quant_sim_vpc-bin_indexer-unequal_space-bin_edge_list_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-output_graphs-comb_quant_sim_vpc-bin_indexer-k_means_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-output_graphs-comb_quant_sim_vpc-bin_indexer-k_means-n_bins_spec:

n_bins
""""""

Type: :term:`int <int>`

Number of bins.

Example:-

.. code-block:: pyml

    n_bins: 10


.. _vpc-output_graphs-comb_quant_sim_vpc-bin_indexer-k_means-init_method_spec:

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

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

Initialisation method for k-means algorithm.

Example:-

.. code-block:: pyml

    init_method: random


.. _vpc-output_graphs-comb_quant_sim_vpc-quantile_list_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-output_graphs-comb_quant_sim_vpc-min_bin_count_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-output_graphs-comb_quant_sim_vpc-options_list_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-output_graphs-comb_quant_sim_vpc-conf_interval_prop_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-output_graphs-comb_quant_sim_vpc-y_var_norm_list_spec:

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

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

List of y variable names to normalise y_var_list.

Example:-

.. code-block:: pyml

    y_var_norm_list: ['CONC_DRUG_pred', 'CONC_DRUG_pred']


.. _vpc-output_graphs-comb_quant_sim_vpc-norm_method_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-output_graphs-comb_quant_sim_vpc-split_field_spec:

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

Type: :term:`str <str>`

Data variable to partition graphs.

Example:-

.. code-block:: pyml

    split_field: none



