:orphan:

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


.. _table_spec:



.. _table-x-method-options-x-spec:

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

Type: :term:`dict_record <dict_record>`

method options for TABLE

Example:-

.. code-block:: pyml

    METHOD_OPTIONS:
        py_module: table


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

py_module
=========

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

Python module required to process this script file

Example:-

.. code-block:: pyml

    py_module: table


.. _table-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}


.. _table-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


.. _table-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


.. _table-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


.. _table-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


.. _table-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


.. _table-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


.. _table-x-file-paths-x-spec:

FILE_PATHS
**********

Type: :term:`dict_record <dict_record>`

file paths

Example:-

.. code-block:: pyml

    FILE_PATHS:
        output_folder: auto
        log_folder: auto
        table_file_ext: ['csv']
        delete_old_files_flag: False
        solutions:
            initial_fit_ipred: sol0/solution.pyml
            final_fit_ipred: solN/solution.pyml


.. _table-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


.. _table-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


.. _table-x-file-paths-x-table-file-ext-x-spec:

table_file_ext
==============

Type: :term:`list_of(csv) <list_of>`

Output file extension; determines tabular output file format.

Example:-

.. code-block:: pyml

    table_file_ext: ['csv']


.. _table-x-file-paths-x-delete-old-files-flag-x-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


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

solutions
=========

Type: :term:`dict <dict>`

Solutions to compare

Example:-

.. code-block:: pyml

    solutions:
        initial_fit_ipred: sol0/solution.pyml
        final_fit_ipred: solN/solution.pyml


.. _table-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


.. _table-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


.. _table-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


.. _table-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


.. _table-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: |


.. _table-x-output-tables-x-spec:

OUTPUT_TABLES
*************

Type: :term:`list_record <list_record>`

List of tables to create.

Example:-

.. code-block:: pyml

    OUTPUT_TABLES:
        - TABLE:
            input_solution: final_fit_ipred
            output_file: my_table.csv
            cx_columns: "*"
            mx_columns: "*"
            sx_columns: "*"
            px_columns: "*"


.. _table-x-output-tables-x-table-x-spec:

TABLE
=====

Type: :term:`dict_record <dict_record>`

Table properties.

Example:-

.. code-block:: pyml

    TABLE:
        input_solution: final_fit_ipred
        output_file: my_table.csv
        cx_columns: "*"
        mx_columns: "*"
        sx_columns: "*"
        px_columns: "*"


.. _table-x-output-tables-x-table-x-input-solution-x-spec:

input_solution
--------------

Type: :term:`str <str>`

Label of the solution to parse

Example:-

.. code-block:: pyml

    input_solution: final_fit_ipred


.. _table-x-output-tables-x-table-x-output-file-x-spec:

output_file
-----------

Type: :term:`output_file <output_file>`

Destination file for table

Example:-

.. code-block:: pyml

    output_file: my_table.csv


.. _table-x-output-tables-x-table-x-cx-columns-x-spec:

cx_columns
----------

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

Columns from covariates/observations table to output

Example:-

.. code-block:: pyml

    cx_columns: "*"


.. _table-x-output-tables-x-table-x-mx-columns-x-spec:

mx_columns
----------

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

Columns from model_params table to output

Example:-

.. code-block:: pyml

    mx_columns: "*"


.. _table-x-output-tables-x-table-x-sx-columns-x-spec:

sx_columns
----------

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

Columns from states table to output

Example:-

.. code-block:: pyml

    sx_columns: "*"


.. _table-x-output-tables-x-table-x-px-columns-x-spec:

px_columns
----------

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

Columns from predictions table to output

Example:-

.. code-block:: pyml

    px_columns: "*"



