:orphan:

.. The content of this file was generated
.. automatically by the popy.conf.fio.rstdoc_writer module
.. at 09 Mar 2022, 08:35:58


.. _p2ndat_spec:



.. _p2ndat-method_options_spec:

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

Type: :term:`dict_record <dict_record>`

Root record for p2ndat program.

Example:-

.. code-block:: pyml

    METHOD_OPTIONS:
        py_module: p2ndat


.. _p2ndat-method_options-py_module_spec:

py_module
=========

Type: :term:`one_of(p2ndat) <one_of>`

Python module required to process this script file

Example:-

.. code-block:: pyml

    py_module: p2ndat


.. _p2ndat-file_paths_spec:

FILE_PATHS
**********

Type: :term:`dict_record <dict_record>`

File path options for p2ndat program.

Example:-

.. code-block:: pyml

    FILE_PATHS:
        input_popy_file: input_popy_data.csv
        output_nonmem_file: output_nonmem_data.csv
        output_nonmem_file_format: csv


.. _p2ndat-file_paths-input_popy_file_spec:

input_popy_file
===============

Type: :term:`input_file <input_file>`

path to input comma separated value file in popy data format

Example:-

.. code-block:: pyml

    input_popy_file: input_popy_data.csv


.. _p2ndat-file_paths-output_nonmem_file_spec:

output_nonmem_file
==================

Type: :term:`output_file <output_file>`

path to output nonmem file to be created by script

Example:-

.. code-block:: pyml

    output_nonmem_file: output_nonmem_data.csv


.. _p2ndat-file_paths-output_nonmem_file_format_spec:

output_nonmem_file_format
=========================

Type: :term:`one_of(csv,ssv,bin) <one_of>`

File format for NONMEM output (csv/ssv/bin)

Example:-

.. code-block:: pyml

    output_nonmem_file_format: csv


.. _p2ndat-input_popy_fields_spec:

INPUT_POPY_FIELDS
*****************

Type: :term:`dict_record <dict_record>`

Details for input popy data.

Example:-

.. code-block:: pyml

    INPUT_POPY_FIELDS:
        time_field: ABSTIME
        id_field: ID
        type_field: TYPE
        dv_fields: ['DRUG_CONC']
        amt_fields: ['AMT']
        rate_fields: []
        dur_fields: []
        dose_labels: ['']


.. _p2ndat-input_popy_fields-time_field_spec:

time_field
==========

Type: :term:`str <str>`

Name of input popy time field

Example:-

.. code-block:: pyml

    time_field: ABSTIME


.. _p2ndat-input_popy_fields-id_field_spec:

id_field
========

Type: :term:`str <str>`

Name of input popy id field

Example:-

.. code-block:: pyml

    id_field: ID


.. _p2ndat-input_popy_fields-type_field_spec:

type_field
==========

Type: :term:`str <str>`

Name of input popy type field

Example:-

.. code-block:: pyml

    type_field: TYPE


.. _p2ndat-input_popy_fields-dv_fields_spec:

dv_fields
=========

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

List of input popy fields containing dependent value information

Example:-

.. code-block:: pyml

    dv_fields: ['DRUG_CONC']


.. _p2ndat-input_popy_fields-amt_fields_spec:

amt_fields
==========

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

List of input popy columns containing dosing amount information

Example:-

.. code-block:: pyml

    amt_fields: ['AMT']


.. _p2ndat-input_popy_fields-rate_fields_spec:

rate_fields
===========

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

List of input popy columns containing infusion rate information

Example:-

.. code-block:: pyml

    rate_fields: []


.. _p2ndat-input_popy_fields-dur_fields_spec:

dur_fields
==========

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

List of input popy columns containing infusion duration information

Example:-

.. code-block:: pyml

    dur_fields: []


.. _p2ndat-input_popy_fields-dose_labels_spec:

dose_labels
===========

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

List of input popy dose label values within 
the TYPE field that define different types of dose 
i.e if entry is dose:X then put X in listif entry is dose then put "" in list

Example:-

.. code-block:: pyml

    dose_labels: ['']


.. _p2ndat-output_nonmem_fields_spec:

OUTPUT_NONMEM_FIELDS
********************

Type: :term:`dict_record <dict_record>`

Details for output popy data.

Example:-

.. code-block:: pyml

    OUTPUT_NONMEM_FIELDS:
        comment_prefix: '#'
        column_names: auto
        time_field: TIME
        id_field: ID
        evid_field: EVID
        dv_field: DV
        mdv_field: MDV
        amt_field: AMT
        rate_field: none
        dur_field: none
        cmt_field: CMT
        obs_cmt_numbers: [1]
        dose_cmt_numbers: [1]


.. _p2ndat-output_nonmem_fields-comment_prefix_spec:

comment_prefix
==============

Type: :term:`str <str>`

Characters used to indicate a comment line

Example:-

.. code-block:: pyml

    comment_prefix: '#'


.. _p2ndat-output_nonmem_fields-column_names_spec:

column_names
============

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

List of column names.
"auto" takes names from first row of dataset

Example:-

.. code-block:: pyml

    column_names: auto


.. _p2ndat-output_nonmem_fields-time_field_spec:

time_field
==========

Type: :term:`str <str>`

Name of output nonmem time field

Example:-

.. code-block:: pyml

    time_field: TIME


.. _p2ndat-output_nonmem_fields-id_field_spec:

id_field
========

Type: :term:`str <str>`

Name of output nonmem id field

Example:-

.. code-block:: pyml

    id_field: ID


.. _p2ndat-output_nonmem_fields-evid_field_spec:

evid_field
==========

Type: :term:`str <str>`

Name of output nonmem evid field

Example:-

.. code-block:: pyml

    evid_field: EVID


.. _p2ndat-output_nonmem_fields-dv_field_spec:

dv_field
========

Type: :term:`str <str>`

Name of output nonmem dependent value field

Example:-

.. code-block:: pyml

    dv_field: DV


.. _p2ndat-output_nonmem_fields-mdv_field_spec:

mdv_field
=========

Type: :term:`str <str>`

Name of output nonmem missing dependent value column

Example:-

.. code-block:: pyml

    mdv_field: MDV


.. _p2ndat-output_nonmem_fields-amt_field_spec:

amt_field
=========

Type: :term:`str <str>`

Name of output nonmem dose amount column

Example:-

.. code-block:: pyml

    amt_field: AMT


.. _p2ndat-output_nonmem_fields-rate_field_spec:

rate_field
==========

Type: :term:`str <str>`

Name of output nonmem infusion rate column (e.g. RATE)

Example:-

.. code-block:: pyml

    rate_field: none


.. _p2ndat-output_nonmem_fields-dur_field_spec:

dur_field
=========

Type: :term:`str <str>`

Name of output nonmem infusion duration column (e.g. DUR)

Example:-

.. code-block:: pyml

    dur_field: none


.. _p2ndat-output_nonmem_fields-cmt_field_spec:

cmt_field
=========

Type: :term:`str <str>`

Name of output nonmem compartment column

Example:-

.. code-block:: pyml

    cmt_field: CMT


.. _p2ndat-output_nonmem_fields-obs_cmt_numbers_spec:

obs_cmt_numbers
===============

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

For each output nonmem dv field specify 
a compartment number has to be same length as PoPy 
dv_fields list

Example:-

.. code-block:: pyml

    obs_cmt_numbers: [1]


.. _p2ndat-output_nonmem_fields-dose_cmt_numbers_spec:

dose_cmt_numbers
================

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

For each output nonmem amt field specify a 
compartment number, has to be same length as PoPy 
amt_fields list

Example:-

.. code-block:: pyml

    dose_cmt_numbers: [1]


.. _p2ndat-output_options_spec:

OUTPUT_OPTIONS
**************

Type: :term:`dict_record <dict_record>`

Output options for n2pdat/p2ndat programs.

Example:-

.. code-block:: pyml

    OUTPUT_OPTIONS:
        drop_fields: []


.. _p2ndat-output_options-drop_fields_spec:

drop_fields
===========

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

Columns to remove from the output

Example:-

.. code-block:: pyml

    drop_fields: []



