.. _script_file_sections:

Script File Sections
##############################

A |popy| script file is hierarchical and based on :term:`YAML`.

The file is indented with the main sections defined at the start of a line. Subsections are indented within the main sections.

In :numref:`table_popy_sections` we list the main sections that are common to many :ref:`script_formats`.


.. _table_popy_sections:

.. list-table:: Common Script Sections
    :header-rows: 1
    
    * - Section
      - Purpose
      
    * - :ref:`method_options`
      - Script type and run options
      
    * - :ref:`description`
      - Title and summary of model
      
    * - :ref:`file_paths`
      - Paths to load and output data
      
    * - :ref:`data_fields`
      - Define type/id/time fields for data
      
    * - :ref:`preprocess`
      - Filter or expand the input data
  
    * - :ref:`level_params`
      - Define population |fx| and |rx| variable structure 
  
    * - :ref:`model_params`
      - Define |mx| for each data row, given |fx|, |rx| and |cx|
      
    * - :ref:`states`
      - Define initial value |sx|, given |mx| and |cx|
  
    * - :ref:`derivatives`
      - Define |dx| |wrt| time, given |mx|, |cx| and |sx|
  
    * - :ref:`predictions`
      - Define |px| for each data row, given |mx|, |cx| and |sx|
  
    * - :ref:`ode_solver`
      - Define |ode| method and parameters
  
    * - :ref:`fit_methods`
      - Define fit methods and parameters
      
    * - :ref:`covariance`
      - If true, compute :ref:`standard errors<uncertainty>`
      
    * - :ref:`output_scripts`
      - Declare child scripts for post processing
  
    * - :ref:`output_options`
      - Miscellaneous output parameters
       
.. toctree::
    :maxdepth: 1
    :hidden:

    method_options
    description
    file_paths
    data_fields
    preprocess
    level_params
    model_params
    states
    derivatives
    predictions
    ode_solver
    fit_methods
    covariance
    output_scripts
    output_options
    
    
.. comment
   unused sections - don't mention parallel yet
    parallel
    
    
    
