cgeniepy.ecology
================

.. py:module:: cgeniepy.ecology


Classes
-------

.. autoapisummary::

   cgeniepy.ecology.EcoModel


Module Contents
---------------

.. py:class:: EcoModel(*args, **kwargs)

   Bases: :py:obj:`cgeniepy.model.GenieModel`


   EcoModel is an subclass of GenieModel, as EcoGENIE to cGENIE

   It facilitates the access of ecophysiological parameters and plankton variables

   Initialise a EcoModel object with a path to cGENIE output directory


   Example
   -----------

   >>> from cgeniepy.ecology import EcoModel
   >>> model = EcoModel("path_to_GENIE_output")


   .. py:attribute:: eco_varlist


   .. py:attribute:: plank_n


   .. py:attribute:: phyto_indices


   .. py:attribute:: zoo_indices


   .. py:attribute:: mixo_indices


   .. py:attribute:: phyto_n


   .. py:attribute:: zoo_n


   .. py:attribute:: mixo_n


   .. py:method:: eco_pars()

      Get all the ecophysiological parameters used in the model

      :return: a pandas DataFrame object



   .. py:method:: get_pft(pft_index, prefix='Plankton', element='C')

      a variant of GenieModel's `get_var`, to select plankton functional type

      :param pft_index: the index of plankton functional type
      :param prefix: 'Plankton' or 'Export'
      :param element: 'C', 'Fe', 'P', 'Si', 'N'

      :return: a GenieArray object


      Example
      ----------------------------------------

      >>> from cgeniepy.ecology import EcoModel

      >>> ### initialise a model object
      >>> model = EcoModel("path_to_GENIE_output")

      >>> ### get PFT-1 carbon biomass data
      >>> model.get_pft(1, "Plankton", "C")

      >>> ### get a list of PFT carbon biomass data
      >>> model.get_pft([1, 2, 3], "Plankton", "C")

      >>> ### get all phytoplankton carbon biomass data
      >>> model.get_pft('phyto', "Plankton", "C")

      >>> ### get all zooplankton carbon biomass data
      >>> model.get_pft('zoo', "Plankton", "C")

      >>> ### get all plankton carbon biomass data
      >>> model.get_pft('all', "Plankton", "C")