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docs: Tweak multi-valued element docs
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wmayner committed Apr 2, 2021
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24 changes: 12 additions & 12 deletions docs/examples/multivalued_elements.rst
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Expand Up @@ -9,9 +9,8 @@ multivalued p53-Mdm2 network from
*Entropy*. 2021; 23(1):6.
https://doi.org/10.3390/e23010006

To begin, we need to checkout the ``nonbinary`` branch from GitHub, found at
https://github.com/wmayner/pyphi/tree/nonbinary. You can install it with this
command:
To begin, we need to install the ``nonbinary`` branch of the PyPhi repository
`on GitHub <https://github.com/wmayner/pyphi/tree/nonbinary>`_:

.. code-block:: bash
Expand Down Expand Up @@ -41,6 +40,15 @@ Before computation, we need to configure PyPhi with the settings used in the pap
Note that ``'TRI'`` as a partition type is an approximation; ``'ALL'`` will
consider all possible partitions and give the true value.

.. warning::
There may be issues using the ``pyphi.config`` to change settings via
direct assignment if you are not using Linux. If you encounter any, you
can instead use a ``pyphi_config.yml`` file in the working directory. An
example with the default settings is available `here
<https://github.com/wmayner/pyphi/blob/nonbinary/pyphi_config.yml>`_.
Note that this will affect all computations with PyPhi performed from
that directory. See :mod:`pyphi.conf` for more information.

.. important::
The EMD measure is not supported in the ``nonbinary`` branch. IIT's
measure of choice for mechanism integrated information is the intrinsic
Expand All @@ -51,17 +59,9 @@ consider all possible partitions and give the true value.
*Entropy*. 2021; 23(3):362.
https://doi.org/10.3390/e23030362

Other options include 'L1' and 'KLD' (see
Other options include ``'L1'`` and ``'KLD'`` (see
:attr:`~pyphi.conf.PyphiConfig.MEASURE`).

.. warning::
There may be issues using the ``pyphi.config`` to change settings via
direct assignment if you are not using Linux. If you encounter any, you
can instead use a ``pyphi_config.yml`` file in the working directory. An
example with the default settings is available `here
<https://github.com/wmayner/pyphi/blob/nonbinary/pyphi_config.yml>`_.
Note that this will affect all computations with PyPhi performed from
that directory. See :mod:`pyphi.conf` for more information.

State-by-state transition probability matrix
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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