Package
=======

Configuration
-------------

Persistent user configuration (email and optional OpenAlex API key) stored at
``~/.config/collabnet/config.json``. Interactive first-time setup runs automatically
when no configuration file exists.

.. autofunction:: collabnet.config.get_config
.. autofunction:: collabnet.config.setup_config
.. autofunction:: collabnet.config.load_config
.. autofunction:: collabnet.config.save_config

QueryOA
-------

A utility class to collect works for the research question at hand.
This can be a collection of topic IDs, a list of journal IDs, or
several institutions, identified by their ROR IDs. By default
all records within the defined year range are gathered. This can take
several minutes for large numbers and requires sufficient disc space.

.. autoclass:: collabnet.utils.QueryOA
   :private-members:

search_topics
-------------

Search OpenAlex topic names and descriptions by keyword to discover
topic IDs suitable for use with :class:`QueryOA`.

.. autofunction:: collabnet.utils.search_topics

TransformOA
-----------

Transform collected OpenAlex work collections into suitable format for
further analysis. The full OpenAlex data is reduced and certain sub-fields
are extracted to have a flat structure. Each source file is transformed
and saved in the output format as a JSON file. This allows the processing
of large files also for machines with less memory. None the less for edge
cases the routine might lead to Out-of-Memory errors.

.. autoclass:: collabnet.data.TransformOA
   :private-members:

join_to_df
----------

A routine to join all transformed files into a single pandas DataFrame.

.. autofunction:: collabnet.data.join_to_df

CreateNetwork
-------------

Create networks for co-author and co-country analysis from the gathered
and transformed data as described above.

.. autoclass:: collabnet.analysis.CreateNetwork
   :private-members:

CalculateAICI
-------------

Calculate adjusted internationalization collaboration index (AICI) from
a collection of publication records.

.. autoclass:: collabnet.analysis.CalculateAICI
   :private-members:

AffiliationBias
---------------

Quantify how affiliation-data availability depends on research field,
journal, year, and publication type via logistic regression.

.. autoclass:: collabnet.analysis.AffiliationBias
   :private-members:

ror2name
--------

Resolve a ROR identifier to the institution's display name via the ROR API.

.. autofunction:: collabnet.analysis.ror2name

generateCirclePlot
------------------

Generate a polar circle plot showing the collaboration partners of a given
institution (identified by its ROR ID) over a specified year range.

.. autofunction:: collabnet.analysis.generateCirclePlot