:py:mod:`medcat.utils.ner`
==========================

.. py:module:: medcat.utils.ner


Submodules
----------
.. toctree::
   :titlesonly:
   :maxdepth: 1

   deid/index.rst
   helpers/index.rst
   metrics/index.rst
   model/index.rst


Package Contents
----------------


Functions
~~~~~~~~~

.. autoapisummary::

   medcat.utils.ner.metrics
   medcat.utils.ner.make_or_update_cdb



.. py:function:: metrics(p, return_df=False, plus_recall=0, tokenizer=None, dataset=None, merged_negative={0, 1, -100}, padding_label=-100, csize=15, subword_label=1, verbose=False)

   Calculate metrics for a model's predictions, based off the tokenized output of a MedCATTrainer project.

   :param p: The model's predictions.
   :param return_df: Whether to return a DataFrame of metrics.
   :param plus_recall: The recall to add to the model's predictions.
   :param tokenizer: The tokenizer used to tokenize the texts.
   :param dataset: The dataset used to train the model.
   :param merged_negative: The negative labels to merge.
   :param padding_label: The padding label.
   :param csize: The size of the context window.
   :param subword_label: The subword label.
   :param verbose: Whether to print the metrics.

   :Returns: **Dict** -- A dictionary of metrics.


.. py:function:: make_or_update_cdb(json_path, cdb = None, min_count = 0)

   Creates a new CDB or updates an existing one with new
   concepts if the cdb argument is provided. All concepts that are less frequent
   than min_count will be ignored.

   :param json_path: The json path
   :type json_path: str
   :param cdb: The CDB if present. Defaults to None.
   :type cdb: Optional[CDB]
   :param min_count: Minimum count to include. Defaults to 0.
   :type min_count: int

   :Returns: **CDB** -- The same or new CDB.