Quick start guide
=================

Installation
------------

Open a command line and type:

.. code-block:: bash

    $ pip install ititer

Usage
-----

Load data, and (if necessary) compute log dilutions:

.. code-block:: python

    import ititer as it
    import pandas as pd

    df = pd.read_csv("path/to/data.csv")

    df["Log Dilution"] = it.titer_to_index(df["Dilution"], start=40, fold=4)

    df.head().round(2)

.. csv-table::
   :header: Sample,OD,Dilution,Log Dilution
   :widths: 20, 10, 10, 10

   21-P0004-v001sr01,1.371,40,0.0
   21-P0004-v001sr01,0.981,160,1.0
   21-P0004-v001sr01,0.535,640,2.0
   21-P0004-v001sr01,0.182,2560,3.0
   21-P0004-v001sr01,0.064,10240,4.0

Fit and visualize sigmoid curves:

.. code-block:: python

    sigmoid = it.Sigmoid().fit(
        response="OD",
        sample_labels="Sample",
        log_dilution="Log Dilution",
        data=df,
    )

    sigmoid.plot_samples(["21-P0833-v001sr01", "21-P0834-v001sr01"])

.. image:: 2-samples.png

Export inflection (or endpoint) titers and their highest density intervals:

.. code-block:: python

    df_inflections = sigmoid.inflections(hdi_prob=0.95)

    df_inflection_titers = it.index_to_titer(df_inflections, start=40, fold=4)

    df_inflection_titers.head().round(2)

.. csv-table::
    :header: sample,mean,median,hdi low,hdi high
    :widths: 20, 12, 12, 12, 12

    21-P0425-v001sr01,141.43,141.58,117.89,169.98
    21-P0917-v001sr01,501.36,501.69,422.53,601.65
    21-P0796-v001sr01,1294.1,1294.03,1102.35,1544.14
    21-P0680-v001sr01,676.47,676.82,563.92,807.78
    21-P0800-v001sr01,19699.43,19744.58,16530.67,23644.44