Quick Start
===========

This guide will help you get started with ResPredAI in just a few minutes.

Step 1: Create a Configuration File
------------------------------------

Generate a template configuration file:

.. code-block:: bash

    respredai create-config my_config.ini

Step 2: Edit the Configuration
------------------------------

Open ``my_config.ini`` and customize it for your data:

.. code-block:: ini

    [Data]
    data_path = ./data/my_data.csv
    targets = Target1,Target2
    continuous_features = Feature1,Feature2,Feature3
    # group_column = PatientID  # Optional: prevents data leakage

    [Pipeline]
    models = LR,RF,XGB,CatBoost
    outer_folds = 5
    inner_folds = 3
    calibrate_threshold = false
    threshold_method = auto
    calibrate_probabilities = false
    probability_calibration_method = sigmoid

    [Reproducibility]
    seed = 42

    [Log]
    verbosity = 1
    log_basename = respredai.log

    [Resources]
    n_jobs = -1

    [ModelSaving]
    enable = true
    compression = 3

    [Imputation]
    method = none
    strategy = mean
    n_neighbors = 5
    estimator = bayesian_ridge

    [Output]
    out_folder = ./output/

Configuration Sections
~~~~~~~~~~~~~~~~~~~~~~

.. list-table::
   :header-rows: 1
   :widths: 30 70

   * - Section
     - Description
   * - ``[Data]``
     - Input data path, target columns, feature types
   * - ``[Pipeline]``
     - Models to train, CV folds, threshold optimization and probability calibration
   * - ``[Reproducibility]``
     - Random seed for reproducibility
   * - ``[Log]``
     - Logging verbosity and file name
   * - ``[Resources]``
     - Parallel processing settings
   * - ``[ModelSaving]``
     - Model persistence options
   * - ``[Imputation]``
     - Missing data imputation settings
   * - ``[Output]``
     - Output directory path

Step 3: Validate Configuration (Optional)
-----------------------------------------

Check that your configuration is valid before running:

.. code-block:: bash

    respredai validate-config my_config.ini --check-data

Step 4: Run the Pipeline
------------------------

Execute the nested cross-validation pipeline:

.. code-block:: bash

    respredai run --config my_config.ini

Step 5: Explore Results
-----------------------

After the pipeline completes, check your output folder:

- ``report.html`` - Comprehensive HTML report with all results
- ``metrics/`` - Performance metrics with 95% confidence intervals
- ``confusion_matrices/`` - Visualization of model performance
- ``models/`` - Saved models for feature importance extraction

Step 6: Extract Feature Importance (Optional)
---------------------------------------------

Analyze which features are most important:

.. code-block:: bash

    respredai feature-importance --output ./output --model LR --target Target1

Available Models
----------------

.. list-table::
   :header-rows: 1
   :widths: 20 80

   * - Code
     - Model
   * - ``LR``
     - Logistic Regression
   * - ``RF``
     - Random Forest
   * - ``XGB``
     - XGBoost
   * - ``CatBoost``
     - CatBoost
   * - ``MLP``
     - Neural Network
   * - ``TabPFN``
     - TabPFN
   * - ``RBF_SVC``
     - RBF SVM
   * - ``Linear_SVC``
     - Linear SVM
   * - ``KNN``
     - K-Nearest Neighbors

Next Steps
----------

- Read the :doc:`../cli-reference/index` for detailed command options
- Check the :doc:`../cli-reference/run-command` for advanced configuration