API Reference
=============


adelie.bcd
----------


.. currentmodule:: adelie.bcd


.. automodule:: adelie.bcd
    :no-index:


.. autosummary::
    :toctree: generated/


    objective
    root
    root_function
    root_lower_bound
    root_upper_bound
    solve


adelie.configs
--------------


.. currentmodule:: adelie.configs


.. automodule:: adelie.configs


.. autosummary::
    :toctree: generated/


    set_configs


adelie.constraint
-----------------


.. currentmodule:: adelie.constraint


.. automodule:: adelie.constraint


.. autosummary::
    :toctree: generated/


    box
    linear
    lower
    one_sided
    upper


adelie.cv
---------


.. currentmodule:: adelie.cv


.. automodule:: adelie.cv


.. autosummary::
    :toctree: generated/


    CVGrpnetResult
    cv_grpnet


adelie.data
-----------


.. currentmodule:: adelie.data


.. automodule:: adelie.data


.. autosummary::
    :toctree: generated/


    dense
    snp_phased_ancestry
    snp_unphased


adelie.diagnostic
-----------------


.. currentmodule:: adelie.diagnostic


.. automodule:: adelie.diagnostic


.. autosummary::
    :toctree: generated/

    DiagnosticCov
    DiagnosticNaive
    coefficient
    diagnostic
    gradients
    gradient_norms
    gradient_scores
    objective
    plot_benchmark
    plot_coefficients
    plot_devs
    plot_kkt
    plot_set_sizes
    predict
    residuals


adelie.glm
----------


.. currentmodule:: adelie.glm


.. automodule:: adelie.glm


.. autosummary::
    :toctree: generated/


    binomial
    cox
    gaussian
    multigaussian
    multinomial
    poisson


adelie.io
---------


.. currentmodule:: adelie.io


.. automodule:: adelie.io


.. autosummary::
    :toctree: generated/


    snp_phased_ancestry
    snp_unphased


adelie.matrix
-------------


.. currentmodule:: adelie.matrix


.. automodule:: adelie.matrix


.. autosummary::
    :toctree: generated/


    block_diag
    concatenate
    dense
    eager_cov
    interaction
    kronecker_eye
    lazy_cov
    one_hot
    snp_phased_ancestry
    snp_unphased
    sparse
    standardize
    subset


adelie.solver
-------------


.. currentmodule:: adelie.solver


.. automodule:: adelie.solver
    

.. autosummary::
    :toctree: generated/


    gaussian_cov
    grpnet


adelie.state
------------


.. currentmodule:: adelie.state


.. automodule:: adelie.state


.. autosummary::
    :toctree: generated/


    gaussian_cov
    gaussian_naive
    gaussian_pin_cov
    gaussian_pin_naive
    glm_naive
    multigaussian_naive
    multiglm_naive


.. toctree::
    :maxdepth: 1
    :hidden:


    internal