from pharmpy.modeling.block_rvs import create_joint_distribution, split_joint_distribution
from pharmpy.modeling.common import (
    bump_model_number,
    convert_model,
    copy_model,
    fix_parameters,
    fix_parameters_to,
    generate_model_code,
    get_config_path,
    get_model_covariates,
    load_example_model,
    print_model_code,
    print_model_symbols,
    read_model,
    read_model_from_database,
    read_model_from_string,
    remove_unused_parameters_and_rvs,
    set_initial_estimates,
    set_name,
    unfix_parameters,
    unfix_parameters_to,
    write_model,
)
from pharmpy.modeling.covariate_effect import add_covariate_effect
from pharmpy.modeling.error import (
    has_additive_error_model,
    has_combined_error_model,
    has_proportional_error_model,
    remove_error_model,
    set_additive_error_model,
    set_combined_error_model,
    set_dtbs_error_model,
    set_proportional_error_model,
    set_time_varying_error_model,
    set_weighted_error_model,
    use_thetas_for_error_stdev,
)
from pharmpy.modeling.estimation_steps import (
    add_covariance_step,
    add_estimation_step,
    append_estimation_step_options,
    remove_covariance_step,
    remove_estimation_step,
    set_estimation_step,
    set_evaluation_step,
)
from pharmpy.modeling.eta_additions import add_iiv, add_iov, add_pk_iiv
from pharmpy.modeling.eta_transformations import (
    transform_etas_boxcox,
    transform_etas_john_draper,
    transform_etas_tdist,
)
from pharmpy.modeling.iiv_on_ruv import set_iiv_on_ruv
from pharmpy.modeling.math import (
    calculate_corr_from_cov,
    calculate_corr_from_inf,
    calculate_cov_from_corrse,
    calculate_cov_from_inf,
    calculate_inf_from_corrse,
    calculate_inf_from_cov,
    calculate_se_from_cov,
    calculate_se_from_inf,
)
from pharmpy.modeling.ml import (
    predict_influential_individuals,
    predict_influential_outliers,
    predict_outliers,
)
from pharmpy.modeling.odes import (
    add_individual_parameter,
    add_lag_time,
    add_peripheral_compartment,
    has_first_order_elimination,
    has_michaelis_menten_elimination,
    has_mixed_mm_fo_elimination,
    has_zero_order_absorption,
    has_zero_order_elimination,
    remove_lag_time,
    remove_peripheral_compartment,
    set_bolus_absorption,
    set_first_order_absorption,
    set_first_order_elimination,
    set_michaelis_menten_elimination,
    set_mixed_mm_fo_elimination,
    set_ode_solver,
    set_peripheral_compartments,
    set_seq_zo_fo_absorption,
    set_transit_compartments,
    set_zero_order_absorption,
    set_zero_order_elimination,
)
from pharmpy.modeling.parameter_sampling import (
    create_rng,
    sample_individual_estimates,
    sample_parameters_from_covariance_matrix,
    sample_parameters_uniformly,
)
from pharmpy.modeling.power_on_ruv import set_power_on_ruv
from pharmpy.modeling.remove_iiv import remove_iiv
from pharmpy.modeling.remove_iov import remove_iov
from pharmpy.modeling.run import create_results, fit, read_results, run_tool
from pharmpy.modeling.update_inits import update_inits
from pharmpy.modeling.write_csv import write_csv

from .allometry import add_allometry
from .amd import run_amd, run_iiv
from .data import (
    add_time_after_dose,
    check_dataset,
    drop_columns,
    drop_dropped_columns,
    expand_additional_doses,
    get_baselines,
    get_concentration_parameters_from_data,
    get_covariate_baselines,
    get_doseid,
    get_doses,
    get_ids,
    get_mdv,
    get_number_of_individuals,
    get_number_of_observations,
    get_number_of_observations_per_individual,
    get_observations,
    list_time_varying_covariates,
    remove_loq_data,
    translate_nmtran_time,
    undrop_columns,
)
from .evaluation import (
    evaluate_epsilon_gradient,
    evaluate_eta_gradient,
    evaluate_expression,
    evaluate_individual_prediction,
    evaluate_population_prediction,
    evaluate_weighted_residuals,
)
from .expressions import (
    calculate_epsilon_gradient_expression,
    calculate_eta_gradient_expression,
    create_symbol,
    get_individual_prediction_expression,
    get_observation_expression,
    get_population_prediction_expression,
    mu_reference_model,
    simplify_expression,
)
from .iterators import omit_data, resample_data
from .plots import plot_individual_predictions, plot_iofv_vs_iofv
from .reporting import create_report
from .results import (
    calculate_aic,
    calculate_bic,
    calculate_eta_shrinkage,
    calculate_individual_parameter_statistics,
    calculate_individual_shrinkage,
    calculate_pk_parameters_statistics,
    check_high_correlations,
    check_parameters_near_bounds,
    print_fit_summary,
    summarize_modelfit_results,
    write_results,
)
from .units import get_unit_of

# Remember to sort __all__ alphabetically for order in documentation
__all__ = [
    'add_allometry',
    'add_covariance_step',
    'add_covariate_effect',
    'add_estimation_step',
    'add_iiv',
    'add_individual_parameter',
    'add_iov',
    'add_lag_time',
    'add_peripheral_compartment',
    'add_pk_iiv',
    'add_time_after_dose',
    'append_estimation_step_options',
    'bump_model_number',
    'calculate_aic',
    'calculate_bic',
    'calculate_corr_from_cov',
    'calculate_corr_from_inf',
    'calculate_cov_from_corrse',
    'calculate_cov_from_inf',
    'calculate_epsilon_gradient_expression',
    'calculate_eta_gradient_expression',
    'calculate_eta_shrinkage',
    'calculate_individual_parameter_statistics',
    'calculate_individual_shrinkage',
    'calculate_inf_from_corrse',
    'calculate_inf_from_cov',
    'calculate_pk_parameters_statistics',
    'calculate_se_from_cov',
    'calculate_se_from_inf',
    'check_dataset',
    'check_high_correlations',
    'check_parameters_near_bounds',
    'convert_model',
    'copy_model',
    'create_joint_distribution',
    'create_report',
    'create_results',
    'create_rng',
    'create_symbol',
    'drop_columns',
    'drop_dropped_columns',
    'evaluate_epsilon_gradient',
    'evaluate_eta_gradient',
    'evaluate_expression',
    'evaluate_individual_prediction',
    'evaluate_population_prediction',
    'evaluate_weighted_residuals',
    'expand_additional_doses',
    'fit',
    'fix_parameters',
    'fix_parameters_to',
    'get_baselines',
    'get_concentration_parameters_from_data',
    'get_covariate_baselines',
    'get_doses',
    'get_doseid',
    'get_ids',
    'get_individual_prediction_expression',
    'get_number_of_individuals',
    'get_number_of_observations',
    'get_number_of_observations_per_individual',
    'generate_model_code',
    'get_config_path',
    'get_mdv',
    'get_model_covariates',
    'get_observations',
    'get_observation_expression',
    'get_population_prediction_expression',
    'get_unit_of',
    'has_additive_error_model',
    'has_combined_error_model',
    'has_first_order_elimination',
    'has_michaelis_menten_elimination',
    'has_mixed_mm_fo_elimination',
    'has_proportional_error_model',
    'has_zero_order_absorption',
    'has_zero_order_elimination',
    'list_time_varying_covariates',
    'load_example_model',
    'mu_reference_model',
    'omit_data',
    'plot_individual_predictions',
    'plot_iofv_vs_iofv',
    'predict_influential_individuals',
    'predict_influential_outliers',
    'predict_outliers',
    'print_fit_summary',
    'print_model_code',
    'print_model_symbols',
    'read_model',
    'read_model_from_database',
    'read_model_from_string',
    'read_results',
    'remove_covariance_step',
    'remove_error_model',
    'remove_estimation_step',
    'remove_iiv',
    'remove_iov',
    'remove_lag_time',
    'remove_loq_data',
    'remove_peripheral_compartment',
    'remove_unused_parameters_and_rvs',
    'resample_data',
    'run_amd',
    'run_iiv',
    'run_tool',
    'sample_parameters_from_covariance_matrix',
    'sample_individual_estimates',
    'sample_parameters_uniformly',
    'set_additive_error_model',
    'set_bolus_absorption',
    'set_combined_error_model',
    'set_dtbs_error_model',
    'set_estimation_step',
    'set_evaluation_step',
    'set_first_order_absorption',
    'set_first_order_elimination',
    'set_iiv_on_ruv',
    'set_initial_estimates',
    'set_michaelis_menten_elimination',
    'set_mixed_mm_fo_elimination',
    'set_name',
    'set_ode_solver',
    'set_peripheral_compartments',
    'set_power_on_ruv',
    'set_proportional_error_model',
    'set_seq_zo_fo_absorption',
    'set_time_varying_error_model',
    'set_transit_compartments',
    'set_weighted_error_model',
    'set_zero_order_absorption',
    'set_zero_order_elimination',
    'simplify_expression',
    'split_joint_distribution',
    'summarize_modelfit_results',
    'transform_etas_boxcox',
    'transform_etas_john_draper',
    'transform_etas_tdist',
    'translate_nmtran_time',
    'unfix_parameters',
    'unfix_parameters_to',
    'update_inits',
    'use_thetas_for_error_stdev',
    'write_csv',
    'write_model',
    'write_results',
    'undrop_columns',
]
