from pharmpy.modeling.block_rvs import create_joint_distribution, split_joint_distribution
from pharmpy.modeling.common import (
    add_estimation_step,
    append_estimation_step_options,
    convert_model,
    copy_model,
    fix_parameters,
    fix_parameters_to,
    generate_model_code,
    get_model_covariates,
    load_example_model,
    print_model_symbols,
    read_model,
    read_model_from_database,
    read_model_from_string,
    remove_estimation_step,
    set_estimation_step,
    set_initial_estimates,
    set_name,
    unfix_parameters,
    unfix_parameters_to,
    write_model,
)
from pharmpy.modeling.covariate_effect import add_covariate_effect
from pharmpy.modeling.data import (
    get_number_of_individuals,
    get_number_of_observations,
    get_number_of_observations_per_individual,
    get_observations,
)
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_weighted_error_model,
    use_thetas_for_error_stdev,
)
from pharmpy.modeling.eta_additions import add_iiv, add_iov
from pharmpy.modeling.eta_transformations import (
    transform_etas_boxcox,
    transform_etas_john_draper,
    transform_etas_tdist,
)
from pharmpy.modeling.evaluation import evaluate_expression
from pharmpy.modeling.iiv_on_ruv import set_iiv_on_ruv
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_zero_order_absorption,
    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.results import (
    calculate_eta_shrinkage,
    calculate_individual_parameter_statistics,
    calculate_individual_shrinkage,
    calculate_pk_parameters_statistics,
    summarize_modelfit_results,
)
from pharmpy.modeling.run import create_results, fit, read_results, run_tool
from pharmpy.modeling.update_inits import update_inits

from .plots import plot_individual_predictions, plot_iofv_vs_iofv

# Remember to sort __all__ alphabetically for order in documentation
__all__ = [
    'add_covariate_effect',
    'add_estimation_step',
    'add_iiv',
    'add_individual_parameter',
    'add_iov',
    'add_lag_time',
    'add_peripheral_compartment',
    'append_estimation_step_options',
    'calculate_eta_shrinkage',
    'calculate_individual_parameter_statistics',
    'calculate_individual_shrinkage',
    'calculate_pk_parameters_statistics',
    'convert_model',
    'copy_model',
    'create_joint_distribution',
    'create_results',
    'create_rng',
    'evaluate_expression',
    'fit',
    'fix_parameters',
    'fix_parameters_to',
    'get_number_of_individuals',
    'get_number_of_observations',
    'get_number_of_observations_per_individual',
    'generate_model_code',
    'get_model_covariates',
    'get_observations',
    'has_additive_error_model',
    'has_combined_error_model',
    'has_proportional_error_model',
    'has_zero_order_absorption',
    'load_example_model',
    'plot_individual_predictions',
    'plot_iofv_vs_iofv',
    'predict_influential_individuals',
    'predict_influential_outliers',
    'predict_outliers',
    'print_model_symbols',
    'read_model',
    'read_model_from_database',
    'read_model_from_string',
    'read_results',
    'remove_error_model',
    'remove_estimation_step',
    'remove_iiv',
    'remove_iov',
    'remove_lag_time',
    'remove_peripheral_compartment',
    '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_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_transit_compartments',
    'set_weighted_error_model',
    'set_zero_order_absorption',
    'set_zero_order_elimination',
    'split_joint_distribution',
    'summarize_modelfit_results',
    'transform_etas_boxcox',
    'transform_etas_john_draper',
    'transform_etas_tdist',
    'unfix_parameters',
    'unfix_parameters_to',
    'update_inits',
    'use_thetas_for_error_stdev',
    'write_model',
]
