Interface to the 'Pharmpy' 'Pharmacometrics' Library
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Documentation for package ‘pharmr’ version 1.0.1
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A B C D E F G H I L M O P R S T U W
-- A --
| add_admid | add_admid |
| add_allometry | add_allometry |
| add_bioavailability | add_bioavailability |
| add_cmt | add_cmt |
| add_covariate_effect | add_covariate_effect |
| add_derivative | add_derivative |
| add_effect_compartment | add_effect_compartment |
| add_estimation_step | add_estimation_step |
| add_iiv | add_iiv |
| add_indirect_effect | add_indirect_effect |
| add_individual_parameter | add_individual_parameter |
| add_iov | add_iov |
| add_lag_time | add_lag_time |
| add_metabolite | add_metabolite |
| add_parameter_uncertainty_step | add_parameter_uncertainty_step |
| add_pd_iiv | add_pd_iiv |
| add_peripheral_compartment | add_peripheral_compartment |
| add_pk_iiv | add_pk_iiv |
| add_population_parameter | add_population_parameter |
| add_predictions | add_predictions |
| add_residuals | add_residuals |
| add_time_after_dose | add_time_after_dose |
| append_estimation_step_options | append_estimation_step_options |
-- B --
| bin_observations | bin_observations |
| bump_model_number | bump_model_number |
-- C --
| calculate_aic | calculate_aic |
| calculate_bic | calculate_bic |
| calculate_corr_from_cov | calculate_corr_from_cov |
| calculate_corr_from_prec | calculate_corr_from_prec |
| calculate_cov_from_corrse | calculate_cov_from_corrse |
| calculate_cov_from_prec | calculate_cov_from_prec |
| calculate_epsilon_gradient_expression | calculate_epsilon_gradient_expression |
| calculate_eta_gradient_expression | calculate_eta_gradient_expression |
| calculate_eta_shrinkage | calculate_eta_shrinkage |
| calculate_individual_parameter_statistics | calculate_individual_parameter_statistics |
| calculate_individual_shrinkage | calculate_individual_shrinkage |
| calculate_parameters_from_ucp | calculate_parameters_from_ucp |
| calculate_pk_parameters_statistics | calculate_pk_parameters_statistics |
| calculate_prec_from_corrse | calculate_prec_from_corrse |
| calculate_prec_from_cov | calculate_prec_from_cov |
| calculate_se_from_cov | calculate_se_from_cov |
| calculate_se_from_prec | calculate_se_from_prec |
| calculate_ucp_scale | calculate_ucp_scale |
| check_dataset | check_dataset |
| check_high_correlations | check_high_correlations |
| check_parameters_near_bounds | check_parameters_near_bounds |
| check_pharmpy | Checks version of Pharmpy/pharmr |
| cleanup_model | cleanup_model |
| convert_model | convert_model |
| create_basic_pk_model | create_basic_pk_model |
| create_config_template | create_config_template |
| create_joint_distribution | create_joint_distribution |
| create_report | create_report |
| create_rng | create_rng |
| create_symbol | create_symbol |
-- D --
| deidentify_data | deidentify_data |
| display_odes | display_odes |
| drop_columns | drop_columns |
| drop_dropped_columns | drop_dropped_columns |
-- E --
| evaluate_epsilon_gradient | evaluate_epsilon_gradient |
| evaluate_eta_gradient | evaluate_eta_gradient |
| evaluate_expression | evaluate_expression |
| evaluate_individual_prediction | evaluate_individual_prediction |
| evaluate_population_prediction | evaluate_population_prediction |
| evaluate_weighted_residuals | evaluate_weighted_residuals |
| expand_additional_doses | expand_additional_doses |
-- F --
| filter_dataset | filter_dataset |
| find_clearance_parameters | find_clearance_parameters |
| find_volume_parameters | find_volume_parameters |
| fit | fit |
| fix_or_unfix_parameters | fix_or_unfix_parameters |
| fix_parameters | fix_parameters |
| fix_parameters_to | fix_parameters_to |
-- G --
| get_admid | get_admid |
| get_baselines | get_baselines |
| get_bioavailability | get_bioavailability |
| get_central_volume_and_clearance | get_central_volume_and_clearance |
| get_cmt | get_cmt |
| get_concentration_parameters_from_data | get_concentration_parameters_from_data |
| get_config_path | get_config_path |
| get_covariate_baselines | get_covariate_baselines |
| get_covariate_effects | get_covariate_effects |
| get_doseid | get_doseid |
| get_doses | get_doses |
| get_dv_symbol | get_dv_symbol |
| get_evid | get_evid |
| get_ids | get_ids |
| get_individual_parameters | get_individual_parameters |
| get_individual_prediction_expression | get_individual_prediction_expression |
| get_initial_conditions | get_initial_conditions |
| get_lag_times | get_lag_times |
| get_mdv | get_mdv |
| get_model_code | get_model_code |
| get_model_covariates | get_model_covariates |
| get_number_of_individuals | get_number_of_individuals |
| get_number_of_observations | get_number_of_observations |
| get_number_of_observations_per_individual | get_number_of_observations_per_individual |
| get_number_of_peripheral_compartments | get_number_of_peripheral_compartments |
| get_number_of_transit_compartments | get_number_of_transit_compartments |
| get_observations | get_observations |
| get_observation_expression | get_observation_expression |
| get_omegas | get_omegas |
| get_parameter_rv | get_parameter_rv |
| get_pd_parameters | get_pd_parameters |
| get_pk_parameters | get_pk_parameters |
| get_population_prediction_expression | get_population_prediction_expression |
| get_rv_parameters | get_rv_parameters |
| get_sigmas | get_sigmas |
| get_thetas | get_thetas |
| get_unit_of | get_unit_of |
| get_zero_order_inputs | get_zero_order_inputs |
| greekify_model | greekify_model |
-- H --
| has_additive_error_model | has_additive_error_model |
| has_combined_error_model | has_combined_error_model |
| has_covariate_effect | has_covariate_effect |
| has_first_order_absorption | has_first_order_absorption |
| has_first_order_elimination | has_first_order_elimination |
| has_instantaneous_absorption | has_instantaneous_absorption |
| has_linear_odes | has_linear_odes |
| has_linear_odes_with_real_eigenvalues | has_linear_odes_with_real_eigenvalues |
| has_michaelis_menten_elimination | has_michaelis_menten_elimination |
| has_mixed_mm_fo_elimination | has_mixed_mm_fo_elimination |
| has_odes | has_odes |
| has_presystemic_metabolite | has_presystemic_metabolite |
| has_proportional_error_model | has_proportional_error_model |
| has_random_effect | has_random_effect |
| has_seq_zo_fo_absorption | has_seq_zo_fo_absorption |
| has_weighted_error_model | has_weighted_error_model |
| has_zero_order_absorption | has_zero_order_absorption |
| has_zero_order_elimination | has_zero_order_elimination |
-- I --
| install_pharmpy | Install Pharmpy |
| install_pharmpy_devel | Install Pharmpy (with specified version) |
| is_linearized | is_linearized |
| is_real | is_real |
| is_strictness_fulfilled | is_strictness_fulfilled |
-- L --
| list_time_varying_covariates | list_time_varying_covariates |
| load_dataset | load_dataset |
| load_example_model | load_example_model |
| load_example_modelfit_results | load_example_modelfit_results |
-- M --
| make_declarative | make_declarative |
| mu_reference_model | mu_reference_model |
-- O --
| omit_data | omit_data |
-- P --
| plot_abs_cwres_vs_ipred | plot_abs_cwres_vs_ipred |
| plot_cwres_vs_idv | plot_cwres_vs_idv |
| plot_dv_vs_ipred | plot_dv_vs_ipred |
| plot_dv_vs_pred | plot_dv_vs_pred |
| plot_eta_distributions | plot_eta_distributions |
| plot_individual_predictions | plot_individual_predictions |
| plot_iofv_vs_iofv | plot_iofv_vs_iofv |
| plot_transformed_eta_distributions | plot_transformed_eta_distributions |
| plot_vpc | plot_vpc |
| predict_influential_individuals | predict_influential_individuals |
| predict_influential_outliers | predict_influential_outliers |
| predict_outliers | predict_outliers |
| print_fit_summary | print_fit_summary |
| print_model_code | print_model_code |
| print_model_symbols | print_model_symbols |
| print_pharmpy_version | Print pharmpy version |
-- R --
| read_dataset_from_datainfo | read_dataset_from_datainfo |
| read_model | read_model |
| read_modelfit_results | read_modelfit_results |
| read_model_from_string | read_model_from_string |
| read_results | read_results |
| remove_bioavailability | remove_bioavailability |
| remove_covariate_effect | remove_covariate_effect |
| remove_derivative | remove_derivative |
| remove_error_model | remove_error_model |
| remove_estimation_step | remove_estimation_step |
| remove_iiv | remove_iiv |
| remove_iov | remove_iov |
| remove_lag_time | remove_lag_time |
| remove_loq_data | remove_loq_data |
| remove_parameter_uncertainty_step | remove_parameter_uncertainty_step |
| remove_peripheral_compartment | remove_peripheral_compartment |
| remove_predictions | remove_predictions |
| remove_residuals | remove_residuals |
| remove_unused_parameters_and_rvs | remove_unused_parameters_and_rvs |
| rename_symbols | rename_symbols |
| replace_non_random_rvs | replace_non_random_rvs |
| resample_data | resample_data |
| reset_index | Reset index |
| reset_indices_results | Reset result indices |
| retrieve_models | retrieve_models |
| run_allometry | run_allometry |
| run_amd | run_amd |
| run_bootstrap | run_bootstrap |
| run_covsearch | run_covsearch |
| run_estmethod | run_estmethod |
| run_iivsearch | run_iivsearch |
| run_iovsearch | run_iovsearch |
| run_linearize | run_linearize |
| run_modelfit | run_modelfit |
| run_modelsearch | run_modelsearch |
| run_retries | run_retries |
| run_ruvsearch | run_ruvsearch |
| run_simulation | run_simulation |
| run_structsearch | run_structsearch |
| run_tool | run_tool |
-- S --
| sample_individual_estimates | sample_individual_estimates |
| sample_parameters_from_covariance_matrix | sample_parameters_from_covariance_matrix |
| sample_parameters_uniformly | sample_parameters_uniformly |
| set_additive_error_model | set_additive_error_model |
| set_baseline_effect | set_baseline_effect |
| set_combined_error_model | set_combined_error_model |
| set_covariates | set_covariates |
| set_dataset | set_dataset |
| set_direct_effect | set_direct_effect |
| set_dtbs_error_model | set_dtbs_error_model |
| set_dvid | set_dvid |
| set_estimation_step | set_estimation_step |
| set_evaluation_step | set_evaluation_step |
| set_first_order_absorption | set_first_order_absorption |
| set_first_order_elimination | set_first_order_elimination |
| set_iiv_on_ruv | set_iiv_on_ruv |
| set_initial_condition | set_initial_condition |
| set_initial_estimates | set_initial_estimates |
| set_instantaneous_absorption | set_instantaneous_absorption |
| set_lloq_data | set_lloq_data |
| set_lower_bounds | set_lower_bounds |
| set_michaelis_menten_elimination | set_michaelis_menten_elimination |
| set_mixed_mm_fo_elimination | set_mixed_mm_fo_elimination |
| set_name | set_name |
| set_ode_solver | set_ode_solver |
| set_peripheral_compartments | set_peripheral_compartments |
| set_power_on_ruv | set_power_on_ruv |
| set_proportional_error_model | set_proportional_error_model |
| set_reference_values | set_reference_values |
| set_seq_zo_fo_absorption | set_seq_zo_fo_absorption |
| set_simulation | set_simulation |
| set_time_varying_error_model | set_time_varying_error_model |
| set_tmdd | set_tmdd |
| set_transit_compartments | set_transit_compartments |
| set_upper_bounds | set_upper_bounds |
| set_weighted_error_model | set_weighted_error_model |
| set_zero_order_absorption | set_zero_order_absorption |
| set_zero_order_elimination | set_zero_order_elimination |
| set_zero_order_input | set_zero_order_input |
| simplify_expression | simplify_expression |
| solve_ode_system | solve_ode_system |
| split_joint_distribution | split_joint_distribution |
| summarize_modelfit_results | summarize_modelfit_results |
-- T --
| transform_blq | transform_blq |
| transform_etas_boxcox | transform_etas_boxcox |
| transform_etas_john_draper | transform_etas_john_draper |
| transform_etas_tdist | transform_etas_tdist |
| translate_nmtran_time | translate_nmtran_time |
-- U --
| unconstrain_parameters | unconstrain_parameters |
| undrop_columns | undrop_columns |
| unfix_parameters | unfix_parameters |
| unfix_parameters_to | unfix_parameters_to |
| unload_dataset | unload_dataset |
| update_initial_individual_estimates | update_initial_individual_estimates |
| use_thetas_for_error_stdev | use_thetas_for_error_stdev |
-- W --
| write_csv | write_csv |
| write_model | write_model |
| write_results | write_results |