Files in pharmpy/pharmr

Interface to the 'Pharmpy' 'Pharmacometrics' Library

R/check_pharmpy.R R/check_setup.R R/functions_wrapper.R R/install.R R/internals.R R/overloads.R R/printing.R R/utils.R R/zzz.R README.md man/add_admid.Rd man/add_allometry.Rd man/add_bioavailability.Rd man/add_cmt.Rd man/add_covariate_effect.Rd man/add_derivative.Rd man/add_effect_compartment.Rd man/add_estimation_step.Rd man/add_iiv.Rd man/add_indirect_effect.Rd man/add_individual_parameter.Rd man/add_iov.Rd man/add_lag_time.Rd man/add_metabolite.Rd man/add_parameter_uncertainty_step.Rd man/add_pd_iiv.Rd man/add_peripheral_compartment.Rd man/add_pk_iiv.Rd man/add_population_parameter.Rd man/add_predictions.Rd man/add_residuals.Rd man/add_time_after_dose.Rd man/append_estimation_step_options.Rd man/bin_observations.Rd man/bump_model_number.Rd man/calculate_aic.Rd man/calculate_bic.Rd man/calculate_corr_from_cov.Rd man/calculate_corr_from_prec.Rd man/calculate_cov_from_corrse.Rd man/calculate_cov_from_prec.Rd man/calculate_epsilon_gradient_expression.Rd man/calculate_eta_gradient_expression.Rd man/calculate_eta_shrinkage.Rd man/calculate_individual_parameter_statistics.Rd man/calculate_individual_shrinkage.Rd man/calculate_parameters_from_ucp.Rd man/calculate_pk_parameters_statistics.Rd man/calculate_prec_from_corrse.Rd man/calculate_prec_from_cov.Rd man/calculate_se_from_cov.Rd man/calculate_se_from_prec.Rd man/calculate_ucp_scale.Rd man/check_dataset.Rd man/check_high_correlations.Rd man/check_parameters_near_bounds.Rd man/check_pharmpy.Rd man/check_setup.Rd man/cleanup_model.Rd man/convert_model.Rd man/create_basic_pk_model.Rd man/create_config_template.Rd man/create_context.Rd man/create_joint_distribution.Rd man/create_report.Rd man/create_rng.Rd man/create_symbol.Rd man/deidentify_data.Rd man/display_odes.Rd man/drop_columns.Rd man/drop_dropped_columns.Rd man/evaluate_epsilon_gradient.Rd man/evaluate_eta_gradient.Rd man/evaluate_expression.Rd man/evaluate_individual_prediction.Rd man/evaluate_population_prediction.Rd man/evaluate_weighted_residuals.Rd man/expand_additional_doses.Rd man/filter_dataset.Rd man/find_clearance_parameters.Rd man/find_volume_parameters.Rd man/fit.Rd man/fix_or_unfix_parameters.Rd man/fix_parameters.Rd man/fix_parameters_to.Rd man/get_admid.Rd man/get_baselines.Rd man/get_bioavailability.Rd man/get_central_volume_and_clearance.Rd man/get_cmt.Rd man/get_concentration_parameters_from_data.Rd man/get_config_path.Rd man/get_covariate_baselines.Rd man/get_covariate_effects.Rd man/get_doseid.Rd man/get_doses.Rd man/get_dv_symbol.Rd man/get_evid.Rd man/get_ids.Rd man/get_individual_parameters.Rd man/get_individual_prediction_expression.Rd man/get_initial_conditions.Rd man/get_lag_times.Rd man/get_mdv.Rd man/get_model_code.Rd man/get_model_covariates.Rd man/get_mu_connected_to_parameter.Rd man/get_number_of_individuals.Rd man/get_number_of_observations.Rd man/get_number_of_observations_per_individual.Rd man/get_number_of_peripheral_compartments.Rd man/get_number_of_transit_compartments.Rd man/get_observation_expression.Rd man/get_observations.Rd man/get_omegas.Rd man/get_parameter_rv.Rd man/get_pd_parameters.Rd man/get_pk_parameters.Rd man/get_population_prediction_expression.Rd man/get_rv_parameters.Rd man/get_sigmas.Rd man/get_thetas.Rd man/get_unit_of.Rd man/get_zero_order_inputs.Rd man/greekify_model.Rd man/has_additive_error_model.Rd man/has_combined_error_model.Rd man/has_covariate_effect.Rd man/has_first_order_absorption.Rd man/has_first_order_elimination.Rd man/has_instantaneous_absorption.Rd man/has_linear_odes.Rd man/has_linear_odes_with_real_eigenvalues.Rd man/has_michaelis_menten_elimination.Rd man/has_mixed_mm_fo_elimination.Rd man/has_mu_reference.Rd man/has_odes.Rd man/has_presystemic_metabolite.Rd man/has_proportional_error_model.Rd man/has_random_effect.Rd man/has_seq_zo_fo_absorption.Rd man/has_weighted_error_model.Rd man/has_zero_order_absorption.Rd man/has_zero_order_elimination.Rd man/install_pharmpy.Rd man/install_pharmpy_devel.Rd man/is_linearized.Rd man/is_real.Rd man/is_strictness_fulfilled.Rd man/list_time_varying_covariates.Rd man/load_dataset.Rd man/load_example_model.Rd man/load_example_modelfit_results.Rd man/make_declarative.Rd man/mu_reference_model.Rd man/omit_data.Rd man/plot_abs_cwres_vs_ipred.Rd man/plot_cwres_vs_idv.Rd man/plot_dv_vs_ipred.Rd man/plot_dv_vs_pred.Rd man/plot_eta_distributions.Rd man/plot_individual_predictions.Rd man/plot_iofv_vs_iofv.Rd man/plot_transformed_eta_distributions.Rd man/plot_vpc.Rd man/predict_influential_individuals.Rd man/predict_influential_outliers.Rd man/predict_outliers.Rd man/print_fit_summary.Rd man/print_log.Rd man/print_model_code.Rd man/print_model_symbols.Rd man/print_pharmpy_version.Rd man/read_dataset_from_datainfo.Rd man/read_model.Rd man/read_model_from_string.Rd man/read_modelfit_results.Rd man/read_results.Rd man/remove_bioavailability.Rd man/remove_covariate_effect.Rd man/remove_derivative.Rd man/remove_error_model.Rd man/remove_estimation_step.Rd man/remove_iiv.Rd man/remove_iov.Rd man/remove_lag_time.Rd man/remove_loq_data.Rd man/remove_parameter_uncertainty_step.Rd man/remove_peripheral_compartment.Rd man/remove_predictions.Rd man/remove_residuals.Rd man/remove_unused_parameters_and_rvs.Rd man/rename_symbols.Rd man/replace_fixed_thetas.Rd man/replace_non_random_rvs.Rd man/resample_data.Rd man/reset_index.Rd man/reset_indices_results.Rd man/retrieve_model.Rd man/retrieve_modelfit_results.Rd man/retrieve_models.Rd man/run_allometry.Rd man/run_amd.Rd man/run_bootstrap.Rd man/run_covsearch.Rd man/run_estmethod.Rd man/run_iivsearch.Rd man/run_iovsearch.Rd man/run_linearize.Rd man/run_modelfit.Rd man/run_modelsearch.Rd man/run_retries.Rd man/run_ruvsearch.Rd man/run_simulation.Rd man/run_structsearch.Rd man/run_tool.Rd man/sample_individual_estimates.Rd man/sample_parameters_from_covariance_matrix.Rd man/sample_parameters_uniformly.Rd man/set_additive_error_model.Rd man/set_baseline_effect.Rd man/set_combined_error_model.Rd man/set_covariates.Rd man/set_dataset.Rd man/set_description.Rd man/set_direct_effect.Rd man/set_dtbs_error_model.Rd man/set_dvid.Rd man/set_estimation_step.Rd man/set_evaluation_step.Rd man/set_first_order_absorption.Rd man/set_first_order_elimination.Rd man/set_iiv_on_ruv.Rd man/set_initial_condition.Rd man/set_initial_estimates.Rd man/set_instantaneous_absorption.Rd man/set_lloq_data.Rd man/set_lower_bounds.Rd man/set_michaelis_menten_elimination.Rd man/set_mixed_mm_fo_elimination.Rd man/set_name.Rd man/set_ode_solver.Rd man/set_peripheral_compartments.Rd man/set_power_on_ruv.Rd man/set_proportional_error_model.Rd man/set_reference_values.Rd man/set_seq_zo_fo_absorption.Rd man/set_simulation.Rd man/set_time_varying_error_model.Rd man/set_tmdd.Rd man/set_transit_compartments.Rd man/set_upper_bounds.Rd man/set_weighted_error_model.Rd man/set_zero_order_absorption.Rd man/set_zero_order_elimination.Rd man/set_zero_order_input.Rd man/simplify_expression.Rd man/solve_ode_system.Rd man/split_joint_distribution.Rd man/summarize_modelfit_results.Rd man/transform_blq.Rd man/transform_etas_boxcox.Rd man/transform_etas_john_draper.Rd man/transform_etas_tdist.Rd man/translate_nmtran_time.Rd man/unconstrain_parameters.Rd man/undrop_columns.Rd man/unfix_parameters.Rd man/unfix_parameters_to.Rd man/unload_dataset.Rd man/update_initial_individual_estimates.Rd man/use_thetas_for_error_stdev.Rd man/write_csv.Rd man/write_model.Rd man/write_results.Rd tests/testthat.R tests/testthat/test-installed.R tests/testthat/test-reset_index.R tests/testthat/test-transform.R