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pharmr  

Interface to the 'Pharmpy' 'Pharmacometrics' Library
View on CRAN: Click here


Download and install pharmr package within the R console
Install from CRAN:
install.packages("pharmr")

Install from Github:
library("remotes")
install_github("cran/pharmr")

Install by package version:
library("remotes")
install_version("pharmr", "1.4.0")



Attach the package and use:
library("pharmr")
Maintained by
Rikard Nordgren
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-10-15
Latest Update: 2023-06-15
Description:
Interface to the 'Pharmpy' 'pharmacometrics' library. The 'Reticulate' package is used to interface Python from R.
How to cite:
Rikard Nordgren (2021). pharmr: Interface to the 'Pharmpy' 'Pharmacometrics' Library. R package version 1.4.0, https://cran.r-project.org/web/packages/pharmr. Accessed 22 Dec. 2024.
Previous versions and publish date:
0.33.1 (2021-10-15 09:30), 0.73.1 (2022-06-23 14:20), 0.96.0 (2023-06-15 15:50), 1.0.0 (2024-06-04 11:48), 1.0.1 (2024-06-17 12:00)
Other packages that cited pharmr R package
View pharmr citation profile
Other R packages that pharmr depends, imports, suggests or enhances
Complete documentation for pharmr
Functions, R codes and Examples using the pharmr R package
Some associated functions: add_allometry . add_covariance_step . add_covariate_effect . add_estimation_step . add_iiv . add_individual_parameter . add_iov . add_lag_time . add_metabolite . add_peripheral_compartment . add_pk_iiv . add_population_parameter . add_time_after_dose . append_estimation_step_options . bump_model_number . calculate_aic . calculate_bic . calculate_corr_from_cov . calculate_corr_from_prec . calculate_cov_from_corrse . calculate_cov_from_prec . calculate_epsilon_gradient_expression . calculate_eta_gradient_expression . calculate_eta_shrinkage . calculate_individual_parameter_statistics . calculate_individual_shrinkage . calculate_parameters_from_ucp . calculate_pk_parameters_statistics . calculate_prec_from_corrse . calculate_prec_from_cov . calculate_se_from_cov . calculate_se_from_prec . calculate_ucp_scale . check_dataset . check_high_correlations . check_parameters_near_bounds . check_pharmpy . cleanup_model . convert_model . create_basic_pk_model . create_config_template . create_joint_distribution . create_report . create_results . create_rng . create_symbol . deidentify_data . display_odes . 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 . find_clearance_parameters . find_volume_parameters . fit . fix_or_unfix_parameters . fix_parameters . fix_parameters_to . get_baselines . get_bioavailability . get_cmt . get_concentration_parameters_from_data . get_config_path . get_covariate_baselines . get_doseid . get_doses . get_dv_symbol . get_evid . get_ids . get_individual_parameters . get_individual_prediction_expression . get_initial_conditions . get_lag_times . get_mdv . get_model_code . get_model_covariates . get_number_of_individuals . get_number_of_observations . get_number_of_observations_per_individual . get_observation_expression . get_observations . get_omegas . get_pk_parameters . get_population_prediction_expression . get_rv_parameters . get_sigmas . get_thetas . get_unit_of . get_zero_order_inputs . greekify_model . has_additive_error_model . has_combined_error_model . has_covariate_effect . has_first_order_elimination . has_linear_odes . has_linear_odes_with_real_eigenvalues . has_michaelis_menten_elimination . has_mixed_mm_fo_elimination . has_odes . has_proportional_error_model . has_random_effect . has_weighted_error_model . has_zero_order_absorption . has_zero_order_elimination . install_pharmpy . install_pharmpy_devel . is_linearized . is_real . list_time_varying_covariates . load_example_model . load_example_modelfit_results . make_declarative . mu_reference_model . omit_data . plot_individual_predictions . plot_iofv_vs_iofv . plot_transformed_eta_distributions . predict_influential_individuals . predict_influential_outliers . predict_outliers . print_fit_summary . print_model_code . print_model_symbols . print_pharmpy_version . rank_models . read_dataset_from_datainfo . read_model . read_model_from_string . read_modelfit_results . read_results . remove_covariance_step . remove_covariate_effect . remove_error_model . remove_estimation_step . remove_iiv . remove_iov . remove_lag_time . remove_loq_data . remove_peripheral_compartment . remove_unused_parameters_and_rvs . rename_symbols . resample_data . reset_index . reset_indices_results . resume_tool . retrieve_final_model . retrieve_models . run_allometry . run_amd . run_bootstrap . run_covsearch . run_estmethod . run_iivsearch . run_iovsearch . run_modelfit . run_modelsearch . run_ruvsearch . run_tool . sample_individual_estimates . sample_parameters_from_covariance_matrix . sample_parameters_uniformly . set_additive_error_model . set_bolus_absorption . set_combined_error_model . set_covariates . set_dtbs_error_model . set_dvid . set_estimation_step . set_evaluation_step . set_first_order_absorption . set_first_order_elimination . set_iiv_on_ruv . set_initial_condition . set_initial_estimates . set_lower_bounds . 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_tmdd . set_transit_compartments . set_upper_bounds . set_weighted_error_model . set_zero_order_absorption . set_zero_order_elimination . set_zero_order_input . simplify_expression . solve_ode_system . split_joint_distribution . summarize_errors . summarize_individuals . summarize_individuals_count_table . summarize_modelfit_results . transform_blq . transform_etas_boxcox . transform_etas_john_draper . transform_etas_tdist . translate_nmtran_time . unconstrain_parameters . undrop_columns . unfix_parameters . unfix_parameters_to . update_initial_individual_estimates . update_inits . use_thetas_for_error_stdev . write_csv . write_model . write_results . 
Some associated R codes: check_pharmpy.R . functions_wrapper.R . install.R . internals.R . printing.R . utils.R . zzz.R .  Full pharmr package functions and examples
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