R: Interface to the 'Pharmpy' 'Pharmacometrics' Library

# Interface to the 'Pharmpy' 'Pharmacometrics' Library

## Documentation for package ‘pharmr’ version 2.1.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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_output_variables | add_output_variables
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
add_time_of_last_dose | add_time_of_last_dose
append_estimation_step_options | append_estimation_step_options

## -- B --

binarize_dataset | binarize_dataset
bin_observations | bin_observations
broadcast_log | broadcast_log
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_summary_statistic | calculate_summary_statistic
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
check_setup | Checks setup of Pharmpy/pharmr
cholesky_decompose | cholesky_decompose
cleanup_model | cleanup_model
convert_model | convert_model
convert_unit | convert_unit
create_basic_kpd_model | create_basic_kpd_model
create_basic_pd_model | create_basic_pd_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
export_model_files | export_model_files

## -- 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_column_name | get_column_name
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_mu_connected_to_parameter | get_mu_connected_to_parameter
get_nested_model | get_nested_model
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_mu_reference | has_mu_reference
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_weibull_absorption | has_weibull_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 --

infer_datatypes | infer_datatypes
insert_ebes_into_dataset | insert_ebes_into_dataset
install_pharmpy | Install Pharmpy
install_pharmpy_devel | Install Pharmpy (with specified version)
is_binary | is_binary
is_linearized | is_linearized
is_real | is_real
is_simulation_model | is_simulation_model
is_strictness_fulfilled | is_strictness_fulfilled

## -- L --

list_models | list_models
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
map_eta_parameters | map_eta_parameters
mu_reference_model | mu_reference_model

## -- O --

omit_data | omit_data
open_context | open_context

## -- 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_log | print_log
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_columns | remove_unused_columns
remove_unused_parameters_and_rvs | remove_unused_parameters_and_rvs
rename_symbols | rename_symbols
replace_fixed_thetas | replace_fixed_thetas
replace_non_random_rvs | replace_non_random_rvs
resample_data | resample_data
reset_index | Reset index
reset_indices_results | Reset result indices
retrieve_model | retrieve_model
retrieve_modelfit_results | retrieve_modelfit_results
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_modelrank | run_modelrank
run_modelsearch | run_modelsearch
run_pdsearch | run_pdsearch
run_qa | run_qa
run_retries | run_retries
run_ruvsearch | run_ruvsearch
run_simulation | run_simulation
run_structsearch | run_structsearch
run_tool | run_tool
run_vpc | run_vpc

## -- 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_description | set_description
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_n_transit_compartments | set_n_transit_compartments
set_ode_solver | set_ode_solver
set_peripheral_compartments | set_peripheral_compartments
set_placebo_model | set_placebo_model
set_power_on_ruv | set_power_on_ruv
set_property | set_property
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_unit | set_unit
set_upper_bounds | set_upper_bounds
set_weibull_absorption | set_weibull_absorption
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_dataset | write_dataset
write_model | write_model
write_results | write_results