Package: pharmr 1.3.0

Rikard Nordgren

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

Interface to the 'Pharmpy' 'pharmacometrics' library. The 'Reticulate' package is used to interface Python from R.

Authors:Rikard Nordgren [aut, cre, cph], Stella Belin [aut, cph], Mats O. Karlsson [sad], Andrew C. Hooker [sad], Xiaomei Chen [sad], Sebastian Ueckert [sad], Simon Buatois [rev], João A. Abrantes [rev], Emilie Schindler [rev], F. Hoffmann-La Roche Ltd. [fnd], Bayer AG [fnd]

pharmr_1.3.0.tar.gz
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pharmr.pdf |pharmr.html✨
pharmr/json (API)

# Install 'pharmr' in R:
install.packages('pharmr', repos = c('https://pharmpy.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/pharmpy/pharmr/issues

On CRAN:

5.68 score 19 stars 5 scripts 296 downloads 257 exports 45 dependencies

Last updated 2 days agofrom:9ee9d31ed6. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-winOKNov 20 2024
R-4.5-linuxOKNov 20 2024
R-4.4-winOKNov 20 2024
R-4.4-macOKNov 20 2024
R-4.3-winOKNov 20 2024
R-4.3-macOKNov 20 2024

Exports:add_admidadd_allometryadd_bioavailabilityadd_cmtadd_covariate_effectadd_derivativeadd_effect_compartmentadd_estimation_stepadd_iivadd_indirect_effectadd_individual_parameteradd_iovadd_lag_timeadd_metaboliteadd_parameter_uncertainty_stepadd_pd_iivadd_peripheral_compartmentadd_pk_iivadd_population_parameteradd_predictionsadd_residualsadd_time_after_doseappend_estimation_step_optionsbin_observationsbump_model_numbercalculate_aiccalculate_biccalculate_corr_from_covcalculate_corr_from_preccalculate_cov_from_corrsecalculate_cov_from_preccalculate_epsilon_gradient_expressioncalculate_eta_gradient_expressioncalculate_eta_shrinkagecalculate_individual_parameter_statisticscalculate_individual_shrinkagecalculate_parameters_from_ucpcalculate_pk_parameters_statisticscalculate_prec_from_corrsecalculate_prec_from_covcalculate_se_from_covcalculate_se_from_preccalculate_ucp_scalecheck_datasetcheck_high_correlationscheck_parameters_near_boundscleanup_modelconvert_modelcreate_basic_pk_modelcreate_config_templatecreate_joint_distributioncreate_reportcreate_rngcreate_symboldeidentify_datadisplay_odesdrop_columnsdrop_dropped_columnsevaluate_epsilon_gradientevaluate_eta_gradientevaluate_expressionevaluate_individual_predictionevaluate_population_predictionevaluate_weighted_residualsexpand_additional_dosesfilter_datasetfind_clearance_parametersfind_volume_parametersfitfix_or_unfix_parametersfix_parametersfix_parameters_toget_admidget_baselinesget_bioavailabilityget_central_volume_and_clearanceget_cmtget_concentration_parameters_from_dataget_config_pathget_covariate_baselinesget_covariate_effectsget_doseidget_dosesget_dv_symbolget_evidget_idsget_individual_parametersget_individual_prediction_expressionget_initial_conditionsget_lag_timesget_mdvget_model_codeget_model_covariatesget_mu_connected_to_parameterget_number_of_individualsget_number_of_observationsget_number_of_observations_per_individualget_number_of_peripheral_compartmentsget_number_of_transit_compartmentsget_observation_expressionget_observationsget_omegasget_parameter_rvget_pd_parametersget_pk_parametersget_population_prediction_expressionget_rv_parametersget_sigmasget_thetasget_unit_ofget_zero_order_inputsgreekify_modelhas_additive_error_modelhas_combined_error_modelhas_covariate_effecthas_first_order_absorptionhas_first_order_eliminationhas_instantaneous_absorptionhas_linear_odeshas_linear_odes_with_real_eigenvalueshas_michaelis_menten_eliminationhas_mixed_mm_fo_eliminationhas_mu_referencehas_odeshas_presystemic_metabolitehas_proportional_error_modelhas_random_effecthas_seq_zo_fo_absorptionhas_weighted_error_modelhas_zero_order_absorptionhas_zero_order_eliminationinstall_pharmpyis_linearizedis_realis_strictness_fulfilledlist_time_varying_covariatesload_datasetload_example_modelload_example_modelfit_resultsmake_declarativemu_reference_modelomit_dataplot_abs_cwres_vs_ipredplot_cwres_vs_idvplot_dv_vs_ipredplot_dv_vs_predplot_eta_distributionsplot_individual_predictionsplot_iofv_vs_iofvplot_transformed_eta_distributionsplot_vpcpredict_influential_individualspredict_influential_outlierspredict_outliersprint_fit_summaryprint_model_codeprint_model_symbolsprint_pharmpy_versionread_dataset_from_datainforead_modelread_model_from_stringread_modelfit_resultsread_resultsremove_bioavailabilityremove_covariate_effectremove_derivativeremove_error_modelremove_estimation_stepremove_iivremove_iovremove_lag_timeremove_loq_dataremove_parameter_uncertainty_stepremove_peripheral_compartmentremove_predictionsremove_residualsremove_unused_parameters_and_rvsrename_symbolsreplace_fixed_thetasreplace_non_random_rvsresample_datareset_indexretrieve_modelsrun_allometryrun_amdrun_bootstraprun_covsearchrun_estmethodrun_iivsearchrun_iovsearchrun_linearizerun_modelfitrun_modelsearchrun_retriesrun_ruvsearchrun_simulationrun_structsearchrun_toolsample_individual_estimatessample_parameters_from_covariance_matrixsample_parameters_uniformlyset_additive_error_modelset_baseline_effectset_combined_error_modelset_covariatesset_datasetset_descriptionset_direct_effectset_dtbs_error_modelset_dvidset_estimation_stepset_evaluation_stepset_first_order_absorptionset_first_order_eliminationset_iiv_on_ruvset_initial_conditionset_initial_estimatesset_instantaneous_absorptionset_lloq_dataset_lower_boundsset_michaelis_menten_eliminationset_mixed_mm_fo_eliminationset_nameset_ode_solverset_peripheral_compartmentsset_power_on_ruvset_proportional_error_modelset_reference_valuesset_seq_zo_fo_absorptionset_simulationset_time_varying_error_modelset_tmddset_transit_compartmentsset_upper_boundsset_weighted_error_modelset_zero_order_absorptionset_zero_order_eliminationset_zero_order_inputsimplify_expressionsolve_ode_systemsplit_joint_distributionsummarize_modelfit_resultstransform_blqtransform_etas_boxcoxtransform_etas_john_drapertransform_etas_tdisttranslate_nmtran_timeunconstrain_parametersundrop_columnsunfix_parametersunfix_parameters_tounload_datasetupdate_initial_individual_estimatesuse_thetas_for_error_stdevwrite_csvwrite_modelwrite_results

Dependencies:altairassertthatbase64encbslibcachemclidigestevaluatefansifastmapfontawesomefsglueherehighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlatticelifecyclemagrittrMatrixmemoisemimepillarpngR6rappdirsRcppRcppTOMLreprreticulaterlangrmarkdownrprojrootsasstinytexutf8vctrsvegawidgetwithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
add_admidadd_admid
add_allometryadd_allometry
add_bioavailabilityadd_bioavailability
add_cmtadd_cmt
add_covariate_effectadd_covariate_effect
add_derivativeadd_derivative
add_effect_compartmentadd_effect_compartment
add_estimation_stepadd_estimation_step
add_iivadd_iiv
add_indirect_effectadd_indirect_effect
add_individual_parameteradd_individual_parameter
add_iovadd_iov
add_lag_timeadd_lag_time
add_metaboliteadd_metabolite
add_parameter_uncertainty_stepadd_parameter_uncertainty_step
add_pd_iivadd_pd_iiv
add_peripheral_compartmentadd_peripheral_compartment
add_pk_iivadd_pk_iiv
add_population_parameteradd_population_parameter
add_predictionsadd_predictions
add_residualsadd_residuals
add_time_after_doseadd_time_after_dose
append_estimation_step_optionsappend_estimation_step_options
bin_observationsbin_observations
bump_model_numberbump_model_number
calculate_aiccalculate_aic
calculate_biccalculate_bic
calculate_corr_from_covcalculate_corr_from_cov
calculate_corr_from_preccalculate_corr_from_prec
calculate_cov_from_corrsecalculate_cov_from_corrse
calculate_cov_from_preccalculate_cov_from_prec
calculate_epsilon_gradient_expressioncalculate_epsilon_gradient_expression
calculate_eta_gradient_expressioncalculate_eta_gradient_expression
calculate_eta_shrinkagecalculate_eta_shrinkage
calculate_individual_parameter_statisticscalculate_individual_parameter_statistics
calculate_individual_shrinkagecalculate_individual_shrinkage
calculate_parameters_from_ucpcalculate_parameters_from_ucp
calculate_pk_parameters_statisticscalculate_pk_parameters_statistics
calculate_prec_from_corrsecalculate_prec_from_corrse
calculate_prec_from_covcalculate_prec_from_cov
calculate_se_from_covcalculate_se_from_cov
calculate_se_from_preccalculate_se_from_prec
calculate_ucp_scalecalculate_ucp_scale
check_datasetcheck_dataset
check_high_correlationscheck_high_correlations
check_parameters_near_boundscheck_parameters_near_bounds
Checks version of Pharmpy/pharmrcheck_pharmpy
cleanup_modelcleanup_model
convert_modelconvert_model
create_basic_pk_modelcreate_basic_pk_model
create_config_templatecreate_config_template
create_joint_distributioncreate_joint_distribution
create_reportcreate_report
create_rngcreate_rng
create_symbolcreate_symbol
deidentify_datadeidentify_data
display_odesdisplay_odes
drop_columnsdrop_columns
drop_dropped_columnsdrop_dropped_columns
evaluate_epsilon_gradientevaluate_epsilon_gradient
evaluate_eta_gradientevaluate_eta_gradient
evaluate_expressionevaluate_expression
evaluate_individual_predictionevaluate_individual_prediction
evaluate_population_predictionevaluate_population_prediction
evaluate_weighted_residualsevaluate_weighted_residuals
expand_additional_dosesexpand_additional_doses
filter_datasetfilter_dataset
find_clearance_parametersfind_clearance_parameters
find_volume_parametersfind_volume_parameters
fitfit
fix_or_unfix_parametersfix_or_unfix_parameters
fix_parametersfix_parameters
fix_parameters_tofix_parameters_to
get_admidget_admid
get_baselinesget_baselines
get_bioavailabilityget_bioavailability
get_central_volume_and_clearanceget_central_volume_and_clearance
get_cmtget_cmt
get_concentration_parameters_from_dataget_concentration_parameters_from_data
get_config_pathget_config_path
get_covariate_baselinesget_covariate_baselines
get_covariate_effectsget_covariate_effects
get_doseidget_doseid
get_dosesget_doses
get_dv_symbolget_dv_symbol
get_evidget_evid
get_idsget_ids
get_individual_parametersget_individual_parameters
get_individual_prediction_expressionget_individual_prediction_expression
get_initial_conditionsget_initial_conditions
get_lag_timesget_lag_times
get_mdvget_mdv
get_model_codeget_model_code
get_model_covariatesget_model_covariates
get_mu_connected_to_parameterget_mu_connected_to_parameter
get_number_of_individualsget_number_of_individuals
get_number_of_observationsget_number_of_observations
get_number_of_observations_per_individualget_number_of_observations_per_individual
get_number_of_peripheral_compartmentsget_number_of_peripheral_compartments
get_number_of_transit_compartmentsget_number_of_transit_compartments
get_observation_expressionget_observation_expression
get_observationsget_observations
get_omegasget_omegas
get_parameter_rvget_parameter_rv
get_pd_parametersget_pd_parameters
get_pk_parametersget_pk_parameters
get_population_prediction_expressionget_population_prediction_expression
get_rv_parametersget_rv_parameters
get_sigmasget_sigmas
get_thetasget_thetas
get_unit_ofget_unit_of
get_zero_order_inputsget_zero_order_inputs
greekify_modelgreekify_model
has_additive_error_modelhas_additive_error_model
has_combined_error_modelhas_combined_error_model
has_covariate_effecthas_covariate_effect
has_first_order_absorptionhas_first_order_absorption
has_first_order_eliminationhas_first_order_elimination
has_instantaneous_absorptionhas_instantaneous_absorption
has_linear_odeshas_linear_odes
has_linear_odes_with_real_eigenvalueshas_linear_odes_with_real_eigenvalues
has_michaelis_menten_eliminationhas_michaelis_menten_elimination
has_mixed_mm_fo_eliminationhas_mixed_mm_fo_elimination
has_mu_referencehas_mu_reference
has_odeshas_odes
has_presystemic_metabolitehas_presystemic_metabolite
has_proportional_error_modelhas_proportional_error_model
has_random_effecthas_random_effect
has_seq_zo_fo_absorptionhas_seq_zo_fo_absorption
has_weighted_error_modelhas_weighted_error_model
has_zero_order_absorptionhas_zero_order_absorption
has_zero_order_eliminationhas_zero_order_elimination
Install Pharmpyinstall_pharmpy
Install Pharmpy (with specified version)install_pharmpy_devel
is_linearizedis_linearized
is_realis_real
is_strictness_fulfilledis_strictness_fulfilled
list_time_varying_covariateslist_time_varying_covariates
load_datasetload_dataset
load_example_modelload_example_model
load_example_modelfit_resultsload_example_modelfit_results
make_declarativemake_declarative
mu_reference_modelmu_reference_model
omit_dataomit_data
plot_abs_cwres_vs_ipredplot_abs_cwres_vs_ipred
plot_cwres_vs_idvplot_cwres_vs_idv
plot_dv_vs_ipredplot_dv_vs_ipred
plot_dv_vs_predplot_dv_vs_pred
plot_eta_distributionsplot_eta_distributions
plot_individual_predictionsplot_individual_predictions
plot_iofv_vs_iofvplot_iofv_vs_iofv
plot_transformed_eta_distributionsplot_transformed_eta_distributions
plot_vpcplot_vpc
predict_influential_individualspredict_influential_individuals
predict_influential_outlierspredict_influential_outliers
predict_outlierspredict_outliers
print_fit_summaryprint_fit_summary
print_model_codeprint_model_code
print_model_symbolsprint_model_symbols
Print pharmpy versionprint_pharmpy_version
read_dataset_from_datainforead_dataset_from_datainfo
read_modelread_model
read_model_from_stringread_model_from_string
read_modelfit_resultsread_modelfit_results
read_resultsread_results
remove_bioavailabilityremove_bioavailability
remove_covariate_effectremove_covariate_effect
remove_derivativeremove_derivative
remove_error_modelremove_error_model
remove_estimation_stepremove_estimation_step
remove_iivremove_iiv
remove_iovremove_iov
remove_lag_timeremove_lag_time
remove_loq_dataremove_loq_data
remove_parameter_uncertainty_stepremove_parameter_uncertainty_step
remove_peripheral_compartmentremove_peripheral_compartment
remove_predictionsremove_predictions
remove_residualsremove_residuals
remove_unused_parameters_and_rvsremove_unused_parameters_and_rvs
rename_symbolsrename_symbols
replace_fixed_thetasreplace_fixed_thetas
replace_non_random_rvsreplace_non_random_rvs
resample_dataresample_data
Reset indexreset_index
Reset result indicesreset_indices_results
retrieve_modelsretrieve_models
run_allometryrun_allometry
run_amdrun_amd
run_bootstraprun_bootstrap
run_covsearchrun_covsearch
run_estmethodrun_estmethod
run_iivsearchrun_iivsearch
run_iovsearchrun_iovsearch
run_linearizerun_linearize
run_modelfitrun_modelfit
run_modelsearchrun_modelsearch
run_retriesrun_retries
run_ruvsearchrun_ruvsearch
run_simulationrun_simulation
run_structsearchrun_structsearch
run_toolrun_tool
sample_individual_estimatessample_individual_estimates
sample_parameters_from_covariance_matrixsample_parameters_from_covariance_matrix
sample_parameters_uniformlysample_parameters_uniformly
set_additive_error_modelset_additive_error_model
set_baseline_effectset_baseline_effect
set_combined_error_modelset_combined_error_model
set_covariatesset_covariates
set_datasetset_dataset
set_descriptionset_description
set_direct_effectset_direct_effect
set_dtbs_error_modelset_dtbs_error_model
set_dvidset_dvid
set_estimation_stepset_estimation_step
set_evaluation_stepset_evaluation_step
set_first_order_absorptionset_first_order_absorption
set_first_order_eliminationset_first_order_elimination
set_iiv_on_ruvset_iiv_on_ruv
set_initial_conditionset_initial_condition
set_initial_estimatesset_initial_estimates
set_instantaneous_absorptionset_instantaneous_absorption
set_lloq_dataset_lloq_data
set_lower_boundsset_lower_bounds
set_michaelis_menten_eliminationset_michaelis_menten_elimination
set_mixed_mm_fo_eliminationset_mixed_mm_fo_elimination
set_nameset_name
set_ode_solverset_ode_solver
set_peripheral_compartmentsset_peripheral_compartments
set_power_on_ruvset_power_on_ruv
set_proportional_error_modelset_proportional_error_model
set_reference_valuesset_reference_values
set_seq_zo_fo_absorptionset_seq_zo_fo_absorption
set_simulationset_simulation
set_time_varying_error_modelset_time_varying_error_model
set_tmddset_tmdd
set_transit_compartmentsset_transit_compartments
set_upper_boundsset_upper_bounds
set_weighted_error_modelset_weighted_error_model
set_zero_order_absorptionset_zero_order_absorption
set_zero_order_eliminationset_zero_order_elimination
set_zero_order_inputset_zero_order_input
simplify_expressionsimplify_expression
solve_ode_systemsolve_ode_system
split_joint_distributionsplit_joint_distribution
summarize_modelfit_resultssummarize_modelfit_results
transform_blqtransform_blq
transform_etas_boxcoxtransform_etas_boxcox
transform_etas_john_drapertransform_etas_john_draper
transform_etas_tdisttransform_etas_tdist
translate_nmtran_timetranslate_nmtran_time
unconstrain_parametersunconstrain_parameters
undrop_columnsundrop_columns
unfix_parametersunfix_parameters
unfix_parameters_tounfix_parameters_to
unload_datasetunload_dataset
update_initial_individual_estimatesupdate_initial_individual_estimates
use_thetas_for_error_stdevuse_thetas_for_error_stdev
write_csvwrite_csv
write_modelwrite_model
write_resultswrite_results