Man pages for john-harrold/ubiquity
PKPD, PBPK, and Systems Pharmacology Modeling Tools
| apply_sub_file_COV | Extracts Covariates for a Subject from a Subject Data File |
| archive_estimation | Archive Estimation Results |
| AUC_Bailers_method | Calculate AUC for Sparse Data |
| build_system | Build the System File |
| calculate_halflife | Calculate the halflife of data |
| calculate_objective | Calculates the Value of the Specified Objective Function |
| calculate_objective_ga | 'GA' Wrapper for calculate_objective |
| calculate_objective_pso | 'pso' Wrapper for calculate_objective |
| calculate_variance | Calculates the Variance in od_general |
| check_steady_state | Verify System Steady State |
| compare_estimate | Compares Estimate to Bounds |
| estimate_parameters | Performs parameter estimation |
| fetch_full_parameters | Create Full Parameter Vector from Estimation Subset |
| find_bracketed_arguments | Parse Prototype Functions for Arguments |
| generate_parameter | Generates a Parameter Based on '<IIV:?>' in the System File |
| generate_report | Generate Text Report with Estimation Results |
| generate_subject | Generate Subject |
| gg_axis | Make Pretty ggplot x- or y-Axis Log 10 Scale |
| gg_log10_xaxis | Make Pretty ggplot x-Axis Log 10 Scale |
| gg_log10_yaxis | Make Pretty ggplot y-Axis Log 10 Scale |
| GUI_log_entry | Wrapper for system_log_entry Used in ShinyApp |
| linspace | Implementation of the 'linspace' Function from Matlab |
| logspace | Implementation of the 'logspace' Function from Matlab |
| make_forcing_function | Makes Forcing Function From Times and Values |
| nm_select_records | Select Records from NONMEM-ish Data Set |
| pad_string | Pad String with Spaces |
| parse_patterns | Parse String for Prototype Functions |
| prepare_figure | Make ggplot Figure Pretty |
| run_simulation_titrate | Simulate With Titration or Rule-Based Inputs |
| run_simulation_ubiquity | Simulate Individual Response |
| sample_around | Define Sample Times Around Events |
| simulate_subjects | Run Population Simulations |
| solution_statistics | Calculate Solution Statistics |
| som_to_df | Converts the Wide/Verbose Output Simulation Functions into... |
| system_check_requirements | Check For Perl and C Tools |
| system_check_steady_state | Verify System Steady State |
| system_clear_cohorts | Clear all Cohorts |
| system_define_cohort | Define Estimation Cohort |
| system_define_cohorts_nm | Define Cohorts from NONMEM Input File |
| system_estimate_parameters | Control Estimation Process |
| system_fetch_guess | Fetch Current Parameter Guesses |
| system_fetch_iiv | Fetch Variability Terms |
| system_fetch_nca | Fetch NCA Results |
| system_fetch_nca_columns | Columns in NCA Analysis |
| system_fetch_parameters | Fetch System Parameters |
| system_fetch_rpt_officer_object | Extracts the officer Object From the Specified ubiquity... |
| system_fetch_rpt_onbrand_object | Extracts the onbrand Object From the Specified ubiquity... |
| system_fetch_set | Fetch Mathematical Set |
| system_fetch_template | Create New Analysis Template |
| system_fetch_TSsys | Fetch System Timescale |
| system_glp_init | Initialize GLP study design |
| system_glp_scenario | Design GLP Study For a Scenario |
| system_load_data | Loading Datasets |
| system_log_debug_save | Save variables to files |
| system_log_entry | Add Log Entry |
| system_log_init | Initialize System Log File |
| system_nca_parameters_meta | List NCA parameters, text names and descriptions |
| system_nca_run | Automatic NCA |
| system_nca_summary | Summarize NCA Results in Tabular Format |
| system_new | Create New 'system.txt' File |
| system_new_list | Fetch List of Available System Templates |
| system_new_tt_rule | Titration Rules |
| system_nm_check_ds | Check NONMEM Dataset for Automatic Definitions |
| system_od_general | General Observation Details Function |
| system_plot_cohorts | Plot Estimation Results |
| system_req | Require Suggested Packages |
| system_rpt_add_doc_content | Adds Content to a Word Report |
| system_rpt_add_slide | Add Slide to a Powerpoint Report |
| system_rpt_estimation | Generate a Report from Parameter Estimation |
| system_rpt_nca | Report NCA |
| system_rpt_read_template | Initialize a New Report |
| system_rpt_save_report | Save Report to a File |
| system_rpt_template_details | Generate Details about Report Template |
| system_select_set | Selecting Parameter Sets |
| system_set_bolus | Set Bolus Inputs |
| system_set_covariate | Set Covariate Values |
| system_set_guess | Alter Initial Guess and Parameter Bounds |
| system_set_iiv | Set Variability Terms |
| system_set_option | Setting Analysis Options |
| system_set_parameter | Set Value for Parameter |
| system_set_rate | Set Infusion Rate Inputs |
| system_set_rpt_officer_object | Sets the officer Object for the Specified ubiquity Report |
| system_set_rpt_onbrand_object | Sets the onbrand Object for the Specified ubiquity Report |
| system_set_tt_bolus | Actual Function Called by 'SI_TT_BOLUS' |
| system_set_tt_cond | Define Titration Triggers and Actions |
| system_set_tt_rate | Actual Function Called by 'SI_TT_RATE' |
| system_simulate_estimation_results | Simulate Results at Estimates |
| system_ts_to_simtime | Convert Time in Timescale to Simulation Time |
| system_view | View Information About the System |
| system_zero_inputs | Zero All Model Inputs |
| tic | Implementation of Matlab 'tic()' command |
| timecourse_stats | Calculate Timecourse Statistics for a Matrix of Responses |
| toc | Implementation of Matlab 'toc()' command |
| ubiquity_name_check | Check Names of Cohorts, Analyses, Reports, etc. |
| var2string | Converts Numeric Variables into Padded Strings |
| var2string_gen | Convert R Objects to Strings |
| vp | Print and Log Messages |
| workshop_fetch | Fetch Ubiquity Workshop Sections |
