System Basics

Building systems, setting options, access workshop elements etc.

build_system()

Building The System

system_new()

Create New system.txt File

system_new_list()

Fetch List of Available System Templates

workshop_fetch()

Fetch Ubiquity Workshop Sections

system_fetch_parameters()

Fetch System Parameters

system_fetch_iiv()

Fetch Variability Terms

system_fetch_set()

Fetch Mathematical Set

system_fetch_template()

Create New Analysis Template

system_fetch_TSsys()

Fetch System Timescale

system_view()

View Information About the System

system_check_requirements()

Check For Perl and C Tools

system_set_option()

Setting Analysis Options

system_set_iiv()

Set Variability Terms

Simulation

Individual and population simulations

run_simulation_ubiquity()

Simulate Individual Response

simulate_subjects()

Run Population Simulations

system_load_data()

Loading Datasets

system_select_set()

Selecting Parameter Sets

som_to_df()

Converts the Wide/Verbose Output Simulation Functions into Data Frames

system_check_steady_state()

Verify System Steady State

system_zero_inputs()

Zero All Model Inputs

system_set_bolus()

Set Bolus Inputs

system_set_rate()

Set Infusion Rate Inputs

system_set_covariate()

Set Covariate Values

run_simulation_titrate()

Simulate With Titration or Rule-Based Inputs

system_new_tt_rule()

Titration Rules

system_set_tt_cond()

Define Titration Triggers and Actions

system_set_tt_rate()

Actual Function Called by SI_TT_RATE

Estimation

Naive-pooled parameters estimation

system_estimate_parameters()

Control Estimation Process

system_set_guess()

Alter Initial Guess and Parameter Bounds

system_plot_cohorts()

Plot Estimation Results

system_clear_cohorts()

Clear all Cohorts

system_define_cohort()

Define Estimation Cohort

system_define_cohorts_nm()

Define Cohorts from NONMEM Input File

system_simulate_estimation_results()

Simulate Results at Estimates

system_od_general()

General Observation Details Function

Reporting

The following functions are used to create, modify and save Word and PowerPoint reports

system_rpt_add_doc_content()

Adds Content to a Word Report

system_rpt_add_slide()

Add Slide to Report

system_rpt_estimation()

Generate a Report from Parameter Estimation

system_rpt_nca()

Report NCA

system_rpt_read_template()

Initialize a New Officer Report

system_rpt_save_report()

Save Report to a File

system_rpt_template_details()

Generate Details about Report Template

system_fetch_rpt_officer_object()

Extracts the officer Object From the Specified ubiquity Report

system_fetch_rpt_onbrand_object()

Extracts the onbrand Object From the Specified ubiquity Report

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

NCA

The following functions are used to run NCA and summarize results

system_fetch_nca()

Fetch NCA Results

system_fetch_nca_columns()

Columns in NCA Analysis

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

General Functions

calculate_halflife()

Calculate the halflife of data

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

linspace()

Implementation of the linspace Function from Matlab

logspace()

Implementation of the logspace Function from Matlab

pad_string()

Pad String with Spaces

prepare_figure()

Make ggplot Figure Pretty

vp()

Print and Log Messages

var2string()

Converts Numeric Variables into Padded Strings

system_log_debug_save()

Save variables to files

system_log_init()

Initialize System Log File

tic()

Implementation of Matlab tic() command

toc()

Implementation of Matlab toc() command