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System Basics

Building systems, setting options, access workshop elements etc.

build_system()
Build the System File
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_parameter()
Set Value for Parameter
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_parameter()
Set Value for Parameter
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_fetch_guess()
Fetch Current Parameter Guesses
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 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_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
estimate_parameters()
Performs parameter estimation
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