PKPD, PBPK, and Systems Pharmacology Modeling Tools

---

Documentation for package ‘ubiquity’ version 2.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

build_system	Build the System File
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
run_simulation_titrate	Simulate With Titration or Rule-Based Inputs
run_simulation_ubiquity	Simulate Individual Response
simulate_subjects	Run Population Simulations
som_to_df	Converts the Wide/Verbose Output Simulation Functions into Data Frames
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 Report
system_fetch_rpt_onbrand_object	Extracts the onbrand Object From the Specified ubiquity Report
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_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_od_general	General Observation Details Function
system_plot_cohorts	Plot Estimation Results
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_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_view	View Information About the System
system_zero_inputs	Zero All Model Inputs
tic	Implementation of Matlab 'tic()' command
toc	Implementation of Matlab 'toc()' command
var2string	Converts Numeric Variables into Padded Strings
vp	Print and Log Messages
workshop_fetch	Fetch Ubiquity Workshop Sections