# PKPD, PBPK, and Systems Pharmacology Modeling Tools

## Documentation for package ‘ubiquity’ version 1.0.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

build_system | Building The System
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
md_to_officer | Parse Markdown for OfficeR
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_parameters | Fetch System Parameters
system_fetch_set | Fetch Mathematical Set
system_fetch_template | Create New Template After Building System File
system_fetch_TSsys | Fetch System Timescale
system_glp_init | Initialize GLP study design
system_glp_save | Save results from a 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_run | Automatic NCA
system_new | Create New 'system.txt' File
system_new_list | Fetch list of internal system templates
system_new_tt_rule | Titration Rules
system_od_general | General Observation Details Function
system_plot_cohorts | Plot Estimation Results
system_report_doc_add_content | Add content to Body of a Word Document Report
system_report_doc_format_section | Formats the Current Document Section
system_report_doc_set_ph | Sets Placeholder Content for Word Document Report
system_report_estimation | Generate a Report from Parameter Estimation
system_report_fetch | Retrieve the officer Object of a Report
system_report_glp | Report GLP Study
system_report_init | Initialize a New Officer Report
system_report_nca | Report NCA
system_report_ph_content | Populate Placeholder In Officer Report
system_report_save | Save Report to File
system_report_set | Overwrite officer Object for a Given Report
system_report_slide_content | Add Slide With Main Body of Content
system_report_slide_section | Generate Slide with Section Break
system_report_slide_title | Generate Title Slide
system_report_slide_two_col | Generate Slide with Two Column Layout
system_report_view_layout | Generate Annotated Layout for Report Templates
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_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