Package index • ubiquity

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

In development

The following are under development

system_glp_init(): Initialize GLP study design

system_glp_scenario(): Design GLP Study For a Scenario