Man pages for john-harrold/ubiquity
PKPD, PBPK, and Systems Pharmacology Modeling Tools

apply_sub_file_COVExtracts Covariates for a Subject from a Subject Data File
archive_estimationArchive Estimation Results
AUC_Bailers_methodAUC for sparse data
build_systemBuilding The System
calculate_halflifeCalculate the halflife of data
calculate_objectiveCalculates the Value of the Specified Objective Function
calculate_objective_ga'GA' Wrapper for calculate_objective
calculate_objective_pso'pso' Wrapper for calculate_objective
calculate_varianceCalculates the Variance in od_general
check_steady_stateVerify System Steady State
compare_estimateCompares Estimate to Bounds
estimate_parametersPerforms parameter estimation
fetch_full_parametersCreate Full Parameter Vector from Estimation Subset
find_bracketed_argumentsParse Prototype Functions for Arguments
generate_parameterGenerates a Parameter Based on '<IIV:?>' in the System File
generate_reportGenerate Text Report with Estimation Results
generate_subjectGenerate Subject
gg_axisMake Pretty ggplot x- or y-Axis Log 10 Scale
gg_log10_xaxisMake Pretty ggplot x-Axis Log 10 Scale
gg_log10_yaxisMake Pretty ggplot y-Axis Log 10 Scale
GUI_log_entryWrapper for system_log_entry Used in ShinyApp
linspaceImplementation of the 'linspace' Function from Matlab
logspaceImplementation of the 'logspace' Function from Matlab
make_forcing_functionMakes Forcing Function From Times and Values
nm_select_recordsSelect Records from NONMEM-ish Data Set
pad_stringPad String with Spaces
parse_patternsParse String for Prototype Functions
prepare_figureMake ggplot Figure Pretty
run_simulation_titrateSimulate With Titration or Rule-Based Inputs
run_simulation_ubiquitySimulate Individual Response
sample_aroundDefine Sample Times Around Events
simulate_subjectsRun Population Simulations
solution_statisticsCalculate Solution Statistics
som_to_dfConverts the Wide/Verbose Output Simulation Functions into...
system_check_requirementsCheck For Perl and C Tools
system_check_steady_stateVerify System Steady State
system_clear_cohortsClear all Cohorts
system_define_cohortDefine Estimation Cohort
system_define_cohorts_nmDefine Cohorts from NONMEM Input File
system_estimate_parametersControl Estimation Process
system_fetch_guessFetch Current Parameter Guesses
system_fetch_iivFetch Variability Terms
system_fetch_parametersFetch System Parameters
system_fetch_templateCreate New Template After Building System File
system_fetch_TSsysFetch System Timescale
system_glp_initInitialize GLP study design
system_glp_saveSave results from a GLP Study design
system_glp_scenarioDesign GLP Study For a Scenario
system_load_dataLoading Datasets
system_log_entryAdd Log Entry
system_log_initInitialize System Log File
system_nca_runAutomatic NCA
system_newCreate New 'system.txt' File
system_new_tt_ruleTitration Rules
system_nm_check_dsCheck NONMEM Dataset for Automatic Definitions
system_od_generalGeneral Observation Details Function
system_plot_cohortsPlot Estimation Results
system_report_doc_add_contentAdd content to Body of a Word Document Report
system_report_doc_set_phSets Placeholder Content for Word Document Report
system_report_estimationGenerate a Report from Parameter Estimation
system_report_fetchRetrieve the officer Object of a Report
system_report_glpReport GLP Study
system_report_initInitialize a New Officer Report
system_report_ncaReport NCA
system_report_ph_contentPopulate Placeholder In Officer Report
system_report_saveSave Report to File
system_report_setOverwrite officer Object for a Given Report
system_report_slide_contentAdd Slide With Main Body of Content
system_report_slide_sectionGenerate Slide with Section Break
system_report_slide_titleGenerate Title Slide
system_report_slide_two_colGenerate Slide with Two Column Layout
system_report_view_layoutGenerate Annotated Layout for Report Templates
system_reqRequire Suggested Packages
system_select_setSelecting Parameter Sets
system_set_bolusSet Bolus Inputs
system_set_covariateSet Covariate Values
system_set_guessAlter Initial Guess and Parameter Bounds
system_set_iivSet Variability Terms
system_set_optionSetting Analysis Options
system_set_parameterSet Value for Parameter
system_set_rateSet Infusion Rate Inputs
system_set_tt_bolusActual Function Called by 'SI_TT_BOLUS'
system_set_tt_condDefine Titration Triggers and Actions
system_set_tt_rateActual Function Called by 'SI_TT_RATE'
system_simulate_estimation_resultsSimulate Results at Estimates
system_ts_to_simtimeConvert Time in Timescale to Simulation Time
system_viewView Information About the System
system_zero_inputsZero All Model Inputs
ticImplementation of Matlab 'tic()' command
timecourse_statsCalculate Timecourse Statistics for a Matrix of Responses
tocImplementation of Matlab 'toc()' command
ubiquity_name_checkCheck Names of Cohorts, Analyses, Reports, etc.
var2stringConverts Numeric Variables into Padded Strings
var2string_genConvert R Objects to Strings
vpPrint and Log Messages
workshop_fetchFetch Ubiquity Workshop Sections
john-harrold/ubiquity documentation built on Nov. 7, 2019, 12:13 p.m.