Package: ubiquity 2.1.1

ubiquity: PKPD, PBPK, and Systems Pharmacology Modeling Tools

Complete work flow for the analysis of pharmacokinetic pharmacodynamic (PKPD), physiologically-based pharmacokinetic (PBPK) and systems pharmacology models including: creation of ordinary differential equation-based models, pooled parameter estimation, individual/population based simulations, rule-based simulations for clinical trial design and modeling assays, deployment with a customizable 'Shiny' app, and non-compartmental analysis. System-specific analysis templates can be generated and each element includes integrated reporting with 'PowerPoint' and 'Word'.

Authors:John Harrold [aut, cre]

ubiquity_2.1.1.tar.gz
ubiquity_2.1.1.zip(r-4.7)ubiquity_2.1.1.zip(r-4.6)ubiquity_2.1.1.zip(r-4.5)
ubiquity_2.1.1.tgz(r-4.6-any)ubiquity_2.1.1.tgz(r-4.5-any)
ubiquity_2.1.1.tar.gz(r-4.7-any)ubiquity_2.1.1.tar.gz(r-4.6-any)
ubiquity_2.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ubiquity/json (API)
NEWS

# Install 'ubiquity' in R:
install.packages('ubiquity', repos = c('https://john-harrold.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/john-harrold/ubiquity/issues

Pkgdown/docs site:https://r.ubiquity.tools

On CRAN:

Conda:

modelingpkpd

6.59 score 14 stars 35 scripts 315 downloads 84 exports 101 dependencies

Last updated from:a6af2e725c. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE618
source / vignettesOK278
linux-release-x86_64NOTE642
macos-release-arm64NOTE556
macos-oldrel-arm64NOTE557
windows-develNOTE735
windows-releaseNOTE814
windows-oldrelNOTE670
wasm-releaseOK189

Exports:apply_sub_file_COVbuild_systemcalculate_halflifecalculate_objectivecheck_depsfetch_full_parametersfind_bracketed_argumentsgenerate_parametergenerate_subjectgg_axisgg_log10_xaxisgg_log10_yaxisGUI_log_entrylinspacelogspacenm_select_recordspad_stringparse_patternsprepare_figurerun_simulation_titraterun_simulation_ubiquitysimulate_subjectssom_to_dfsystem_check_requirementssystem_check_steady_statesystem_clear_cohortssystem_define_cohortsystem_define_cohorts_nmsystem_estimate_parameterssystem_fetch_guesssystem_fetch_iivsystem_fetch_ncasystem_fetch_nca_columnssystem_fetch_parameterssystem_fetch_rpt_officer_objectsystem_fetch_rpt_onbrand_objectsystem_fetch_setsystem_fetch_templatesystem_fetch_TSsyssystem_glp_initsystem_glp_scenariosystem_load_datasystem_log_debug_savesystem_log_entrysystem_log_initsystem_nca_parameters_metasystem_nca_runsystem_nca_summarysystem_newsystem_new_listsystem_new_tt_rulesystem_od_generalsystem_plot_cohortssystem_rpt_add_doc_contentsystem_rpt_add_slidesystem_rpt_estimationsystem_rpt_ncasystem_rpt_read_templatesystem_rpt_save_reportsystem_rpt_template_detailssystem_select_setsystem_set_bolussystem_set_covariatesystem_set_guesssystem_set_iivsystem_set_optionsystem_set_parametersystem_set_ratesystem_set_rpt_officer_objectsystem_set_rpt_onbrand_objectsystem_set_tt_bolussystem_set_tt_condsystem_set_tt_ratesystem_simulate_estimation_resultssystem_ts_to_simtimesystem_viewsystem_zero_inputstictimecourse_statstocvar2stringvar2string_genvpworkshop_fetch

Dependencies:askpassbackportsbase64encbslibcachemcellrangercheckmateclicodetoolscommonmarkcpp11crayondata.tabledeSolvedigestdoParalleldplyrevaluatefarverfastmapflextablefontawesomefontBitstreamVerafontLiberationfontquiverforeachfsgdtoolsgenericsggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelifecyclemagrittrMASSmemoisemimenlmenloptrnumDerivofficeronbrandopenssloptimxotelpillarpkgconfigPKNCApracmaprettyunitsprogresspromisespsopurrrR6raggrappdirsRColorBrewerRcppreadxlrematchrhandsontablerlangrmarkdownS7sassscalesshinysourcetoolsstringistringrsyssystemfontstextshapingtibbletidyrtidyselecttinytexutf8uuidvctrsviridisLitewithrxfunxml2xtableyamlzip

Model Deployment

John Harrold & Anson K Abraham

Rendered fromDeployment.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2021-12-05
Started: 2018-04-27

Naive-Pooled Parameter Estimation

Rendered fromEstimation.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2026-01-03
Started: 2018-03-04

Analysis of Static Systems, an In Vitro Example

Rendered fromIn_Vitro.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2025-03-22
Started: 2024-10-20

Modeling Language

Rendered fromLanguage.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2025-03-21
Started: 2018-03-04

Noncompartmental Analysis

Rendered fromNCA.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2025-12-30
Started: 2019-07-08

Report Generation

Rendered fromReporting.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2024-03-07
Started: 2018-03-04

Individual and Population Simulations

Rendered fromSimulation.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2025-03-22
Started: 2018-03-04

Titration/Rule-Based Simulations

Rendered fromTitration.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2025-03-22
Started: 2018-03-04

Readme and manuals

Help Manual

Help pageTopics
Build the System Filebuild_system
Calculate the halflife of datacalculate_halflife
Implementation of Matlab 'toc()' commandcheck_deps
Make Pretty ggplot x- or y-Axis Log 10 Scalegg_axis
Make Pretty ggplot x-Axis Log 10 Scalegg_log10_xaxis
Make Pretty ggplot y-Axis Log 10 Scalegg_log10_yaxis
Implementation of the 'linspace' Function from Matlablinspace
Implementation of the 'logspace' Function from Matlablogspace
Pad String with Spacespad_string
Make ggplot Figure Prettyprepare_figure
Simulate With Titration or Rule-Based Inputsrun_simulation_titrate
Simulate Individual Responserun_simulation_ubiquity
Run Population Simulationssimulate_subjects
Converts the Wide/Verbose Output Simulation Functions into Data Framessom_to_df
Check For Perl and C Toolssystem_check_requirements
Verify System Steady Statesystem_check_steady_state
Clear all Cohortssystem_clear_cohorts
Define Estimation Cohortsystem_define_cohort
Define Cohorts from NONMEM Input Filesystem_define_cohorts_nm
Control Estimation Processsystem_estimate_parameters
Fetch Current Parameter Guessessystem_fetch_guess
Fetch Variability Termssystem_fetch_iiv
Fetch NCA Resultssystem_fetch_nca
Columns in NCA Analysissystem_fetch_nca_columns
Fetch System Parameterssystem_fetch_parameters
Extracts the officer Object From the Specified ubiquity Reportsystem_fetch_rpt_officer_object
Extracts the onbrand Object From the Specified ubiquity Reportsystem_fetch_rpt_onbrand_object
Fetch Mathematical Setsystem_fetch_set
Create New Analysis Templatesystem_fetch_template
Fetch System Timescalesystem_fetch_TSsys
Initialize GLP study designsystem_glp_init
Design GLP Study For a Scenariosystem_glp_scenario
Loading Datasetssystem_load_data
Save variables to filessystem_log_debug_save
Initialize System Log Filesystem_log_init
List NCA parameters, text names and descriptionssystem_nca_parameters_meta
Automatic NCAsystem_nca_run
Summarize NCA Results in Tabular Formatsystem_nca_summary
Create New 'system.txt' Filesystem_new
Fetch List of Available System Templatessystem_new_list
Titration Rulessystem_new_tt_rule
General Observation Details Functionsystem_od_general
Plot Estimation Resultssystem_plot_cohorts
Adds Content to a Word Reportsystem_rpt_add_doc_content
Add Slide to a Powerpoint Reportsystem_rpt_add_slide
Generate a Report from Parameter Estimationsystem_rpt_estimation
Report NCAsystem_rpt_nca
Initialize a New Reportsystem_rpt_read_template
Save Report to a Filesystem_rpt_save_report
Generate Details about Report Templatesystem_rpt_template_details
Selecting Parameter Setssystem_select_set
Set Bolus Inputssystem_set_bolus
Set Covariate Valuessystem_set_covariate
Alter Initial Guess and Parameter Boundssystem_set_guess
Set Variability Termssystem_set_iiv
Setting Analysis Optionssystem_set_option
Set Value for Parametersystem_set_parameter
Set Infusion Rate Inputssystem_set_rate
Sets the officer Object for the Specified ubiquity Reportsystem_set_rpt_officer_object
Sets the onbrand Object for the Specified ubiquity Reportsystem_set_rpt_onbrand_object
Define Titration Triggers and Actionssystem_set_tt_cond
Actual Function Called by 'SI_TT_RATE'system_set_tt_rate
Simulate Results at Estimatessystem_simulate_estimation_results
View Information About the Systemsystem_view
Zero All Model Inputssystem_zero_inputs
Implementation of Matlab 'tic()' commandtic
Implementation of Matlab 'toc()' commandtoc
Converts Numeric Variables into Padded Stringsvar2string
Print and Log Messagesvp
Fetch Ubiquity Workshop Sectionsworkshop_fetch