Introduction | Current modules | formods framework | Expected functions | Expected UI components | Module interaction | Module state and reacting to changes | Helper functions in formods | Setting holds on UI elements | Dataframe formatting information | Notifications | Adding tooltips | Pausing the screen | formods state objects | App information in MM | Checklist | Configuration file | YAML configuration files

Introduction | Least squares estimation/single output (analysis_parent.r) | Automated Reporting | PowerPoint | Word | Maximum likelihood/two outputs (analysis_parent_metabolite.r) | Global estimation routines (analysis_parent_metabolite_global.r) | Cohorts from NONMEM dataset (analysis_parent_metabolite_nm_data.r) | Contents of system.txt

Introduction | Quick Template for Running NCA | Single Dose Data | Expected Format of Data | NCA and Outputs | Automated Reporting | PowerPoint | Word | Summarizing Data | Multiple Dose Data | Sparse Sampling

Introduction | General workflow | The yaml report file structure | placeholders | parameters | covariates | options | Building figures & tables | figures | tables | pptx | docx | Customizing reports for your organization | PowerPoint | Word | Report configuration file report_fit.yaml

Introduction | Creating figures and tables | Using report objects in RMarkdown

Introduction | The sysem file: system-in_vitro.txt | The dataset: in_vitro_er_data.csv | The analysis script: analysis_in_vitro.R | Output times | Making a dynamic simulation static: | Datasets | Defining cohorts | Postprocessing | Results | Contents of system-in_vitro.txt

Introduction | Simulating an Individual Response (analysis_single.r) | Simulating Population Response From IIV (analysis_multiple.r) | Simulating Population Response From File (analysis_multiple_file.r) | Parallelization | Contents of system.txt

Introduction | Repeated Bolus Dosing (analysis_repeat_dosing.r) | Repeated Infusions (analysis_repeat_infusion.r) | Titrated Dosing (analysis_visit_dosing_titration.r) | Monte Carlo Simulations (analysis_visit_dosing_titration_stochastic.r) | Performing State/Compartment Resets (analysis_state_reset.r) | Contents of system.txt

Introduction | Parameters | System parameters <P> | Parameter sets | Secondary parameters <As> and <Ad> | Variance parameters <VP> | Parameter estimation information <EST:?>? | Variability: defining the variance/covariance Matrix <IIV:?>? & <IIVCOR:?>? | IIV and parameter sets <IIVSET:?>? & <IIVCORSET:?>? | Differential equations | Writing ODEs <ODE:?> | Rate equations =?=> | Equilibrium relationships <=kforward:kreverse=> | Sources and sinks <S:?> | Movement between compartments <C> | Bringing it all together | Initial conditions <I> | Model inputs | Bolus dosing <B:times>, <B:events> | Continuous infusions <R:?> | Covariates <CV:?>, <CVSET:?:?> | Simple covariates | Complicated covariates | Model outputs | Output error model <OE:?> ? | Functions and operators | Current simulation time | Modeling quasi-equilibrium of target-mediated drugs | Timescales | Mathematical sets | Set notation <SET:?>? | Aligning Sets | Set Functions | Set Evaluation | Piecewise-continuous functions/parameters <IF:?:?> | Constructing a piece-wise continuous function/parameter | Controlling indices | Concentrations vs amounts | Options | Example system files | Templates | R workflow | Matlab workflow | Other Software Targets | References

Introduction | Implementation | Avialable modules | Using a module | Compact UI elements | Deployment | Server functions | YAML configuration files | App State Management (ASM) | Upload Data (UD) | Data Management (DM) | Data Wrangling (DW) | Figure Generation (FG) | Known Issues | 413 Request Entity too large. | Disconnected from the server

Introduction | PowerPoint | Loading your presentation template | Adding content to placeholders | Lists | Figures | Tables | Adding content in user-defined locations | Saving presentations | Accessing the PowerPoint mapping information | Word | Loading your Word template | Adding content | Table of contents | Text | Styles | Formats | Formatting sections | Placeholder text | Formatting sections (again) | Multi-page figures and tables | Cross referencing figures and tables | Saving the Word report | Accessing the Word mapping information | Formatting with markdown | Using onbrand::ft_apply_md to format tables | Accessing the officer object directly | Mapping file

Introduction | Saving and loading an analysis | Creating automated workflows | Preloading the app with content

Introduction | Mapping and the yaml file format | PowerPoint | Step 1: Read the PowerPoint template | Step 2: Create the PowerPoint mapping | Defining markdown defaults | Post-processing | Step 3: Testing and previewing your template | Word | Step 1: Read the Word document | Step 2: Create the Word mapping | styles | doc_def | formatting | md_def | post_processing | Switching templates | Using your new template | Mapping file

Introduction | Implenting onbrand in ubiquity | Reporting workshop files | PowerPoint reports (make_report_PowerPoint.R) | Creating some content | Creating a new report | Adding slides to a report | Adding lists | Adding figures | Adding tables | Saving the report | Word reports (make_report_Word.R) | Adding content to the report | Adding text | Other content and formatting | Using custom organizational templates | PowerPoint | Word | Using the custom templates | Integration with ubiquity workflows | Parameter estimation | Non-compartmental analysis (NCA) | Modifying reports directly with officer | Wrapper mapping between ubiquity and onbrand functions

Introduction | Running the model | Altering dosing | Population simulations | Saving model results | Model scripts | Controlling what is saved | Model documentation | Model diagram | Model reports | User definable functions | Custom simulation commands | Custom plotting commands | Deployment on a Shiny Server