Introduction | Initial Setup | Setting up the data | Population Simulation Data | Time Profile Plots | Population Data Aggregation | Showing Individual Dataset Names | Custom Aesthetic Mappings | Predicted vs Observed Plots | Customizing Fold Distance | Swapping Axes | Scaling Options | Residuals vs Covariate Plots | Residuals vs Observed Values | Residuals vs Time | Residuals vs Predicted Values | Residual Scale Options | Residuals as Histogram | Quantile-Quantile (Q-Q) Plot | Automatic Unit Conversion | Specifying Units Directly | Handling Mixed Error Types | Using data.table Instead of DataCombined | Further Customization | Legend title | Legend position | Saving Plots

Calculating PK parameters | Extracting a dataframe | Import and export of PK-analyses | User-Defined PK Parameters | Examples | Calculate AUC between for a specific time interval. | Calculate CMax between the 4th and 5th application of a multiple applications simulation. | Calculate CMax between the 4th and 5th application of a multiple applications simulation and apply a time offset | Update Dimension of a standard parameter for correct visualization

Changing initial values | Formula types | Changing parameters and molecules initial values

Adding enzyme ontogenies

Unit conversion

Life cycle of a simulation run | Running a single simulation once | Running a single simulation multiple times and varying some parameters/initial values between each run | Optimized loading for running simulations with predefined set of variable parameters | Varying state variable parameters with SimulationBatch

Overview | Quick Start: Basic Simulation | Step-by-Step Tutorial | Loading Simulations | Exploring Model Structure | Modifying Parameters | Customizing Simulation Settings | Running Simulations | Visualizing Results | Option 1: Built-in Plotting Functions | Option 2: Custom Plotting with ggplot2 | Complete Workflow Example | Understanding ospsuite Objects | Object-Oriented Approach | Key Classes | General Workflow Summary | Next Steps | Essential Next Steps: | Population Studies: | Analysis and Optimization: | Data Integration: | Advanced Topics: | General Information

Loading a simulation | Accessing entities of the model and their properties - the path concept | Loading simulation tree

DataSet | Importing data

Not required for {ospsuite} version equal or above 12.1.0 | Versions below 12.1.0 | Install PK-Sim Globally | Install and use PK-Sim in a project

Loading population file | Creating populations | Running population simulation

Running individual simulation and retrieving the results | Running multiple individual simulations and retrieving the results | Adding new outputs | Changing simulation intervals | Adjusting solver settings

Performing a sensitivity analysis | Understanding numberOfSteps and variationRange | Customizing sensitivity analysis settings | Import and export of sensitivity analysis results

Changing table parameter values

Introduction | Time profile plots | Observed versus simulated scatter plot | Residuals versus time or vs simulated scatter plot | Customizing plots | Creating multi-panel plots | Saving plots | Implementation details

Introduction | Creating DataCombined object | Grouping | Transformations | Extracting a combined data frame | Further functionalities | Visualizations with DataCombined

Get started | Basic usage | Spec constructors | integerOption() | numericOption() | characterOption() | logicalOption() | Common parameters | nullAllowed | naAllowed | expectedLength | Error aggregation | Practical example

Get started | Taking advantage of glue and cli formatting | Catching messages | Masking messages

1. Introduction | 2. Label configuration: labels | 2.1. Label and Label configuration objects | 2.2. Label configuration in plots | 2.3. Changing plot labels | 2.4. Smart plot configurations | 3. Background configuration: background | 3.1. Background configuration properties | 3.2. Background configuration in plots | 3.3. Changing background properties | 3.3.1. Set Background | 3.3.2. Set Grid | 3.3.3. Set Watermark | 4. X/Y axes configurations: xAxis/yAxis | 4.1. Axis configuration in plots | Changing axis properties | 5. Legend configuration: legend | 5.1. Legend configuration in plots | 6. Default plot configuration: Theme objects | 7. Exporting/Saving a plot | Export code to re-create a PlotConfiguration object

Introduction to atom plots | initializePlot | addScatter | addLine | addRibbon | addErrorbar

1. Introduction | 2. Definition of the boxplot functions and classes | 2.1. The plotBoxWhisker function | 2.2. The BoxWhiskerDataMapping class | 3. Examples | 3.1. Data | 3.2. Minimal example | 3.3. Difference x vs fill input | 3.4. Boxplot functions | 3.5. Outlier functions | 3.4. plotConfiguration of boxplots: BoxWhiskerPlotConfiguration | 4. Further utility of BoxWhiskerDataMapping

1. Introduction | 2. Illustration of basic histograms | 2.1. Data | 2.2. plotHistogram | 2.3. Minimal examples | 2.4. Examples using data and dataMapping | 2.5. Focus on binning | 2.6. Focus on distribution fit

1. Introduction | 1.1. Objectives | 1.2. Libraries | 1.3. tlf typical workflow | 1.4. Naming Conventions | 2. Data pre-processing: AggregationSummary class | 2.1. Data format | 2.2. MetaData | 2.3. Aggregation | 3. Mapping and grouping of data: DataMapping class | 3.1. GroupMapping | 3.1.1. Grouping class | 3.1.2. GroupMapping class | 3.2. DataMapping

1. Introduction | 2. Illustration of basic PK ratio plots | 2.1. Data | 2.2. plotPKRatio | 2.3. Minimal example | 2.4. Examples with dataMapping | 2.4.1 groupMapping | 2.4.2 PK values defined in lines | 2.5. Qualification of PK Ratios | 2.6. Plot Configuration

1. Introduction | 2. How to start | 3. How to update theme properties | 4. How to export and re-use a theme

1. Introduction | 2. Definition of the time profile functions and classes | 2.1. plotTimeProfile | 2.2. Data Mappings | 2.2.1. dataMapping argument | 2.2.2. observedDataMapping argument | 2.2.3. Remaining TODOs | 3. Examples | 3.1. Plot simulated data only | 3.1.1 Single simulation | 3.1.2. Single simulation with confidence interval | 3.1.3. Multiple simulations | 3.1.4. Multiple simulations with confidence interval | 3.2. Plot observed data only | 3.2.1. Single observed data set | 3.2.2. Single simulation with confidence interval | 3.2.3. Multiple observed data sets | 3.2.4. Multiple observed data sets with confidence interval | 3.2.4. Missing Dependent Variable (mdv) | 3.3. Plot simulated and observed data | 3.3.1. Single simulation and observed data set | 3.3.2. Single simulation and observed data set with their confidence intervals | 3.3.3. Multiple simulations and observed data sets | 3.3.4. Multiple simulations and observed data sets with their confidence intervals | 3.4. Plot Configuration

1. Introduction | 2. How to start | 3. How to import data | 4. How to plot the imported data | 4.1. Select the plot and its variables | 4.2. Update plot properties | 5. Save/export a plot | 6. Plot-specific properties | 6.1. Add a regression line | 6.1. Tornado plot