# Simulx User Guide – version 3.1

**New versions of the User Guide published with bookdown are also available: HTML – pdf**

Download the R scripts, Mlxtran and pharmML codes used for this user guide

**Introduction**

**Calculation of functions of time**

**Calculation of functions of time**

- Function of time with analytical expression
- Function of time solution of a system of ordinary differential equations (ODEs)
- Function of time solution of a system of delay differential equations (DDEs)
- Model with regression variables

**Simulation of dynamical systems – PK models**

**Simulation of dynamical systems – PK models**

- ODE based system with source terms
- Simulation of PK models: single route of administration
- Simulation of PK models: multiple routes of administration

**Simulation of longitudinal data**

**Simulation of longitudinal data**

- Continuous data
- Categorical data
- Categorical data with Markovian dependence
- Count data
- Time to event data
- Joint model
- Censored data (below or above a limit of quantification)

**Simulation of hierarchical models**

**Simulation of hierarchical models**

- Introduction
- Model with random individual parameters
- Model with random continuous covariates
- Model with random population parameters

**Extensions of the statistical model**

**Extensions of the statistical model**

**Simulation of several individuals and replicates**

**Simulation of several individuals and replicates**

- Defining groups: part I
- Defining groups: part II
- Simulating several replicates of the same experiment
- Computing summary statistics
- Reading data files and using data frames

**Using Simulx with a Monolix project**

**Using Simulx with a Monolix project**

- Using and modifying the original design
- Resampling the patients of the original study
- Introducing uncertainty on the population parameters

**Miscellaneous**

**Miscellaneous**

- Using a model defined “inline”
- Creating outputs not defined in the model (version >=3.1.1)
- Writing the results to a file or a folder
- Reproducing the same random results
- Optimizing the computation time
- Simulating random variables in a block EQUATION
- Using a R model instead of Mlxtran
- Using a PharmML model instead of Mlxtran