Pumas Tutorials
Important
This is a Pumas 2.7 prerelease version of the tutorials page. If you are running Pumas 2.6, please navigate to the Pumas 2.6 version of the tutorials page.
Learning Paths
Getting Started with the Learning Paths
- The Learning Paths are designed to help you navigate through the Pumas ecosystem. Each path consists of a series of modules that cover different aspects of using Pumas, from the fundamentals of Julia programming to advanced modeling techniques.
- The paths are structured to provide a comprehensive learning experience, allowing you to build your knowledge progressively. You can choose to follow a specific path or explore individual modules based on your interests and needs.
- The paths are designed to be flexible, allowing you to learn at your own pace and focus on the areas that are most relevant to you. Whether you are a beginner or an experienced user, the Learning Paths will help you gain the skills and knowledge needed to effectively use Pumas for your modeling and simulation needs.
How to Use the Learning Paths
Path 1: Julia Fundamentals for Pumas
Module 1: Introduction to Julia
Module 2: Data Wrangling and Visualization in Julia
Path 2: Pumas Fundamentals of Data and Model Structure
Module 3: Introduction to Pumas
Module 4: Population PK and PK/PD Modeling with Pumas
- Data Representation
- Model Representation
- Model Representation Using Latexify
- Compartmental PK Models
- Parameter Estimation and Estimating Parameter Uncertainty
- Interpretation of Pumas Model Output
- Model Diagnostics and Evaluation
- Bootstrap and Sampling Importance Resampling
- Sequential and Simultaneous PKPD Models
- Comparison to NONMEM for NONMEM Users (see from NONMEM to Pumas)
Path 3: Pumas Fundamentals of Model Development
Module 5: Structural Model Definitions
Module 6: Absorption Models
Module 7: Random Effect Models
Module 8: Error Models
Module 9: Covariate Model Definitions
Path 4: Pumas Fundamentals of Model Simulation
Module 10: Simulations in Pumas
Module 11: Visual Predictive Checks
Path 5: Pumas Workflows
Module 12: Covariate Modeling
Module 13: Censored Data Modeling
Path 6: Reporting in Pumas
Module 14: Reporting
Path 7: Bioequivalence in Pumas
Module 15: Bioequivalence Overview
Module 16: A Course on Bioequivalence
- BE online course: Unit 1 - What is a Bioequivalence study?
- BE online course: Unit 2 - On log transformed data, geometric means, and the log-normal distribution
- BE online course: Unit 3 - A basic example using parallel design, the TOST idea
- BE online course: Unit 4 - Different experimental designs
- BE online course: Unit 5 - The basic linear model for average bioequivalence
- BE online course: Unit 6 - BE with PumasCP
- BE online course: Unit 7 - Understanding marginal means
- BE online course: Unit 8 - Basics of Power Analysis
- BE online course: Unit 9 - Nonparameteric test
- BE online course: Unit 10 - Details of linear and mixed models
- BE online course: Unit 11 - Intro to Narrow Therapeutic Index Drugs (NTIDs)
- BE online course: Unit 12 - Reference scaling with FDA - part I
- BE online course: Unit 13 - Reference scaling with FDA - part II
- BE online course: Unit 14 - On Type III p-values
- BE online course: Unit 15 - Conclusion and other Pumas BE features
Tutorials Catalog
Julia
Fundamentals
Data Wrangling
Plotting
- Introduction to AlgebraOfGraphics.jl
- Grammar of Graphics with AlgebraOfGraphics.jl
- Geometries
- Statistical Visualizations
- Plot Customization
- Using Wide Data Formats
- Advanced Layouts
- Inserting Custom Vertical/Horizontal Lines
- Add Text Labels
- Adjusting Legend Markers
- Empirical Cumulative Density Function Plots
Pumas
Introduction
- Introduction to Pumas
- Fitting models with Pumas
- Covariate models
- Introduction to Noncompartmental Analysis
- Introduction to Superposition in Pumas
- Understanding Interoccasion Variability (IOV) Modeling in Pumas
- Understanding Correlated Interoccasion Variability (IOV) Modeling in Pumas
- Non-Gaussian Random Effect
- Understanding Normal vs LogNormal for Modeling PK Parameters
Advanced Topics
From NONMEM to Pumas
- Comparing NONMEM and Pumas models
- NONMEM style BQL models (M1-M4) in Pumas
- Translation from NONMEM to Pumas of “Case Study I: Building a Covariate Model”
- Translation from NONMEM to Pumas of “Case Study II: Building a PopPK model with multiple doses”
- Translation from NONMEM to Pumas of “Case Study III: Development of a population PKPD model”
Introduction Tutorials to PKPD modeling in Pumas
Simulations
Discrete Response Models
Covariate Selection Methods
Forests Plots
Bayesian Models
Plot Customization
Reporting
Optimal Design
PK Modeling
Introduction to PK Modeling
Oral Absorption & Bioavailability
Multi-Compartment & Complex Dosing
Nonlinear & Special Kinetics
Physiological & Drug-Specific Models
- PK26: Target mediated drug disposition
- PK27: Allometry - Elementary & Complex Dedrick plot
- PK30: Turnover I - SC Dosing of Hormone
- PK31: Turnover II - Intravenous Dosing of Hormone
- PK32: Turnover III - Non-linear Disposition
- PK33: Transdermal input and kinetics
- PK34: Reversible metabolism
- PK40: Enterohepatic recirculation
- PK45: Reversible metabolism of drug A and its metabolite B
- PK47: Plasma protein binding modeling
- PK49: Turnover IV - Factor II data in healthy volunteers
- PK52: Simulated impact of disease on r-hSOD kinetics