MSA680 Data science for biomedicine Spring 23
This page contains the program of the course: lectures, computer labs, teachers, literature and examination.
Program
The schedule of the course is in TimeEdit.
Exams
Exams from old courses here
Lectures
| Day | Room | Book | Instructor | Content |
|---|---|---|---|---|
| 2022-01-18 | MVF21 | C&L Chapters 1-2 | José Sánchez |
Introduction to course (slides) Introduction to controlled randomised experiments (slides) |
| 2022-01-20 | EC | C&L Chapters 3-4 | Gabriel Abreu | Basic designs and randomisation for controlled experiments (slides) |
| 2022-01-25 | MVF21 | C&L Chapters 7-9 | Gabriel Abreu | Hypothesis testing for efficacy, non-inferiority and bio-equivalence (slides) |
| 2022-01-27 | EA | C&L Chapter 11-12 | Karin Nelander |
Sample size calculation and multiplicity (slides) |
| 2022-02-01 | MVF21 |
C&L Chapter 10 |
Karin Nelander | Survival analysis (slides) |
| 2022-02-03 | Pascal | Lecture notes | Karin Nelander |
Simulation (slides) |
| 2022-02-08 | MVF21 | V&M Chapters 1-4 | José Sánchez | Introduction to linear mixed effects models (slides) |
| 2022-02-10 | Pascal | V&M Chapter 5 | José Sánchez | Estimation for the marginal model (slides) |
| 2022-02-15 | MVF21 | V&M Chapter 6 | José Sánchez | Inference for the marginal model (slides) |
| 2022-02-17 | Pascal | V&M Chapter 7 | José Sánchez | Inference for the random effects (slides) |
| 2022-02-22 | MVF21 | V&M Chapter 8 | José Sánchez | Fitting mixed models (in SAS) (slides) |
| 2022-02-24 | Pascal | Lecture notes/G&H Chapters 11-12 | José Sánchez | Introduction to Bayesian hierarchical models (meta-analysis) (slides) |
| 2022-03-01 | MVF21 | Lecture notes | José Sánchez | Hierarchical models and partial-pooling (lecture notes) |
| 2022-03-03 | Pascal | Lecture notes | José Sánchez | Fitting hierarchical models (in Stan and R) (Meta-analysis code, Radon example code) |
| 2022-03-17 | Exam |
Recommended reading
| Book/Chapter | Section |
|---|---|
| V&M 1-5 | Whole chapter |
| V&M 6 | 6.1 to 6.3.3 |
| V&M 7 | 7.1-7.7 |
| V&M 8 | Whole chapter |
| C&L 1, 2, 3, 4, 7, 8, 9 | Whole chapter |
| C&L 10 |
10.1-10.3 10.4 (Not the part on time dependent covariates) |
| C&L 11 |
11.1-11.3 |
| C&L 12 |
12.6 (Not composite index and subgroup analysis) |
Sofware
- R https://www.r-project.org/
- RStudio https://www.rstudio.com/
- Stan https://mc-stan.org/
- SAS
- SAS OnDemand for Academics
- Course enrollment instructions
- Cours code: d809db1f-b82d-49e0-b47e-f52148818c49
Computer labs
| Files | Computer lab sessions | Report hand-in |
| Lab0 | 2023-01-18 to 2023-01-31 | No report needed |
| Lab1 | 2023-02-01 to 2023-02-14 | 2023-02-14 |
| Lab2 | 2023-02-15 to 2022-02-28 | 2023-02-28 |
| Lab3 | 2023-03-01 to 2023-03-15 | 2023-03-15 |
Contacts
Reference literature
- Design and analysis of Clinical Trials: Concepts and Methodologies, Shein-Chung Chow and Jen-Pei Liu, Third Edition, Wiley. Available as e-book at Chalmers library.
- Linear mixed models for longitudinal data, Geert Verbeke and Geert Molenberghs, Springer Verlag, New York.
- Data analysis using regression and multilevel/hierarchical models, Adrew Gelman and Jennifer Hill, Cambridge University Press.