This repository will contains the content from the summer school in (model-based) multivariate analysis, organised on 21-25 of July 2025, thanks to funding by Nordic Society Oikos.
See https://bertv.folk.ntnu.no/index.html for more details.
This is a preliminary program and thus subject to change.
The days last from 09:00 to 17:00(ish), and a session after dinner. Each day will consist of a mix of lectures, in-class discussion, live demonstration, and interactive exercises / case studies.
- Welcome, logistics, and overview
- Some background of multivariate methods in ecology
- Generalised Linear Models and multispecies extensions
- Introduction to the gllvm R-package
- Multispecies mixed effects Models
- Background of Joint Species Distribution Models
- Accommodating spatial or temporal autocorrelation
- Phylogenetic mixed models
- Background to ordination
- Accommodating nested study designs
- Bringing covariates into the ordination
- Unimodal/quadratic ordination
- Excursion
- GLLVMs from A-Z: application, results, inference
- Participant presentations (more details TBA, but will operate on a first-come basis)
- (Re)analysing article Part I
- Concepts in model-based clustering
- Other packages for (model-based) multivariate analysis
- (Re)analysing article Part II & General Discussion
- Analysis of own data
| Day | Time | Subject | Lecturer |
|---|---|---|---|
| Monday | 09:00 - 09:30 | Welcome, introduction, getting started | Bert |
| 09:30 - 10:15 | Lecture: Modeling data from ecological communities | ||
| 10:15 - 10:45 | ☕ Break | ||
| 10:45 - 11:15 | Icebreaker/group discussion: properties of community data | ||
| 11:15 - 12:00 | Lecture: Generalised Linear Models for multiple species | ||
| 12:30 - 13:30 | 🍽 Lunch | ||
| 13:30 - 14:30 | Practical 2: Fitting GLMs | ||
| 14:30 - 15:15 | Lecture: Finding a good multispecies GLM | ||
| 15:15 - 15:30 | ☕ Break | ||
| 15:30 - 16:30 | Practical 3: Comparing multispecies GLMs | ||
| 16:30 - 17:15 | Lecture: Introduction to the gllvm R-package | Pekka/Bert | |
| 17:15 - 19:30 | Free time + 🍽 Dinner | ||
| 19:30 - 20:30 | Recap of the day | Bert | |
| --------- | ------------- | ---------------------------------------------------------------- | -------- |
| Tuesday | 09:00 - 09:45 | Lecture: Multispecies mixed effects models | Jenni |
| 09:45 - 10:45 | Practical 4: Fitting mixed-effects models | ||
| 10:45 - 11:15 | ☕ Break | ||
| 11:15 - 12:00 | Lecture: Joint Species Distribution Models (JSDMs) | Pekka | |
| 12:00 - 13:00 | 🍽 Lunch | ||
| 13:00 - 14:00 | Practical 5: Fitting JSDMs | ||
| 14:00 - 14:45 | Lecture: Accommodating spatial or temporal autocorrelation | ||
| 14:45 - 15:15 | ☕ Break | ||
| 15:15 - 16:15 | Practical 6: Spatial or temporal JSDMs | ||
| 16:15 - 17:00 | Lecture: Hierarchical environmental responses | Bert | |
| 17:00 - 19:30 | Free time + 🍽 Dinner | ||
| 19:30 - 20:30 | Practical 7: Traits and the phylogenetic model | Bert | |
| --------- | ------------- | ---------------------------------------------------------------- | -------- |
| Wednesday | 09:00 - 09:45 | Lecture: Model-based ordination | Bert |
| 09:45 - 10:45 | Practical 8: Model-based unconstrained | ||
| 10:45 - 11:15 | ☕ Break | ||
| 11:15 - 12:00 | Lecture: Bringing covariates into the ordination | ||
| 12:00 - 13:00 | 🍽 Lunch | ||
| 13:00 - 14:00 | Practical 9: Ordination with covariates | ||
| 14:00 - 14:45 | Lecture: Conditioning and nested designs | ||
| 14:45 - 15:15 | ☕ Break | ||
| 15:15 - 16:15 | Practical 10: Partial ordination | ||
| 16:15 - 17:00 | Lecture: Unimodal responses | ||
| 17:00 - 19:30 | Free time + 🍽 Dinner | ||
| 19:30 - 20:30 | Practical 11: Unimodal responses | Bert | |
| --------- | ------------- | ---------------------------------------------------------------- | -------- |
| Thursday | 09:00 - 12:00 | 🚶 Excursion | |
| 12:00 - 13:00 | 🍽 Lunch | ||
| 13:00 - 13:45 | Lecture: GLLVMs from A-Z | Audun | |
| 13:45 - 17:00 | 🎤 Participant presentations and beyond | ||
| 17:00 - 19:30 | Free time + 🍽 Dinner | ||
| 19:30 - 20:30 | (Re)analysing article Part I | Bert/Audun | |
| --------- | ------------- | ---------------------------------------------------------------- | -------- |
| Friday | 09:05 - 09:45 | Lecture: Concepts in model-based clustering | Francis |
| 09:45 - 10:30 | Lecture: Other packages for multivariate analysis | Bert | |
| 10:30 - 11:30 | Practical 12: Comparing ordinations | ||
| 11:30 - 12:30 | 🍽 Early lunch | ||
| 12:30 - 14:00 | (Re)analysing article Part II / Discussion | ||
| 14:00 - 16:00 | Analysis of own data |
The latest stable version of all of these packages can be installed from CRAN courtesy of the install.packages function.
- gllvm
- DHARMa
- vegan
- labdsv
- ggplot2
- rnaturalearth
- rnaturalearthdata
- sf
- terra
- glmmTMB (mainly for Friday)
- mvabund (mainly for Friday)
- HMSC (mainly for Friday)
- sjSDM (mainly for Friday)
- ecopCopula (mainly for Friday)
- boral (mainly for Friday)