- Course title
- USING GEIGER, PHYTOOLS, AND OTHER COMPUTATIONAL TOOLS TO STUDY MACROEVOLUTION ON PHYLOGENIES
- University / Organization
- Transmitting Science S. L.
- Course website (further registration info)
- Academic level
- Both Msc and PhD
- Course director
- Soledad De Esteban Trivigno
- Course lecturer(s)
- Liam Revel and Luke Harmon
- Course aim
- Course contents / programme
- Tuesday, July 16th, 2019.
1. Introduction to phylogenies and the comparative method. [Lecture]
2. Introduction the basics of the R statistical computing environment. [Exercise]
3. Introduction to reading, writing, manipulating, and visualizing phylogenies and comparative data in R. [Exercise]
4. Models of phenotypic trait evolution on trees: Brownian motion. [Lecture]
5. Simulating Brownian motion on trees using R. [Exercise]
6. Introduction to the phylogenetic comparative method: Phylogenetic independent contrasts. [Lecture]
7. Phylogenetic independent contrasts and exploring the properties of contrasts regression using simulation in R. [Exercise]
8. Phylogenetic generalized least squares regression and phylogenetic generalized ANOVA. [Exercise]
Wednesday, July 17th, 2019.
9. Multivariate statistical methods with phylogenies: Phylogenetic principal components analysis, canonical correlation analysis, and other approaches. [Lecture]
10. Phylogenetic PCA and phylogenetic CCA in R. [Exercise]
11. Continuous character models of trait evolution on phylogenies. [Lecture]
12. Fitting continuous character models to univariate trait data in R. [Exercise]
13. Ancestral state reconstruction I: Continuous characters. [Lecture]
14. Reconstructing ancestral states for continuous traits on phylogenies using R. [Exercise]
Thursday, July 18th, 2019.
15. Ancestral state reconstruction II: Discrete characters. [Lecture]
16. Reconstructing ancestral states for discrete traits on phylogenies using R. [Exercise]
17. Exploring the limitations of ancestral state reconstruction for continuous and discrete characters on phylogenies using R. [Exercise]
18. Testing for the influence of one discrete character on a second using Pagel’s (1994) method. [Lecture]
19. Exploring the promise and limitations of the Pagel (1994) method using R. [Exercise]
20. Analysing discrete character coevolution, and the evolution of discrete and continuous characters using the threshold model. [Lecture]
Friday, July 19th, 2019.
21. Fitting models of discrete and continuous character evolution on trees using the threshold model. [Exercise]
22. Multi-rate, multi-regime, and multivariate models of character evolution on phylogenies. [Lecture]
23. Fitting multi-regime and multivariate models for continuous character evolution in R. [Exercise]
24. Visualizing trees and phylogenetic comparative data. [Lecture]
25. Plotting phylogenies and comparative data using R. [Exercise]
26. Wrap-up and optional additional exercise or lecture.
- Required Knowledge and preparation
- Teaching methods
- Starting month
- Course type
- Consecutive days
- Online course
- Duration (net days)
- 2 ECTS (to be validated by the students University)
- Course fee
- 620 €
- Direct e-mail to register
- Paper submission required?
- Logo of institution
- front approval
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