In-class dynamic: Taming the BEAST tutorial

Instructions: Choose a tutorial from the whole list of BEAST tutorials. Two that stand out:

Create our own reproducible script.

I still have not added these steps to the reproducible script: notebook-log.md.

Take-home message: always read carefully the paper and the documentation of any phylogenetic method you use

Create your own cheatsheet with description, strengths, weaknesses, assumptions and user choices (and other things you find relevant).

Further learning

Checkout all the resources in the Taming the BEAST github repo
Checkout all the BEAST tutorials

Announcements

Final project (deadline coming up)

Final project: 50 points out of 100 total points.
Reproducible script(s) on your github repo: 10 points out of 100 total points
Final presentation: 10 points out of 100 total points

Final project content:

Abstract: 200 words or less
Introduction: convey the background, objective and significance of your analysis
Materials and Methods: describe in details the data and the different methods, software, assumptions or any methodological - choices that you did; appropriately cite other papers or software used
- Use the Methods section in Yi et al (2021) as a template of how to write the Methods section in your project
Results: clearly and effectively describe the results of your analysis
Discussion: summarize the conclusion of your findings and highlight any weaknesses or limitations of your approach
References
Reproducible script: step-by-step description of the methodology that can be easily followed by others. This file should be part of the github repository

Some comments:

There are no page restrictions (based on last year, average of 8-10 pages)
In the Methods section, it is not enough to write “we used X, Y, and Z”. For every software, you should write (not with this wording necessarily):

We used X (reference) which [short description of the methodology]. We chose X because [short description of strengths]. We know that X has the following limitations [short description of weaknesses] and that it has the main following assumptions [short description of the assumptions]. The software X requires the user to input the following parameters: [parameter/user choices selected]

No specific file format: latex, markdown, Rmarkdown, google docs, word
Final project guidelines

Final presentations (on last week of classes)

Final presentation is 7 minutes long (very strict!)
Students divided in the two dates
We meet in class as usual
Students unable to attend in person due to exam or travel conflicts can choose to present remotely or to submit a video recording of their presentation

Student evaluations

Forward me the email after completion of the evaluation and it will count as one HW
- Note that the email does not have information on your answers
I have my own short survey to help me improve the class (on the last class)