VBiTraining2
Materials for the Vectorbite 2019 Training workshops
The 
2019 Training Workshop
Contents
Welcome to the 2019 edition of the VectorBiTE RCN’s Training workshops!
Schedule
The Workshop will consist of lectures, practicals (where you will be guided) and challenges (where you will work more independently, but in groups, to deliver some specific results (a la Hackathons))).
Training Team: Leah Johnson (LJ); Samraat Pawar (SP): Marta Shocket (MS); Zachary Gajewski (ZG); Francis Windram (FW); Matthew Watts (MW)); Deraj Wilson-Aggarwal (DW)
| Date | Time | Topic | Lead Instructor |
|---|---|---|---|
| Monday, 17th June | 08:30 - 09:00 | General Intro (Including to Open Challenge) and Setting up | SP |
| 09:00 - 10:30 | Practicals: Data, Coding and Packages in R | SP+FW | |
| 10:30 - 11:30 | Break | – | |
| 11:00 - 12:00 | Lecture: Model Fitting (General) + Linear/Non-linear) | SP | |
| 12:00 - 13:00 | Lunch | – | |
| 13:00 - 15:00 | Practicals: Model Fitting & Selection | SP+DW+ZG+FW | |
| 15:00 - 15:30 | Break | – | |
| 15:30 - 16:30 | Lecture: Analyses of Abundance (incl. Time Series) Data | SP + LJ | |
| 16:30 - 17:00 | Practicals: Analyses of Abundance Data | All | |
| Tuesday, 18th June | 08:30 - 09:00 | Q & A | All |
| 09:00 - 10:30 | Practicals: Analyses of Abundance Data | All | |
| 10:30 - 11:00 | Break | – | |
| 11:00 - 12:00 | Lecture+Practical: Likelihoods | LJ | |
| 12:00 - 13:00 | Lunch (Start forming final hackathon teams) | – | |
| 13:00 - 14:00 | Lecture: Bayesian Model Fitting | LJ | |
| 14:00 - 15:00 | Practicals: Bayesian Model Fitting | LJ+MS+ZG | |
| 15:00 - 15:30 | Break | – | |
| 15:30 - 16:30 | Practicals: Bayesian Model Fitting | LJ+MS+ZG | |
| 16:30 - 17:00 | Challenge: Traits/Abundances (Intro) | All | |
| Wednesday, 19th June | 08:30 - 09:00 | Q & A | All |
| 09:00 - 10:30 | Challenge: Traits/Abundances (Hackathon) | All | |
| 10:30 - 11:00 | Break | – | |
| 11:00 - 12:00 | Challenge: Traits/Abundances (Hackathon) | ||
| 12:00 - 13:00 | Lunch (Discuss your Open Challenge project/plan!) | – | |
| 13:00 - 13:30 | Challenge: Traits/Abundances (Review; Q&A) | SP + LJ | |
| 14:00 - 15:00 | Open Challenge (Hackathon) | FW+DW+MS+MW+ZG | |
| 15:00 - 15:30 | Break | – | |
| 14:00 - 15:00 | Open Challenge (Hackathon) | FW+DW+MS+MW+ZG | |
| 15:30 - 17:00 | Open Challenge (Hackathon*) | FW+DW+MS+MW+ZG |
*Presentation the next day - see main workshop schedule.
The Teaching/Learning Tools and Materials
Hardware and Software
Please bring a laptop. We will be using R for all data manipulation and analyses/model fitting. Any operating system (Windows, Mac, Linux) will do, as long as you have R (version 3.2 or higher) installed.
You may use any IDE/ GUI for R (VScode, RStudio, Emacs, etc). For most people, RStudio is a good option. Whichever one you decide to use, please make sure it is installed and test it before the workshop. We have budgeted 30 min at the start of Day 1 in case there are any hardware/software issues.
Workshop content
All the teaching materials, including the lectures, jupyter notebooks (practicals + challenges), code, and data are at this git repository.
The practicals have been written as Jupyter notebooks, and can viewed here. Click on any of the .ipynb files, starting with the Intro.ipynb.
If you would like to use jupyter notebooks yourself (not required for the workshop), have a look at this. Or something else online (google “jupyter”) – lots of installation and beginner user guides on the web.
Pre-work / preparation
We are assuming familarity with R basics. In addition, we recommend that you do the following:
- Go to The Multilingual Quantitative Biologist, and read+work through the Intro R Chapter up to the section on Writing R code. Of course, keep going if you want (there is another chapter, on data in R, parts of which we will actually cover in the Workshop on Day 1 (see schedule above)). In particular, you might want to have a look at ggplot. There is a section on this in the data in R chapter.
- In addition / alternatively to pre-work element (1), here are some resources for brushing up on
Rat the end of the Intro R Chapter you can try. But there are many more resources online (e.g., this and this ) – pick something that suits your learning style).
- In addition / alternatively to pre-work element (1), here are some resources for brushing up on
- Inculcate the coding Jedi inside of you - or the Sith - whatever works.