VectorByte Training Materials 2023

Overview

Pre-work and set-up

Hardware and Software

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 3.6 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 will have a channel on Slack dedicated to software/hardware issues and troubleshooting.

We will also be using Slack for additional support during the training. Please have these installed in advance.

Pre-requisites

We are assuming familiarity with R basics. In addition, we recommend that you do the following:

1. Go to The Multilingual Quantitative Biologist, and read+work through the Biological Computing in R Chapter up to the section on Writing R code. Of course, keep going if you want (although we will cover some similar materials here).

2. In addition / alternatively to pre-work element (1), here are some resources for brushing up on R at 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.

3. Review background on introductory probability and statistics (solutions to exercises)

4. Inculcate the coding Jedi inside of you - or the Sith - whatever works.

Introduction to the VecTraits database¹

• This component will be delivered live & synchronously. The VecTraits website can be found here. It might be an idea to explore this prior to the workshop.

Intro to the VecTraits API

Introduction to traits

• Lecture slides

• Cator et al. 2020. The Role of Vector Trait Variation in Vector-Borne Disease Dynamics

Data Wrangling in R

• Practical
• Datasets:
  • Poundhill Data
  • Poundhill Meta Data
  • Huxley et al Trait Data
  • Genome Size
  • Wrangling Practical Data

Introduction to Linear Models

• Lecture Slides, Lecture Video 1, Lecture Video 2, Practical
• Datasets:
  • Genome Size
  • Huxley et al. Trait Data
  • Linear Models Practical Data

Nonlinear Modeling (including Thermal Performance Curves – TPCs)

• Lecture Slides, Lecture Video, Practical
• Datasets:
  • csm7I Data
  • Aedes juvenile mortality data
  • NLLS Practical Data

Intro to Bayes

• Lecture Slides, Practical 1
• Datasets:
  • Midge data

Bayesian computation and MCMC

• Lecture Slides, Practical 2A

bayesTPC

• Practical
• Datasets:
  • Aedes data

Footnotes

1. What is the difference between VectorBiTE and VectorByte? We are glad you asked! VectorBiTE was an RCN or a research coordination network funded by a 5 year grant from the BBSRC. VectorByte is hosting this training which is a newly funded NSF grant to establish a global open access data platform to study disease vectors. All the databases have transitioned to VectorByte but the legacy options will still be available on the VectorBiTE website.