Day Two Pre-workshop Assignment
Overview
Teaching: 0 min
Exercises: 30 minQuestions
What is an ecological network?
Why/How do researchers visualize pairwise interactions and the ecological networks they originate from?
Why/How do researchers quantify pairwise interactions and the networks they originate from?
Objectives
Explore ways to visualize ecological networks
Explore ways to quantify or analyze ecological network
Provide one example of an existing publication that includes interaction data
Articulate benefits of openly sharing research data
Getting Started
Welcome to the description of the pre-workshop assignments for the second day of the Dead Wood 2021 Interaction Data workshop!
You can find the main workshop page here.
In the second day of the Dead Wood 2021 Interaction Data workshop, we’ll be focusing on exploring ways to understand, analyze, visualize, and quantify, ecological networks.
If you haven’t yet introduced yourself in the first pre-workshop assignment, please review/complete part 1. in our second pre-workshop assignment document at https://docs.google.com/document/d/1WaA6xiU6RCpNo6IhHmwSJvHVMQCEycjP-FUngo_MCKE/#. If you’d like to re-use your existing introduction, please copy-paste your existing introduction from the pre-work assignment day 1.
Assignment 1: Introduce Yourself
- Go to https://docs.google.com/document/d/1WaA6xiU6RCpNo6IhHmwSJvHVMQCEycjP-FUngo_MCKE/edit
- Add your name,
- Add your field of work/study/research, and
- Describe a species interaction you enjoy or find interesting.
If you’ve already introduced yourself in the first pre-workshop assignment, feel free to reuse that by copy-pasting it.
If you’d like, you can copy and paste the following example:
Hi, my name is [name]. The pronouns I use are [pronouns]. I am interested in [field of study/research/work]. In this workshop, I’d like to [goals]. One of my favorite biotic interaction is that of a [describe a species interaction].
To help you get started, I filled out mine:
Hi, my name is Jorrit. The pronouns I use are he, him, his. I am interested in biodiversity informatics, open science, and software engineering. In this workshop, I’d like to better understand how to make it easier for students/researchers to share and reuse species interaction data. One of my favorite interactions is of this bird (Sula leucogaster) riding on the back of a sea turtle (Chelonia mydas). See https://www.inaturalist.org/observations/10161815 .
Now, to warm up and prepare for Dr. Talya Hackett’s “Introduction to Network Ecology” and the group assignments that follow, please sharing an example of a definition of what a ecological network is. Also, please provide some published examples of visualizations and quantifications (e.g., network statistics, metrics) you find useful and challenging.
If you need inspiration, you might want to review the literature that Dr. Talya Hackett suggested below.
What is an Ecological Network?
Many definitions of ecological networks exist and are used.
`Assignment 2: Definition of Ecological Network
describe, in your own words, what an ecological network is.
(extra credit) find a cited quote of such definition in published work
please prefix your contributions with your name in parenthesis
Published Ecological Network Visualizations
Species interactions drive the ecological engines that keep us alive. Bluntly said: without pollinators, crops would fail, without predators, populations would grow unchecked. Also recent events suggest that better understanding specific species interactions (e.g., virus-host interactions like bat zoonoses) may help us better predict, manage, or even prevent future pandemics.
Assignment 3a: Published Network Visualizations I Find Useful
Look for a published figure or diagram that contains a visualization of a network that you find useful.
Include a screenshot/image of the visualization in https://docs.google.com/document/d/1WaA6xiU6RCpNo6IhHmwSJvHVMQCEycjP-FUngo_MCKE/edit#heading=h.56n9eiwqsrm1
Provide a short description of why you find the visualization useful.
Include a citation to the publication in which you found the figure/ diagram
Make sure that your figure is not yet included by someone else.
Some visualization are more useful then others, especially when working with complex data like ecological networks.
In the following example, please try and find an example of a published network visualization that you find challenging to interpret and understand. Note that visualization can be beautiful and not so useful at the same time.
Assignment 3b: Published Network Visualizations I Find Challenging
Look for a published figure or diagram that contains a visualization of a network that you find challenging.
Include a screenshot/image of the visualization in https://docs.google.com/document/d/1WaA6xiU6RCpNo6IhHmwSJvHVMQCEycjP-FUngo_MCKE/edit#heading=h.stvhgw7shsa
Provide a short description of why you find the visualization less useful that your previous example.
Include a citation to the publication in which you found the figure/ diagram
Make sure that your figure is not yet included by someone else.
Quantifying (Ecological) Networks
Useful visualizations can help understand complex (ecological) network data. And, quantifying networks using network statistics or other metrics might also help get a grasp on characteristics of a network graph (e.g., nodes connected via edges).
As with visualizations, some quantitative methods are more helpful than others.
Assignment 4a: Published Network Metrics I Find Useful
Look for a published example numeric method or metric that characterizes a network that you find useful.
Include a screenshot/quote of your example in https://docs.google.com/document/d/1WaA6xiU6RCpNo6IhHmwSJvHVMQCEycjP-FUngo_MCKE/edit#heading=h.pxidae6seywp
Provide a short description of why you find the method useful.
Include a citation to the publication in which you found the example
Make sure that your example/method is not yet included by someone else.
Also, add an example of a metric or numeric method that you find not so useful, challenging, or potentially misleading.
Assignment 4b: Published Network Metrics I Find Challenging
Look for a published example numeric method or metric that characterizes a network that you find less useful than your previous examples.
Include a screenshot/quote of your example in https://docs.google.com/document/d/1WaA6xiU6RCpNo6IhHmwSJvHVMQCEycjP-FUngo_MCKE/edit#heading=h.pxidae6seywp
Provide a short description of why you find the method challenging or misleading.
Include a citation to the publication in which you found the example
Make sure that your example/method is not yet included by someone else.
Thanks for taking the time to work through these pre-workshop assignments for day two .
Suggested Reading
Please also consider reading the following references suggested by Dr. Talya Hackett.
Suggested ReadingProulx, S., Promislow, D. & Phillips, P., 2005. Network thinking in ecology and evolution. Trends in Ecology & Evolution, 20(6), pp.345–353. Available at: https://doi.org/10.1016/j.tree.2005.04.004
- “[…] a great intro into networks and their applications […]”
Memmott, J., 1999. The structure of a plant‐pollinator food web. Ecology Letters, 2(5), pp.276–280. Available at: https://doi.org/10.1046/j.1461-0248.1999.00087.x
- “[…] the classic start of quantitative plant-pollinator networks so worth knowing for the history of the field […]”
Blüthgen, Nico, Menzel, F. & Blüthgen, Nils, 2006. BMC Ecology, 6(1), p.9. Available at: https://doi.org/10.1186/1472-6785-6-9.
- “[…] a nice overview of a range of metrics and what they can be used for regarding specialisation and traits (and brings up the important issue of using weighted/quantitative networks)[…]”
If you have troubles accessing the articles, please contact the workshop organizers.
What’s Next?
If you are interested to learn more about what is next, please review the workshop schedule for day 2 of your Dead Wood 2021 workshop.
Key Points
Ecological network data can be multi-faceted and complex
Many existing methods exist to visualize and quantify ecological networks