Tutorial: Topology Weighting
By Simon Martin, 29 January 2020
How to run this exercise
For this activity, you will need to connect to the Amazon instance both via a terminal and via RStudio. For the connection via terminal, you can either use a terminal program on your own computer and then connect using SSH (
ssh [email protected]), or you can use the terminal that comes with Guacamole (ec2-XX-XXX-XX-XXX.compute-1.amazonaws.com:8080/guacamole/). Then navigate to the activity folder:
To run R scripts and view pdf files produced with R, open an RStudio connection in your browser (ec2-XX-XXX-XX-XXX.compute-1.amazonaws.com:8787) and navigate to the directory
Topology weighting activity
The activity is available on Simon Martin’s GitHub repository: Topology Weighting.
Topology weighting is a means to quantify relationships between taxa that are not necessarily monophyletic. The method is published in: Martin and Belleghem 2017.