Biodiversity Facets Practical Session

Matthias Grenié & Marten Winter May 02 2022

This the first practical session in the course “Macroecology and Macroevolution under Global Change”. This it the practical session companion to the lectures on biodiversity facets L2 and L3.

Year: 2022

Instructors: Matthias Grenié & Marten Winter

Contact us via Slack or email for any further questions.

Goals

• Manipulate research open data;
• Learn how to compute functional diversity indices with fundiversity (load trait data, build a functional space, compute indices);
• Learn how to compute phylogenetic diversity indices with ape and picante (load phylogenetic tree, visualize phylogenetic tree, compute indices);
• Familiarize with null models;
• Know the difference between facets of functional and phylogenetic diversity indices;
• Visualize biodiversity facets on the map;
• Show the effect of logging in a tropical forest context on some biodiversity facets.

How to use it?

1. Online It is accessible online at https://rekyt.github.io/biodiversity_facets_tutorial/ click on Setup in the navigation bar to access the tutorial.
2. Online if the website have issue you can access a similar version with the following command: https://htmlpreview.github.io/?https://github.com/Rekyt/biodiversity_facets_tutorial/blob/main/docs/index.html
3. Offline You can download the merged diversity_facets_tutorial.Rmd file by clicking the button below.
4. Offline You can also open the diversity_facets_tutorial.R file in RStudio to get only the code to execute exactly the codes here.

Download Single Rmd file Download Single R file

Data provenance

The data we’ll be using throughout the tutorial comes from the following article:

Döbert, T.F., Webber, B.L., Sugau, J.B., Dickinson, K.J.M. and Didham, R.K. (2017), Logging increases the functional and phylogenetic dispersion of understorey plant communities in tropical lowland rain forest. J Ecol, 105: 1235-1245. https://doi.org/10.1111/1365-2745.12794

The data has been deposited on a open data repository called dryad with the following reference:

Döbert, Timm F. et al. (2018), Data from: Logging increases the functional and phylogenetic dispersion of understorey plant communities in tropical lowland rainforest, Dryad, Dataset, https://doi.org/10.5061/dryad.f77p7

Download Original Data Files

Going Further

Other courses on biodiversity facets and potential interesting papers & tools:

• The FD package is the reference package to compute functional diversity indices.
• The Modern concepts and methods in Macroecology and Biogeography course accessible with this link: http://htmlpreview.github.io/?https://github.com/patrickweigelt/MCMMB/blob/master/index.html.
• The Legras et al. 2018 paper on functional diversity concepts.
• The Community Phylogenetics in R Workshop by Pedro Henrique P. Braga and Katherine Hébert.

License

CC-BY 4.0 Matthias Grenié