5-6-9-10-11 September 2024

This course will provide an in-depth guide to constructing reproducible, automated workflows for biodiversity data acquisition, cleaning, and analysis in R. These workflows will be applicable to both palaeontological and neontological datasets, allowing for their seamless integration during biodiversity analysis through time and across space. We will discuss how sampling links true and observed diversity patterns and through a series of practicals, you will learn how to interrogate biodiversity datasets to identify basic errors and sampling artefacts, then make robust estimates of diversity and diversification rates. Throughout the course, there will be a strong focus on visualising diversity data to ensure that its limitations can be properly understood during analysis.
To provide the context for these practicals, we will discuss theory on the processes which generate biodiversity and its spatial and temporal patterns in both modern and palaeontological contexts, including latitudinal gradients, hotspots, and mass extinctions, and popular hypotheses of how relevant patterns were shaped.

The course is aimed at students, researchers, and practitioners at any career stage with an interest in analysing biodiversity through time and across space. Participants should be accustomed to working with computers, have a good internet connection, and preferably a webcam, as the live online sessions are intended to be highly interactive. Prior experience with base R is recommended (at least an awareness of basic R object and data types). All R scripts will be provided and explained in detail, along with the key R packages which support their workflows, enabling participants to flexibly deploy these tools to meet the demands of their own questions and datasets.

- Understanding of biological occurrence data and their structure, key databases and their limitations.

- Working knowledge of geographic information systems (GIS), chronostratigraphy and palaeogeographic models in R

- An overview of the diversification process, structuring of taxonomic diversity through time and across space, and diversity/diversification rate metrics.

- Understanding of sampling biases, the practical problems they pose for biodiversity analysis, and tools which can help alleviate these issues.

- Appreciation for empirical patterns of diversity through geological time and across geographic space, and how to test hypotheses for these phenomena.

PRE-COURSE (optional)

- Self-guided introduction / refresher on base R language


Thursday 5th Sep – Lectures from 15:00 to 18:00 (CST) + 4 hours practicals

- Types of biodiversity data, and the fundamentals of biological occurrences
- Occurrence databases (GBIF, PBDB, Triton, IUCN Red List)
- Introduction to chronostratigraphy and palaeogeography

- Practical: R as a GIS, palaeorotation, and map making using the terra, sf, rnaturalearth, geodata, chronosphere, rpaleoclim and rgplates packages
- Practical: GBIF, PBDB and IUCN Red List APIs for data acquisition, and data cleaning using CoordinateCleaner, scrubr, fuzzySim and fossilbrush

Friday 6th Sep – Lectures from 15:00 to 18:00 (CST) + 4 hours practicals

- Spatial diversity concepts (alpha, beta gamma)
- Uneven and incomplete sampling across space and through time
- Sampling sensitive diversity metrics (Simpson, Shannon, Hill)
- Subsampling approaches (spatial binning, rarefaction, SQS)

- Practical: sampling metrics and discovery curves, spatial and temporal binning using palaeoverse and icosa
- Practical: diversity metrics under incomplete sampling using vegan, divDyn and iNEXT

Monday 9th Sep – Lectures from 15:00 to 18:00 (CST) + 4 hours practicals

- Diversification models (anagenesis, cladogenesis birth-death-sampling processes)
- Phylogenetic diversification rates
- Occurrence-based diversification rates

- Practical: palaeobiological diversification rates using divDyn, time series and detrending

Tuesday 10th Sep – Lectures from 15:00 to 18:00 (CST) + 4 hours practicals

- Introduction to macroecology and macroevolution
- Mass extinctions and evolutionary radiations
- Red Queen and Court Jester
- Biogeographic diversity patterns

- Practical: simple linear model fitting for diversity data
- Practical: climatic drivers of hotspots

Wednesday 11th Sep – Lectures from 15:00 to 18:00 (CST) + 4 hours practicals

- Bridging modern and palaeontological diversity analysis
- Case study on the Permo-Triassic mass extinction (PTME)

- Practical: spatial and temporal diversity patterns across the PTME