Module 2: Paleodiversity Analyses in R
Welcome to Module 2: Paleodiversity Analyses in R! Across these two days, we’ll focus on how to analyse biodiversity in deep-time through theoretical introductions, hands-on exercises, and mini-assigments in R.
| When | What |
|---|---|
| Aug 23 | Day 3: Community diversity |
| Aug 24 | Day 4: Exploring fossil occurrence data and fossil record biases |
| Aug 25 | Day 5: Global diversity dynamics with traditional approaches |
Day 3: Community diversity
with Wolfgang Kiessling
Purpose
- Introduction to paleodiversity analyses (theory)
- Statistics and diversity metrics
- Mini-assignments in R
Slideshow
R code
Datasets
Reading list
Day 4: Exploring fossil occurrence data and fossil record biases
with Emma Dunne & Lisa Schnetz
Content
There are three main parts to this day and each one has an associated exercise in R:
- Databases in Paleobiology - available databases, futurproofing, accessing the Paleobiology Database and importing datasets into R
- Fossil record biases - exaploring the impact of biases on estimates of diversity through visualisations and simple statistics
- Sampling standardisation - Rarefaction/Extrapolation curves, coverage-based rarefaction with iNEXT, Shareholder Quorum Subsampling (SQS), and squares
Schedule
| From | To | Details |
|---|---|---|
| 9:00 | 10:30 | Databases in paleobiology |
| 10:30 | 10:45 | Coffee |
| 10:45 | 12:00 | Fossil record biases |
| 12:00 | 13:30 | Lunch |
| 13:30 | 15:00 | Sampling standardisation |
| 15:00 | 15:15 | Coffee |
| 15:15 | 16:45 | Sampling standardisation cont. |
Code and files
Slideshows
Suggested papers are hyperlinked in the slideshows - any issues accessing them, just email Emma!
Other useful links
Day 5: Global diversity dynamics
with Ádám Kocsis