Welcome to Module 2: Paleodiversity Analyses in R! Across these three 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 06 Day 2: Community diversity
Aug 07 Day 3: Fossil data structure & sampling standardization
Aug 08 Day 4: Global diversity dynamics



Day 2: 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

Click to download


Day 3: Fossil data structure & sampling standardization

with Emma Dunne


Content

There are three main topics related to this day and each one has an associated exercise in R:

  1. Databases in Paleobiology - available databases, futurproofing, accessing the Paleobiology Database and importing datasets into R
  2. Fossil record data structure - exploring the impact of heterogeneous data structures (biases) on estimates of diversity through visualisations and simple statistics
  3. Sampling standardisation - Rarefaction/Extrapolation curves, coverage-based rarefaction with iNEXT, Shareholder Quorum Subsampling (SQS), and squares


Schedule

From To Details
9:15 10:30 Databases in paleobiology
10:30 10:45 Coffee
10:45 12:00 Fossil record data structure
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 me!


Day 4: Global diversity dynamics

with Ádám Kocsis

Slides and material

PBDB Processing (corrected stb top-bottom mixup)

Other

  • Requests for the chronosphere (has to be published data): Form