Module 2: Paleodiversity Analyses in R

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 19	Day 2: Community diversity
Aug 20-21	Day 3-4: Global diversity

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Day 2: Community diversity

with Wolfgang Kiessling

Purpose

• Introduction to paleodiversity analyses (theory)
• Statistics and diversity metrics
• Mini-assignments in R

Slideshow

• Community diversity

R code

• Alpha_div_2025.R
• Hill_numbers.R
• Beta_div.R
• sqs_Holland.R
• Beta_div_Bangtoupo.R
• Beta_div_Bangtoupo_lecturer.R (lecturer code)

Datasets

• Radiolarians.csv

Reading list

Click to download

Day 3: Global diversity

with Wolfgang Kiessling

Slideshow

• Global diversity

Demo sheet

• FooteMetrics.xls

R code

• ThreeFaunas_new.R
• Sepkoski.R

Datasets

• Gen_link2.csv
• ThreeFaunas.csv
• Stage_sepk.CSV

Day 4: Global diversity dynamics using divDyn

with Ádám Kocsis

Material

• 0. Subsampling again (subsampling.R) - Script written during lecture: (subsampling_adam.R)
• 1. Diversity dynamics - again!
• 2. divDyn - Practicals - Script written during lecture: (divDyn_adam.R)
• 3. The coral example on Evolv-ED

Additional

• Scripts: binningCompare.R
• Result: pbdb_processed_2025-08-19.rds

Other

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