Welcome to Module 5: Global diversity dynamics!

When What
Aug 30 Day 8: Sampling standardisation & diversity dynamics (divDyn)
Aug 31 Day 9: Extinction selectivity & survivorship

Day 8 (Morning): Sampling standardisation

with Emma Dunne


Start End Topic
09:00 10:00 Intro to sampling standardisation
10:00 10:15 COFFEE
10:15 12:00 SQS in R (early tetrapods)
12:00 13:30 LUNCH

Files for SQS in R (early tetrapods):

Useful resources:

Bethany Allen’s squares tutorial Gwen Antell’s package kerneval

Reading list

  • Coming soon!

Day 8 (Afternoon):

with Adam Kocsis


From To What
13:30 14:00 Diversity Dynamics - why
14:00 14:15 Coffee Break
14:15 15:30 The Coral Example
15:30 15:45 Coffee Break
15:54 16:15 The Phanerozoic PBDB Dataset



The Coral Example

Day 9 (Morning): Extinction selectivity & survivorship

with Carl J Reddin


From To What
9:00 9:30 Some logistic regression basics
9:30 10:15 Extinction determined by occupancy and its trajectory
10:15 10:30 Coffee break
10:30 11:45 Extinction selectivity by clades and traits
11:45 13:00 Lunch Break


Example Data
Example Code

Day 9 (Afternoon):

with Adam Kocsis


From To What
13:30 14:30 Phanerozoic marine data preparation and coordinate reconstruction
14:30 14:45 Break
14:45 15:45 Working with Paleogeographic Reconstructions
15:45 16:00 Break
16:00 17:00 Icosahedral gridding (and maybe: bioregionalzation examples)
Papers and resources
Chronosphere calls
Data item Chronosphere calls
The Paleobiology Database fetch("pbdb")
PaleoMAP PaleoDEM fetch("paleomap", "dem")
PaleoMAP Paleoatlas fetch("paleomap", "paleoatlas")
PaleoMAP Polygons and rotation fetch("paleomap", "model")
PaleoMAP Paleocoastlines fetch("paleomap", "paleocoastlines")
Natural Earth Land Polygons fetch("NaturalEarth")

Suggested Exercises

1. data
  • Use chronosphere::datasets("pbdb") to find earlier states of the pbdb and repeat the analyses with that!
  • Set the plateperiod argument of the reconstruct function call in 1_data.R to TRUE and compare the reconstruction results with the original results.
  • Repeat the procedure for an arbitrary set of taxa!
  • Try out the reconstruction model with the previous GPlate standard model. You can use the chronosphere::datasets() function to find and download this!
  • The reconstruction part of the script is using a stage-level discrete timescale. Try repeating the process for 10 my bins!
2. Plotting
  • Write a for loop to repeat the plotting of the DEMS and the PaleoCoastlines for all Phanerozoic stages.
  • Write a for loop to repeat the plotting of occurrences on the platesfor all Phanerozoic stages - but instead of using the 5Ma target ages for the reconstructions, reconstruct the collection coordinates and plates to the stage midpoint ages!
3. Icosahedral gridding
  • Experiment with grid resolutions! How does it affect occupancy values?
  • Write a loop to repeat the calculation of grid occupancy values through the the Phanerozoic, and store the values in a genus by stage ID (stg) matrix!