Global diversity dynamics

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

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Day 8 (Morning): Sampling standardisation

with Emma Dunne

Schedule

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):

• Slideshow
• R code: SQS example (iNEXT v. 2.0.)
• Interval dataset

Useful resources:

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

Reading list

• Coming soon!

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Day 8 (Afternoon):

with Adam Kocsis

Schedule

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

Slides

• Introduction to diversity dynamics and divDyn

divDyn

• CRAN link
• paper
• Phanerozoic-scale marine analysis repository (ddPhanero)

The Coral Example

• Rendered html
• Source R markdown: scleractinian-tutorial_chronos.Rmd
• The paper: web, pdf
• Manual to the divDyn package

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Day 9 (Morning): Extinction selectivity & survivorship

with Carl J Reddin

Schedule

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

Slides

• Slides for logistic regression/extinction selectivity teaching: Extinction selectivity & logistic regression.pptx

Example Data

• Example data for last exercise: Reddin et al. Fossil selectivity supporting data.csv
• Example data for second exercise: dat10.csv
• Example data for last exercise: genus.sizes.ranges.rev.csv

Example Code

• Teaching code used: Logistic_regression.R

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Day 9 (Afternoon):

with Adam Kocsis

Schedule

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)

Code

• Data Preparation: 1_data.R
• Plotting and interaction with paleogeographic reconstructions: 2_plotting.R
• Example uses of icosahedral grids: 3_spatialbins.R
• Bioregionalization example: 4_regionalization.R

Papers and resources

• The PaleoMAP PaleoDEMs
• The PaleoMAP Paleoatlas
• The PaleoMAP Paleocoastlines: article, pdf
• Marine Bioregionalization by Adam: article, pdf
• Intro to the icosa R package: vignette

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!