palaeoverse (version 1.4.0)

palaeorotate: Palaeorotate fossil occurrences

Description

A function to estimate palaeocoordinates for fossil occurrence data (i.e. reconstruct the geographic distribution of organisms' remains at time of deposition). Each occurrence is assigned palaeocoordinates based on its current geographic position and age estimate.

Usage

palaeorotate(
  occdf,
  lng = "lng",
  lat = "lat",
  age = "age",
  model = "MERDITH2021",
  method = "point",
  uncertainty = TRUE,
  round = 3
)

Value

A data.frame containing the original input occurrence data.frame and the reconstructed coordinates (i.e. "p_lng", "p_lat"). The "grid" method also returns the age of rotation ("rot_age") and the reference coordinates rotated ("rot_lng" and "rot_lat"). If only one model is requested, a column containing the rotation model used ("rot_model") is also appended. Otherwise, the name of each model is appended to the name of each column containing palaeocoordinates (e.g. "p_lng_GOLONKA"). If uncertainty is set to TRUE, the palaeolatitudinal range ("range_p_lat") and the maximum geographic distance ("max_dist") in km between palaeocoordinates will also be returned (the latter calculated via distGeo).

Arguments

occdf

data.frame. Fossil occurrences to be palaeogeographically reconstructed. occdf should contain columns with longitudinal and latitudinal coordinates, as well as age estimates. The age of rotation should be supplied in millions of years before present.

lng

character. The name of the column you wish to be treated as longitude (defaults to "lng").

lat

character. The name of the column you wish to be treated as latitude (defaults to "lat").

age

character. The name of the column you wish to be treated as the age for rotation (defaults to "age").

model

character. The name(s) of the Global Plate Model(s) to be used to reconstruct palaeocoordinates. See details for available models.

method

character. Method used to calculate palaeocoordinates for fossil occurrences. Either "grid" to use reconstruction files, or "point" (default) to use the GPlates API service. See details section for specific details.

uncertainty

logical. Should the uncertainty in palaeogeographic reconstructions be returned? If set to TRUE (default), the palaeolatitudinal range and maximum geographic distance (in km) between output palaeocoordinates are calculated. This argument is only relevant if more than one Global Plate Model is specified in model.

round

numeric. Numeric value indicating the number of decimal places lng, lat and age should be rounded to. This functionality is only relevant for the "point" method. Rounding can speed up palaeorotation by reducing the number of unique coordinate pairs. Defaults to a value of 3. If no rounding is desired, set this value to NULL.

Developer(s)

Lewis A. Jones

Reviewer(s)

Kilian Eichenseer, Lucas Buffan & Will Gearty

Details

This function can estimate palaeocoordinates using two different approaches (method):

• Reconstruction files: The "grid" method uses reconstruction files from Jones & Domeier (2024) to spatiotemporally link present-day geographic coordinates and age estimates with a discrete global grid rotated at one million-year time steps throughout the Phanerozoic (540--0 Ma). Here, resolution 3 (~119 km spacing) of the reconstruction files is used. All files, and the process used to generate them, are available and documented in Jones & Domeier (2024). If fine-scale spatial analyses are being conducted, use of the "point" method (see GPlates API below) may be preferred (particularly if occurrences are close to plate boundaries). When using the "grid" method, coordinates within the same grid cell will be assigned equivalent palaeocoordinates due to spatial aggregation. However, this approach enables efficient estimation of the past distribution of fossil occurrences. Note: each reconstruction file is ~45 MB in size.

• GPlates API: The "point" method uses the GPlates Web Service to reconstruct palaeocoordinates for point data. The use of this method is slower than the "grid" method if many unique time intervals exist in your dataset. However, it provides palaeocoordinates with higher precision.

Available models and timespan for each method:

• "MERDITH2021" (Merdith et al., 2021)

  • 0--1000 Ma (point)

  • 0--540 Ma (grid)

• "TorsvikCocks2017" (Torsvik and Cocks, 2016)

  • 0--540 Ma (point/grid)

• "PALEOMAP" (Scotese, 2016)

  • 0--1100 Ma (point)

  • 0--540 Ma (grid)

• "MATTHEWS2016_pmag_ref" (Matthews et al., 2016)

  • 0--410 Ma (grid/point)

• "GOLONKA" (Wright et al., 2013)

  • 0--540 Ma (grid/point)

References

• Jones, L.A., Domeier, M. A Phanerozoic gridded dataset for palaeogeographic reconstructions. Sci Data 11, 710 (2024). tools:::Rd_expr_doi("10.1038/s41597-024-03468-w").

• Matthews, K.J., Maloney, K.T., Zahirovic, S., Williams, S.E., Seton, M., and Müller, R.D. (2016). Global plate boundary evolution and kinematics since the late Paleozoic. Global and Planetary Change, 146, 226-250. tools:::Rd_expr_doi("10.1016/j.gloplacha.2016.10.002").

• Merdith, A., Williams, S.E., Collins, A.S., Tetley, M.G., Mulder, J.A., Blades, M.L., Young, A., Armistead, S.E., Cannon, J., Zahirovic, S., Müller. R.D. (2021). Extending full-plate tectonic models into deep time: Linking the Neoproterozoic and the Phanerozoic. Earth-Science Reviews, 214(103477). tools:::Rd_expr_doi("10.1016/j.earscirev.2020.103477").

• Scotese, C., & Wright, N. M. (2018). PALEOMAP Paleodigital Elevation Models (PaleoDEMs) for the Phanerozoic. PALEOMAP Project.

• Torsvik, T. H. & Cocks, L. R. M. Earth History and Palaeogeography. Cambridge University Press, 2016.

• Wright, N., Zahirovic, S., Müller, R. D., & Seton, M. (2013). Towards community-driven paleogeographic reconstructions: integrating open-access paleogeographic and paleobiology data with plate tectonics. Biogeosciences, 10(3), 1529-1541. tools:::Rd_expr_doi("10.5194/bg-10-1529-2013").

See GPlates documentation for additional information and details.

Examples

if (FALSE) {
#Generic example with a few occurrences
occdf <- data.frame(lng = c(2, -103, -66),
                lat = c(46, 35, -7),
                age = c(88, 125, 200))

#Calculate palaeocoordinates using reconstruction files
ex1 <- palaeorotate(occdf = occdf, method = "grid")

#Calculate palaeocoordinates using the GPlates API
ex2 <- palaeorotate(occdf = occdf, method = "point")

#Calculate uncertainity in palaeocoordinates from models
ex3 <- palaeorotate(occdf = occdf,
                    method = "grid",
                    model = c("MERDITH2021",
                              "GOLONKA",
                              "PALEOMAP"),
                    uncertainty = TRUE)

#Now with some real fossil occurrence data!

#Grab some data from the Paleobiology Database
data(tetrapods)

#Assign midpoint age of fossil occurrence data for reconstruction
tetrapods$age <- (tetrapods$max_ma + tetrapods$min_ma)/2

#Rotate the data
ex3 <- palaeorotate(occdf = tetrapods)

#Calculate uncertainity in palaeocoordinates from models
ex4 <- palaeorotate(occdf = tetrapods,
                    model = c("MERDITH2021",
                              "GOLONKA",
                              "PALEOMAP"),
                    uncertainty = TRUE)
}