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Get speciation rates using the DR statistic (Jetz et al. 2012)

Source: R/estimate_DR.R
estimate_DR.Rd

DR stands for “diversification rate,” but it is ultimately a better estimation of speciation rate than net diversification (Belmaker and Jetz 2015; Quintero and Jetz 2018) and returns results similar to BAMM’s tip speciation rate estimations (Title and Rabosky 2019).

Usage

estimate_DR(tree, label_type = "binomial", occurrences)

Arguments

tree

The dated phylogenetic tree that corresponds with the taxa to be included in a speciation-area relationship

label_type

Either "epithet" or "binomial" (default): describes the type of tip label in the provided tree. If "epithet," only the species epithet will be used to match speciation rates to tips in the returned occurrence dataframe. If "binomial," the full species name (including genus) will be used to match speciation rates to tips in the returned occurrence dataframe.

occurrences

The occurrence record dataframe output from the ssarp pipeline. If you would like to use a custom dataframe, please make sure that there are columns titled "genericName" and "specificEpithet"

Value

A dataframe that includes speciation rates for each species in the occurrence record dataframe

Details

This function uses methodology from Sun and Folk (2020) to calculate the DR statistic for each tip of a given tree and output a dataframe for use in ssarp's speciation-area relationship pipeline. This method also removes any species rows without rates (this is most likely to occur when the tree does not have all of the species included in the occurrence record dataframe). The tree read in the examples below is modified from Patton et al. (2021).

References

  • Belmaker, J., & Jetz, W. (2015). Relative roles of ecological and energetic constraints, diversification rates and region history on global species richness gradients. Ecology Letters, 18: 563–571.

  • Jetz, W., Thomas, G.H, Joy, J.B., Harmann, K., & Mooers, A.O. (2012). The global diversity of birds in space and time. Nature, 491: 444-448.

  • Patton, A.H., Harmon, L.J., del Rosario Castañeda, M., Frank, H.K., Donihue, C.M., Herrel, A., & Losos, J.B. (2021). When adaptive radiations collide: Different evolutionary trajectories between and within island and mainland lizard clades. PNAS, 118(42): e2024451118.

  • Quintero, I., & Jetz, W. (2018). Global elevational diversity and diversification of birds. Nature, 555, 246–250.

  • Sun, M. & Folk, R.A. (2020). Cactusolo/rosid_NCOMMS-19-37964-T: Code and data for rosid_NCOMMS-19-37964 (Version V.1.0). Zenodo. http://doi.org/10.5281/zenodo.3843441

  • Title P.O. & Rabosky D.L. (2019). Tip rates, phylogenies and diversification: What are we estimating, and how good are the estimates? Methods in Ecology and Evolution. 10: 821–834.

Examples

# The GBIF key for the Anolis genus is 8782549
# Read in example dataset filtered from:
#  dat <- rgbif::occ_search(taxonKey = 8782549,
#                           hasCoordinate = TRUE,
#                           limit = 10000)
dat <- read.csv(system.file("extdata",
                            "ssarp_Example_Dat.csv",
                            package = "ssarp"))
#> Warning: file("") only supports open = "w+" and open = "w+b": using the former
#> Error in read.table(file = file, header = header, sep = sep, quote = quote,     dec = dec, fill = fill, comment.char = comment.char, ...): no lines available in input
land <- find_land(occurrences = dat)
#> Error: object 'dat' not found
areas <- find_areas(occs = land)
#> Error: object 'land' not found

# Read tree from Patton et al. (2021), trimmed to Caribbean species
tree <- ape::read.tree(system.file("extdata",
                                   "Patton_Anolis_trimmed.tree",
                                   package = "ssarp"))
#> Warning: empty character string.

occ_speciation <- estimate_DR(tree = tree,
                              label_type = "epithet",
                              occurrences = areas)
#> Error: object 'areas' not found