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Get tip speciation rates from BAMM (Rabosky 2014) analysis

Source: R/estimate_BAMM.R
estimate_BAMM.Rd

Use the BAMMtools package (Rabosky et al. 2014) to extract tip speciation rates from user-supplied BAMM analysis objects.

Usage

estimate_BAMM(label_type = "binomial", occurrences, edata)

Arguments

label_type

Either "epithet" or "binomial" (default): describes the type of tip label in the tree used for the BAMM analysis. 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"

edata

The eventdata object created by using the BAMMtools::getEventData() function

Value

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

References

  • Rabosky, D.L. (2014). Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees. PLOS ONE, 9(2): e89543.

  • Rabosky, D.L., Grundler, M., Anderson, C., Title, P., Shi, J.J., Brown, J.W., Huang, H., & Larson, J.G. (2014), BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees. Methods in Ecology and Evolution, 5: 701-707.

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.

# Event data file from an external BAMM run
event_data <- system.file("extdata",
                          "event_data_Patton_Anolis.txt",
                           package = "ssarp")

edata <- BAMMtools::getEventData(phy = tree, eventdata = event_data)
#> Error in tabulate(phy$edge, n + m): 'bin' must be numeric or a factor

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