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calculate Biogeographical Stochastic Mapping (BSM) with BioGeoBEARS

calc_bsm.Rd

This is a wrapper function to the BioGeoBEARS::runBSM(). It uses the result of a BioGeoBEARS model as input to generate realized range area changes across the tree nodes and branches. This mapping is done stochastically based on the model parameters.

Usage

calc_bsm(
  BioGeoBEARS.data,
  phyllip.file,
  tree.path,
  max.maps = 100,
  n.maps.goal = 50,
  seed = NULL,
  save_after_every_try = FALSE,
  ...
)

Arguments

BioGeoBEARS.data

a BioGeoBEARS result model object

phyllip.file

path to the phyllip file used in the original model

tree.path

path for the phylogenetic tree used in the original model

max.maps

maximum number of stochastic maps to try to generate (passed to maxnum_maps_to_try in runBSM() from {BioGeoBEARS})

n.maps.goal

Target number of successfully generated stochastic maps

seed

Optional seed for reproducibility of stochastic simulations.

save_after_every_try

Logical. If TRUE, results will be saved after each attempt (default is FALSE).

...

Additional arguments passed to runBSM() from {BioGeoBEARS}

Value

A list (BSM output) containing the simulated mappings, including ancestral range estimates and event counts. This output is directly produced by runBSM() from {BioGeoBEARS}.

References

Matzke, N. J. (2013). Probabilistic historical biogeography: new models for founder-event speciation, imperfect detection, and fossils allow improved accuracy and model-testing. Frontiers of Biogeography, 5(4).

Dupin, J., et al. (2017). Bayesian estimation of the global biogeographical history of the Solanaceae. Journal of Biogeography, 44(4), 887–899.

Examples

if (FALSE) { # \dontrun{
data("akodon_newick")
data("resDEC")  # BioGeoBEARS model result

bsm_result <- calc_bsm(
  BioGeoBEARS.data = resDEC,
  phyllip.file = system.file("extdata", "geo_area_akodon.data", package = "Herodotools"),
  tree.path = system.file("extdata", "akodon.new", package = "Herodotools"),
  max.maps = 50,
  n.maps.goal = 10,
  seed = 1234
)
} # }