bsm_DES: Biogeographic stochastic mapping for fossil biogeography
In thauffe/simDES: Simulate fossil biogeography

View source: R/bsm_DES.R

bsm_DES

R Documentation

Biogeographic stochastic mapping for fossil biogeography

Description

This function performs a stochastically simulates the biogeographic history of taxa

Usage

bsm_DES(
  DesIn,
  NumBsm = 1,
  MaxAttempts = 1000,
  Step,
  SimD,
  SimE,
  Qtimes = NULL,
  VarD = NULL,
  VarE = NULL,
  Covariate = NULL,
  DivD = NULL,
  DivE = NULL,
  DdE = NULL,
  Cor = "exponential",
  DataInArea = NULL,
  TraitD = NULL,
  VarTraitD = NULL,
  TraitE = NULL,
  VarTraitE = NULL,
  Verbose = FALSE
)

Arguments

`DesIn`	Input file as for a PyRateDES2 analysis
`NumBsm`	Number of biogeographic stochastic maps
`MaxAttempts`	Maximum number of attempts to stochastically simulate the biogeographic history of a single taxon
`Step`	Time steps for the simulation
`SimD`	Dispersal rates
`SimE`	Extinction rates
`Qtimes`	Shift times in dispersal, extinction, and sampling
`VarD`	Strengths of covariate dependent dispersal and in case of logistic correlation the midpoints
`VarE`	Strengths of covariate dependent extinction and in case of logistic correlation the midpoints
`Covariate`	data.frame with the covariate for e.g. environmental dependent dispersal or extinction
`DivD`	Strengths of diversity dependent dispersal
`DivE`	Strengths of diversity dependent extinction
`DdE`	Strengths of dispersal dependent extinction
`Cor`	Correlation with environment or diversity Options 'exponential' or 'logistic'
`DataInArea`	Simulate dynamic in that area
`TraitD`	Data.frame or matrix of a trait influencing dispersal (first column taxon index and second the trait). Either a continuous trait or a binary trait codes as 1 and exp(1) (internal log transformation)
`VarTraitD`	Strengths of trait dependent dispersal
`TraitE`	Continuous influencing extinction (first column taxon index and second the trait). See TraitD for details
`VarTraitE`	Strengths of trait dependent extinction
`Verbose`	Should progress be printed?