generate_stack: function to perform ABC-SMC

In thijsjanzen/enviDiv:

function to perform ABC-SMC

Description

function to perform ABC-SMC

Usage

generate_stack(
  number_of_replicates = 1000,
  parameters = NULL,
  min_tips = 50,
  max_tips = 150,
  emp_tree = NULL,
  crown_age = NULL,
  write_to_file = FALSE,
  file_name = NULL
)

Arguments

number_of_replicates	number of particles used per iteration of the SMC algorithm
parameters	parameters, a vector with: 1) extinction rate, 2) (sympatric) speciation rate at high water, 3) sympatric speciation rate at low water, 4) allopatric speciation rate at low water, 5) posterior perturbation and 6) the specific model, where 1) model without water level changes, 2) literature water level changes, 3) extrapolated water level changes, 4) standard birth-death model.
min_tips	minimum number of tips
max_tips	maximum number of tips
emp_tree	phy object holding phylogeny of the tree to be fitted on
crown_age	crown age
write_to_file	boolean, if TRUE, results are written to file.
file_name	file name

Value

a tibble containing the results

thijsjanzen/enviDiv documentation built on Feb. 17, 2025, 8:20 p.m.