Extinction event increase for species with negative values after some time

[TGuillerme]

Extinction event increase for species with negative values after some time

Simulating a 1D BM trait (default) for a some time with a default birth-death process. Then changing this process where the extinction is more likely for species with negative values.

What does it do?

What function does it uses?	yes/no	comments
Uses make.bd.params	✅
Uses make.traits	✅	default
Uses make.modifications	✅
Uses make.events	✅

bd.params

A speciation rate of 1 and an extinction rate of 0.1 (10%)

my_bd_params <- make.bd.params(speciation = 1, extinction = 0.1)

modifier

The default modifier (normal birth-death rules)

## birth-death rules (default)
default_modifiers <- make.modifiers()

events

An event that modifies the normal modifier and increases the extinction rate by 1 if the trait value if negative (after time 3).

## New condition and new modifier (increasing speciation if trait is negative)
negative.trait.condition <- function(trait.values, lineage) {
    return(parent.traits(trait.values, lineage) < 0)
}
increase.extinction.1 <- function(x, trait.values, lineage) {
  return(x + 1)
}

## Update the modifier
change.speciation <- make.events(
    condition    = age.condition(3),
    target       = "modifiers",
    modification = modifiers.update(speciation = speciation,
                                    condition  = negative.trait.condition,
                                    modify     = increase.extinction.1))

A running example

## My favorite seed
set.seed(42)

## Some stopping rules
my_stop.rule <- list(max.time = 5)

## The simulation
my_simulation <- treats(stop.rule = my_stop.rule,
                        bd.params = my_bd_params,
                        traits    = make.traits(),
                        modifiers = default_modifiers,
                        events    = change.speciation)

plot(my_simulation)

Reference

If you use this template in a publication, please cite:

• treats
• R