Reducing speciation rate after a certain time (from a distribution to a fixed value)

[TGuillerme]

Reducing speciation rate after a certain time (from a distribution to a fixed value)

Generates a birth death tree with a random speciation rate (from a uniform distributuion (1; 2)) but changing it to a fixed value of 0.25 after four time units

What does it do?

What function does it uses?	yes/no	comments
Uses make.bd.params	✅	using a distribution of rates
Uses make.traits	❌
Uses make.modifications	❌
Uses make.events	✅

bd.params

A birth death parameter with a uniform speciation distribution between 1 and 2:

random_speciation <- make.bd.params(speciation = runif, 
                                    speciation.args = list(min = 1,
                                                           max = 2))

events

Reducing the speciation rate to a fixed rate of 0.25 after time 4.

reduced.speciation <- make.events(
                      condition = time.condition(4),
                      target = "bd.params",
                      modification = bd.params.update(speciation = 0.25))

A running example

## My favorite seed
set.seed(42)

## Some stopping rules
my_stop.rule <- list(max.time = 6)

## The simulation
my_simulation <- treats(stop.rule = my_stop.rule,
                        bd.params = random_speciation,
                        events    = reduced.speciation)
plot(my_simulation, show.tip.label = FALSE)

Reference

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

• treats
• R