Sequential extinctions removing edges of trait distribution (christmas trees!)

[TGuillerme]

My simulation

This simulation template generates a tree with one trait and four sequential extinction events that remove each time 25% of the species with the highest and lowest trait values. It also incidentally make it look like a christmas tree!

What does it do?

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

bd.params

High speciation parameters to create a bushy tree.

my_bd.params <- make.bd.params(speciation = 1.5, extinction = 0.2)

traits

Default BM trait

my_traits <- make.traits()

events

This event triggers 4 times (every one unit of time) and removes 25% of the extreme valued species

## The triggering conditions (every year)
trigger.year1 <- age.condition(x = 1, condition = `>=`)
trigger.year2 <- age.condition(x = 2, condition = `>=`)
trigger.year3 <- age.condition(x = 3, condition = `>=`)
trigger.year4 <- age.condition(x = 4, condition = `>=`)

## Trimming the tree
trim.the.tree <- function(bd.params, lineage, trait.values) {
    ## Get all the trait values
    parent_traits <- parent.traits(trait.values, lineage,  current = FALSE)

    ## Measure the spread of these values
    boundaries <- sort(range(parent_traits[, 1]))
    spread <- diff(boundaries)
    ## Scale the boundaries to 12.5% each side
    boundaries[1] <- boundaries[1] + spread*0.125
    boundaries[2] <- boundaries[2] - spread*0.125

    ## Select all the nodes that are not the boundary
    selected_nodes <- as.numeric(names(which(!(parent_traits[, 1] <= boundaries[2] & parent_traits[, 1] >= boundaries[1]))))

    ## Make them extinct
    extinct <- which(lineage$parents %in% selected_nodes)
    ## Update the lineage object
    lineage$livings <- lineage$livings[!lineage$livings %in% extinct]
    lineage$n <- length(lineage$livings)
    return(lineage)
}

## Make christmas events
christmas <- make.events(target = "taxa",
                         condition = trigger.year1,
                         modification = trim.the.tree,
                         event.name = "year1")
christmas <- make.events(target = "taxa",
                         condition = trigger.year2,
                         modification = trim.the.tree,
                         event.name = "year2",
                         add = christmas)
christmas <- make.events(target = "taxa",
                         condition = trigger.year3,
                         modification = trim.the.tree,
                         event.name = "year3",
                         add = christmas)
christmas <- make.events(target = "taxa",
                         condition = trigger.year4,
                         modification = trim.the.tree,
                         event.name = "year4",
                         add = christmas)

A running example

## My favorite seed
set.seed(19)

## 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    = my_traits,
                        events    = my_events)

plot(my_simulation)

Reference

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

• treats
• R