events.conditions: events.conditions

In treats: Trees and Traits Simulations

events.conditions

Description

Inbuilt conditions functions for helping designing events

Usage

events.condition(x, condition, ...)

Arguments

x	the variable to reach for satisfying a condition (see details)
condition	the logical function for triggering the condition (e.g. '<', '==', '!>', etc...).
...	any optional argument specific for that condition (see details)

Details

The following functions allow to design specific conditions for events:

• age.condition: a conditional function based on the time x. Typically this can be translated into "when time reaches the value x, trigger a condition" (see make.events). There is no optional argument for the function.

• taxa.condition: a conditional function based on the number of taxa x. Typically this can be translated into "when the number of taxa reaches the value x, trigger a condition" (see make.events). This function has one optional argument:

  • living, a logical argument whether to consider the number of taxa alive when the condition is checked (default: living = TRUE) or whether to consider all the taxa simulated so far (living = FALSE).

• trait.condition: a conditional function based on the value x of one or more traits. Typically this can be translated into "when a trait reaches a value x, trigger a condition" (see make.events). This function has three optional argument:

  • trait, one or more integer or numeric value designating the trait(s) to consider. By default, trait = 1, thus considering only the first trait to trigger the condition.

  • what, a function designating what to select from the trait values. By default what = max to select the maximal value of the trait when the condition is triggered (but you can use any function like min, mean, sd, etc. or provide your own function).

  • absolute, a logical designating to consider absolute trait values (TRUE) or not (default; FALSE).

More details about the events functions is explained in the treats manual: http://tguillerme.github.io/treats.

Value

This function outputs a "function" to be passed to make.events.

Author(s)

Thomas Guillerme

See Also

treats make.events events.modifications

Examples

## Generating a mass extinction
## 80% mass extinction at time 4
mass_extinction <- make.events(
                      target       = "taxa",
                      condition    = age.condition(4),
                      modification = random.extinction(0.8))

## Set the simulation parameters
stop.rule <- list(max.time = 5)
bd.params <- list(extinction = 0, speciation = 1)

## Run the simulations
set.seed(123)
results <- treats(bd.params = bd.params,
                stop.rule = stop.rule,
                events    = mass_extinction)
## Plot the results
plot(results, show.tip.label = FALSE)
axisPhylo()

## Changing the trait process
## The 95% upper quantile value of a distribution
upper.95 <- function(x) {
    return(quantile(x, prob = 0.95))
} 
## Create an event to change the trait process
change_process <- make.events(
                  target       = "traits",
                  ## condition is triggered if(upper.95(x) > 3)
                  condition    = trait.condition(3, condition = `>`, what = upper.95),
                  modification = traits.update(process = OU.process))

## Set the simulation parameters
bd.params <- list(extinction = 0, speciation = 1)
stop.rule <- list(max.time = 6)
traits    <- make.traits()

## Run the simulations
set.seed(1)
no_change <- treats(bd.params = bd.params,
                  stop.rule = stop.rule,
                  traits    = traits)
set.seed(1)
process_change <- treats(bd.params = bd.params,
                       stop.rule = stop.rule,
                       traits    = traits,
                       events    = change_process)
## Plot the results
oldpar <- par(mfrow = c(1,2))
plot(no_change, ylim = c(-7, 7))
plot(process_change, ylim = c(-7, 7))
par(oldpar)

treats documentation built on June 8, 2025, 1:43 p.m.