# make.events Making events objects for treats ```r make.events( target, condition, modification, add, test = TRUE, event.name, replications = 0, additional.args ) ``` ## Arguments - `target`: What to modify, can be `"taxa"`, `"bd.params"`, `"traits"` or `"modifiers"` (see details). - `condition`: A `function` returning a logical to trigger the event (see details). - `modification`: A `function` bringing the modification to the event (see details). - `add`: Another `"events"` to object to add this event. - `test`: A `logical`, whether to test if the events object will work (default is `TRUE`) - `event.name`: Optional, a `"character"` string to name the event. - `replications`: A numeric or integer value for repeating the event (by default, the event is not repeated: `replications = 0`). - `additional.args`: Optional, a named `list` of additional arguments to be used in the event. ## Returns This function outputs a `treats` object that is a named list of elements handled internally by the `treats` function. ## Details `target` is a `character` to designate what will be affected by the event. It can be either `"taxa"`, `"bd.params"`, `"traits"` or `"modifiers"`. This means that the `condition` and `modification` functions will target this specific part of the algorithm. `condition` must be a function that returns a `logical` value and intakes any of the following arguments: `bd.params`, `lineage`, `traits` and `time`. See `events.conditions` for examples. `modification` must be a function that intakes a first argument named `"x"` an returns any specific type of class that can be handled internally by treats. For example, if `target = "bd.params"` the `modification` function should typically return an updated `bd.params` object (see `make.bd.params`). See `events.modifications` for examples. ## Examples ```r ## 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) ``` ## See Also `treats` `make.bd.params` `make.traits` `make.modifiers` `events.conditions` `events.modifications` ## Author(s) Thomas Guillerme

make.events function