# Events modifications Inbuilt modifications functions for helping designing events ```r events.modification(x, ...) ``` ## Arguments - `x`: a numerical value to update. - `...`: any specific argument for the modification (see details). ## Returns This function outputs a `"function"` to be passed to `make.events`. ## Details The following functions allow to design specific modifications for events: * modifications for the target `"taxa"` * `random.extinction`: this function removes (makes extinct) a proportion of living taxa when the event is triggered. The proportion of taxa to remove can be changed with the argument `x`. * `trait.extinction`: this function removes (makes extinct) a number of living taxa based on their trait(s) values when the event is triggered. The trait value is specified with the argument `x`.This function has one optional argument: * condition to specify the condition in relation to that trait value (the default is ``condition = `\\\<``` meaning taxa with a trait value lower that `x` will go extinct). * trait to specify which trait will be affected (the default is `trait = 1`, meaning it will only consider the first trait). * modifications for the target `"bd.params"` * `bd.params.update`: this function updates a `"bd.params"` object within the birth death process. It takes any unambiguous named argument to be passed to `make.bd.params`. For example, to update the speciation from any current rate to a new rate of 42, you can use `bd.params.update(speciation = 42)`. * modifications for the target `"traits"` * `traits.update`: this function updates a `"traits"` object within the birth death process. It takes any unambiguous named argument to be passed to `make.traits`. For example, to update the trait process from the current one to an OU process, you can use `traits.update(process = OU.process)`. * modifications for the target `"modifiers"` * `modifiers.update`: this function updates a `"modifiers"` object within the birth death process. It takes any unambiguous named argument to be passed to `make.modifiers`. For example, to update the speciation from the current process to be dependent to trait values, you can use `modifiers.update(speciation = speciation.trait)`. * modifications for the target `"founding"` * `founding.event`: this function runs an independent birth-death process when the condition is met. This function takes any of the arguments normally passed to `treats` (`"bd.params"`, `"traits"`, `"modifiers"` and `"events"`). The `stop.rule` and other arguments are handled internally: namely the `stop.rule` argument is updated to match the time and number of taxa when the founding event is triggered. **Note that this can lead to the simulation stopping just before reaching the `max.taxa` or `max.living` stop rule**. More details about the `events` functions is explained in the `treats` manual: [http://tguillerme.github.io/treats](http://tguillerme.github.io/treats). ## 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.events` `events.conditions` ## Author(s) Thomas Guillerme

events.modifications function