# Simulate under a GeoHiSSE model Simulation function for the GeoHiSSE model ```r SimulateGeoHiSSE(pars, hidden.traits=1, x0="0A", max.taxa=Inf, max.time=Inf, add.jumps=FALSE, add.extinction=FALSE, include.extinct=FALSE, return.GeoHiSSE_pars=FALSE, override.safeties=FALSE) ``` ## Arguments - `pars`: an object of class "GeoHiSSE_pars" generated by `SimulateGeoHiSSE`. See 'Details'. - `hidden.traits`: number of hidden areas in the model. Default is 1. - `x0`: a character value for the starting state. Default is "01A". - `max.taxa`: have the simulation stop at `max.taxa` surviving taxa. - `max.time`: have the simulation stop at `max.time` height (including stem). - `return.GeoHiSSE_pars`: whether to (only) return a "GeoHiSSE_pars" object in the correct format to use in this function. See 'Details'. - `add.jumps`: whether to include jump dispersals in the model. Both for returning the parameters of the model and model estimation. Default is FALSE. - `add.extinction`: whether to separate extirpation and extinction of endemic lineages. Both for returning the parameters of the model and model estimation. Default is FALSE. - `include.extinct`: whether the simulation should keep extinct lineages. Default is FALSE. - `override.safeties`: simulate even if there is no limit on number of taxa or depth of tree. ## Details This function uses `diversitree::tree.classe` function to simulate the tree under the GeoSSE model with hidden states. The parameter `pars` is a list of class "GeoHiSSE_pars" that can be generated using this same function. The best way is to first run `SimulateGeoHiSSE` with empty parameters and `return.GeoHiSSE_pars=TRUE` and with `hidden.areas` equal to the number of desired hidden states in the model. This will return an object in list format with a set of four matrices. Each matrix controls a different set of parameters of the model. All parameters are set to 0 and parameters not used by the model are set to NA. To prepare the simulation, edit these matrices and change the desired parameter values. Leaving a parameter equal to 0 is the same as reducing the model by eliminating this parameter of the model. ## Returns This returns a list, with the following elements: - **$phy**: a phylogeny of class phylo. - **$data**: a data matrix with the species names as the first column and the ranges (in 0, 1, and 2 format) as the second column. - **$hidden.states**: a named vector with the 'true' simulated ranges (include the hidden state information). - **$sim.attempts**: number of times that the simulation tried before reaching desired termination condition. - **$pars**: the parameters used for the simulation. - **$classe.pars**: the parameters in 'make.classe' format for the 'diversitree' package. ## Examples ```r ## Not run: ## Get the a list with the correct parameters to run the simulation: pars <- SimulateGeoHiSSE(hidden.areas=1, return.GeoHiSSE_pars=TRUE) ## Edit the parameter values: pars$model.pars[1:3,] <- 0.1 pars$model.pars[4:5,] <- 0.05 pars$model.pars[6:7,] <- 0.01 pars$q.01[1,2] <- pars$q.01[2,1] <- 0.01 pars$q.1[1,2] <- pars$q.1[2,1] <- 0.02 pars$q.2[1,2] <- pars$q.2[2,1] <- 0.02 ## Run the simulation: sim <- SimulateGeoHiSSE(pars=pars, hidden.areas=1, x0="01A", max.taxa=100) ## End(Not run) ``` ## Author(s) Daniel Caetano

SimulateGeoHiSSE function