# Evolve Birth-Death Trees Evolves one or more trees under the BiSSE (Binary State Speciation and Extinction), MuSSE (Multi-State Speciation and Extinction), BiSSE-ness (BiSSE-node enhanced state shift), ClaSSE (Cladogenetic State change Speciation and Extinction), or GeoSSE (Geographic State Speciation and Extinction) model, or a simple character independent birth-death model. For the SSE models, it simultaneously evolves a character that affects speciation and/or extinction, and the tree itself. ```r trees(pars, type=c("bisse", "bisseness", "bd", "classe", "geosse", "musse", "quasse", "yule"), n=1, max.taxa=Inf, max.t=Inf, include.extinct=FALSE, ...) tree.bisse(pars, max.taxa=Inf, max.t=Inf, include.extinct=FALSE, x0=NA) tree.musse(pars, max.taxa=Inf, max.t=Inf, include.extinct=FALSE, x0=NA) tree.musse.multitrait(pars, n.trait, depth, max.taxa=Inf, max.t=Inf, include.extinct=FALSE, x0=NA) tree.quasse(pars, max.taxa=Inf, max.t=Inf, include.extinct=FALSE, x0=NA, single.lineage=TRUE, verbose=FALSE) tree.bisseness(pars, max.taxa=Inf, max.t=Inf, include.extinct=FALSE, x0=NA) tree.classe(pars, max.taxa=Inf, max.t=Inf, include.extinct=FALSE, x0=NA) tree.geosse(pars, max.taxa=Inf, max.t=Inf, include.extinct=FALSE, x0=NA) tree.bd(pars, max.taxa=Inf, max.t=Inf, include.extinct=FALSE) tree.yule(pars, max.taxa=Inf, max.t=Inf, include.extinct=FALSE) prune(phy, to.drop=NULL) ``` ## Arguments - `pars`: Vector of parameters. The parameters must be in the same order as an unconstrained likelihood function returned by `make.x`, for tree type `x`. The MuSSE simulator automatically detects the appropriate number of states, given a parameter vector. - `type`: Type of tree to generate: May be "bisse" or "bd". - `n`: How many trees to generate? - `max.taxa`: Maximum number of taxa to include in the tree. If `Inf`, then the tree will be evolved until `max.t` time has passed. - `max.t`: Maximum length to evolve the phylogeny over. If `Inf` (the default), then the tree will evolve until `max.taxa` extant taxa are present. - `include.extinct`: Logical: should extinct taxa be included in the final phylogeny? And should extinct trees be returned by `trees`? - `x0`: Initial character state at the root (state 0 or 1). A value of `NA` will randomly choose a state from the model's equilibrium distribution for a BiSSE, ClaSSE, or GeoSSE model, but a non-NA value must be specified for MuSSE and QuaSSE. - `n.trait, depth`: For `tree.musse.multitrait` only, these specify the number of binary traits and the style of parameters (with the same meaning as in `make.musse.multitrait`). The `pars` argument then needs to be in the same order as a likelihood function created by `make.musse.multitrait` with these arguments (this interface may be improved in future -- email me if you find this annoying). - `single.lineage`: (`tree.quasse` only): Start simulation with a single lineage? If `FALSE`, then the simulation starts with two lineages in state `x0` (i.e., immediately following a speciation event). - `verbose`: (`tree.quasse` only): print verbose details about tree simuations. This can be reassuring for really large trees. - `...`: Additional arguments - `phy`: A phylogeny, possibly with extinct species, produced by one of the tree evolving functions. - `to.drop`: Optional vector with the species names to drop. ## Details The phylogeny will begin from a single lineage in state `x0`, but the final phylogeny will include only branches above the first split. `tree.bisse` may return an extinct phylogeny, and `trees` might return extinct phylogenies if `include.extinct` is `TRUE`. ## Note There are some logic problems around the creation of zero and one species trees; this will cause occasional errors when running the above functions. Things will change to fix this soon. All these functions may change in the near future. ## Returns A `phylo` phylogenetic tree (ape format), or for `bisse.trees`, a `list` of `phylo` trees. The trees will have an element `tip.state` that contains the binary state information. ## Examples ```r ## Due to a change in sample() behaviour in newer R it is necessary to ## use an older algorithm to replicate the previous examples if (getRversion() >= "3.6.0") { RNGkind(sample.kind = "Rounding") } pars <- c(0.1, 0.2, 0.03, 0.03, 0.01, 0.01) set.seed(3) phy <- tree.bisse(pars, max.taxa=30, x0=0) phy$tip.state h <- history.from.sim.discrete(phy, 0:1) plot(h, phy) ## Retain extinct species: set.seed(3) phy2 <- tree.bisse(pars, max.taxa=30, x0=0, include.extinct=TRUE) h2 <- history.from.sim.discrete(phy2, 0:1) plot(h2, phy2) #### MuSSE: ## Two states pars <- c(.1, .2, .03, .04, 0.05, 0.1) set.seed(2) phy <- tree.musse(pars, 20, x0=1) h <- history.from.sim.discrete(phy, 1:2) plot(h, phy) ## A 3-state example where movement is only allowed between neighbouring ## states (1 <-> 2 <-> 3), and where speciation and extinction rates ## increase moving from 1 -> 2 -> 3: pars <- c(.1, .15, .2, # lambda 1, 2, 3 .03, .045, .06, # mu 1, 2, 3 .05, 0, # q12, q13 .05, .05, # q21, q23 0, .05) # q31, q32 set.seed(2) phy <- tree.musse(pars, 30, x0=1, include.extinct=TRUE) h <- history.from.sim.discrete(phy, 1:3) plot(h, phy, cex=.7) ## And with extinct taxa pruned: phy2 <- prune(phy) h2 <- history.from.sim.discrete(phy2, 1:3) plot(h2, phy2, cex=.7) ## This can all be done in one step (and is by default): set.seed(2) phy <- tree.musse(pars, 30, x0=1) h <- history.from.sim.discrete(phy, 1:3) plot(h, phy, cex=.7) ``` ## Author(s) Richard G. FitzJohn

simulate function