1d:T7c8,# Prepares the entire set of lambda matrices for cla_secsse. It provides the set of matrices containing all the speciation rates ```r prepare_full_lambdas(traits, num_concealed_states, lambd_and_modeSpe) ``` ## Arguments - `traits`: vector with trait states for each tip in the phylogeny. The order of the states must be the same as the tree tips. For help, see `vignette("starting_secsse", package = "secsse")`. When providing a `multiPhylo` set of multiple phylognies, traits should be a list where each entry in the list corresponds to the matching phylogeny on that position. - `num_concealed_states`: number of concealed states, generally equivalent to the number of examined states in the dataset. - `lambd_and_modeSpe`: a matrix with the 4 models of speciation possible. ## Returns A list of lambdas, its length would be the same than the number of trait states * num_concealed_states.. ## Examples ```r set.seed(13) phylotree <- ape::rcoal(12, tip.label = 1:12) traits <- sample(c(0, 1, 2), ape::Ntip(phylotree), replace = TRUE) num_concealed_states <- 3 # the idparlist for a ETD model (dual state inheritance model of evolution) # would be set like this: idparlist <- secsse::cla_id_paramPos(traits, num_concealed_states) lambd_and_modeSpe <- idparlist$lambdas lambd_and_modeSpe[1, ] <- c(1, 1, 1, 2, 2, 2, 3, 3, 3) idparlist[[1]] <- lambd_and_modeSpe idparlist[[2]][] <- 0 masterBlock <- matrix(4, ncol = 3, nrow = 3, byrow = TRUE) diag(masterBlock) <- NA idparlist[[3]] <- q_doubletrans(traits, masterBlock, diff.conceal = FALSE) # Now, internally, clasecsse sorts the lambda matrices, so they look like # a list with 9 matrices, corresponding to the 9 states # (0A,1A,2A,0B, etc) parameter <- idparlist lambda_and_modeSpe <- parameter$lambdas lambda_and_modeSpe[1, ] <- c(0.2, 0.2, 0.2, 0.4, 0.4, 0.4, 0.01, 0.01, 0.01) parameter[[1]] <- prepare_full_lambdas(traits, num_concealed_states, lambda_and_modeSpe) ```1e:T49a,M7.49933 0.25C3.49635 0.25 0.25 3.49593

prepare_full_lambdas function