prepare_full_lambdas: Prepares the entire set of lambda matrices for cla_secsse. It...

In secsse: Several Examined and Concealed States-Dependent Speciation and Extinction

Prepares the entire set of lambda matrices for cla_secsse. It provides the set of matrices containing all the speciation rates

Description

Prepares the entire set of lambda matrices for cla_secsse. It provides the set of matrices containing all the speciation rates

Usage

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").
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.

Value

A list of lambdas, its length would be the same than the number of trait states * num_concealed_states..

Examples

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)

secsse documentation built on Oct. 22, 2023, 1:13 a.m.