q_doubletrans: Basic Qmatrix Sets a Q matrix where double transitions are...

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

Basic Qmatrix Sets a Q matrix where double transitions are not allowed

Description

This function expands the Q_matrix. If the number of concealed states is not explicitly set by the user, it is assumed to be identical to the number of observed states.

Usage

q_doubletrans(traits, masterBlock, diff.conceal, num_concealed_states = NULL)

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.
masterBlock	matrix of transitions among only examined states, NA in the main diagonal, used to build the full transition rates matrix.
diff.conceal	Boolean stating if the concealed states should be different. E.g. that the transition rates for the concealed states are different from the transition rates for the examined states. Normally it should be FALSE in order to avoid having a huge number of parameters.
num_concealed_states	number of concealed states, generally equivalent to the number of examined states in the dataset.

Value

Q matrix that includes both examined and concealed states, it should be declared as the third element of idparslist.

Examples

traits <- sample(c(0, 1, 2), 45, replace = TRUE) # get some traits
# For a three-state trait
masterBlock <- matrix(99, ncol = 3, nrow = 3, byrow = TRUE)
diag(masterBlock) <- NA
masterBlock[1, 2] <- 6
masterBlock[1, 3] <- 7
masterBlock[2, 1] <- 8
masterBlock[2, 3] <- 9
masterBlock[3, 1] <- 10
masterBlock[3, 2] <- 11
myQ <- q_doubletrans(traits, masterBlock, diff.conceal = FALSE)
# now, it can replace the Q matrix from id_paramPos
num_concealed_states <- 3
param_posit <- id_paramPos(traits,num_concealed_states)
param_posit[[3]] <- myQ

secsse documentation built on May 15, 2026, 5:06 p.m.