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

Source: R/secsse_utils.R
q_doubletrans.Rd

This function expands the Q_matrix, but it does so assuming that the number of concealed traits is equal to the number of examined traits, if you have a different number, you should consider looking at the function expand_q_matrix().

Usage

q_doubletrans(traits, masterBlock, diff.conceal)

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").

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.

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