1d:T738,# Basic Qmatrix Sets a Q matrix where double transitions are not allowed 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()`. ```r 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")`. 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. ## Returns Q matrix that includes both examined and concealed states, it should be declared as the third element of idparslist. ## Examples ```r 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 ```1e:T49a,M7.49933 0.25C3.49635 0.25 0.25 3.49593 0.25 7.50024C0.25 10.703 2.32715 13.4206 5.2081 14.3797C5.57084 14.446 5.70302 14.2222 5.70302 14.0299C5.70302 13.8576 5.69679 13.4019 5.69323 1

q_doubletrans function