The params argument is a numeric vector with the parameters specific to the model being used. Here is the meaning of params for each model:
"JC69","F81": These models have no parameters; params should be NULL.
"K80","HKY85","HKY_CODON": params should be a single value representing the transition-transversion ratio (kappa).
"HKY85+Gap": params should be a numeric vector of length 2; the first element represents the transition/transversion ratio (kappa), and the second is the "gap parameter", the factor by which substitution rates are multiplied if they involve an indel event.
"REV": params should be a numeric vector of length 6 (assuming a model with 4 states). With n states the vector should be of length n*(n-1)/2. The first parameter applies to the entry in the 1st row, 2nd column; the next to the 1st row, 3rd column, etc until the end of the first row; the next parameter applies to the 2nd row, 3rd column; etc.
"SSREV": params should be a numeric vector of length 4. Assuming an alphabet "ACGT", the first parameter is the substitution rate from A->C, C->A, T->G, and G->T. The second is the rate from A->G, G->A, T->C, and C->T, The third is the rate from A->T and T->A, and the last is C->G and G->C.
"UNREST": params should be a numeric vector of length n*n-n (where n is the number of states. params fills in the rate matrix starting at the first row going across, skipping diagonals.
"R2": Parameters should be a numeric vector of length 48. There are 16 states in order AA, AC, AG, AT, CA, ..., TT (assuming alphabet order ACGT). Parameters are filled in starting row 1, column 2, going across and then down, filling in the matrix above the diagonal, and reflecting into the matrix below the diagonal. Only cells which represent a substitution which requires exactly one mutation are filled in; cells requiring greater than 1 mutation have rate 0.
"U2": Similar to R2, except parameters are a numeric vector of length 96. Parameters are filled in starting row 1, column to, going across and then down, filling entire matrix (rather than refelcting across the diagonal)
"R2S": Similar to R2, but with strand symmetry. params should be a vector of length 24. Parameters are filled in a similar fashion as R2, except the same parameter applies to substitutions which are strand symmetric.
"U2S": Similar to U2, but with strand symmetry. params should be a vector of length 48. Parameters are filled in a similar fashion as U2, except the same parameter applies to substitutions which are strand symmetric.
"R3","R3S","U3","U3S": Similar to R2, R2S, U2, and U2S, except there are 64 states instead of 16. params should be numeric vector of length 288, 148, 576, or 288, for models R3, R3S, U3, and U3S respectively.
set.rate.matrix.tm(x, params = NULL, scale = TRUE)An object of type tm.
Parameters specific to the substitution model. Should be a numeric vector of length appropriate for the model. See details below.
A logical value. If TRUE, scale the matrix so that the
expected number of mutations per unit time is one per base pair.
An object of type tm with a rate matrix set according
to params.