Johan's K80+I model

example_K80+I.Rev

# read in the data
data <- readDiscreteCharacterData(data_filename)

# read in a tree (this could also be a stochastic tree variable)
tree <- readTrees(tree_filename)[1]

# assign a lognormal prior to the transition/transversion rate
kappa_sd <- 1.0
kappa_mean <- -0.5 * kappa_sd^2
kappa ~ dnLognormal(kappa_mean, kappa_sd)
moves[1] = mvScale(kappa)

# construct the K80 rate matrix
Q := fnK80(kappa)

# assign a uniform prior to the proportion of invariant sites
p_invar ~ dnUniform(0,1)
moves[2] = mvSlide(p_invar, delta=0.1)

# create the phylogenetic substitution model using K80 and +I
seq ~ dnPhyloCTMC(tree=tree,
                  Q=Q,
                  pInv=p_invar,
                  type="DNA",
                  nSites=data.nchar())
               
# treat the data as observed
seq.clamp(data)