# Select MultiState Analysis 1 # Select MCMC mode of analysis 2 # Two-rate model with uniform [0,1] prior: #PriorAll uniform 0 1 #ratedev 5 # One-rate model with uniform [0,1] prior: #restrict q01 q10 #PriorAll uniform 0 1 #ratedev 5 # Two-rate model with exponential mean 1 prior: #prior q01 exp 1 #prior q10 exp 1 #ratedev 2 # One-rate model with exponential mean 1 prior: #restrict q01 q10 #q10 exp 1 #ratedev 2 # Two-rate model with exponential mean 1 prior: #prior q01 exp 1 #prior q10 exp 1 #ratedev 2 # use rjMCMC with exponential prior and uniform [0,10] hyperprior #rjhp exp 0.0 10 #ratedev 0.2 # Chooses a scale parameter so the acceptance rate is 0.2-0.4 #PriorAll uniform 0 1 #ratedev 0.2 # Specify number of iterations iterations 10100000 # Specify burn-in burnin 100000 # Specify sampling frequency sample 10000 # Specify log file LogFile Adox_trait1_MCMC_log # Reconstruct states at the following specified internal nodes #using conditioned and Most Recent Common Ancestor methods # Run the analysis. run