# BAMM configuration file for speciation/extinction analysis # ========================================================== # # Format # ------ # # - Each option is specified as: option_name = option_value # - Comments start with # and go to the end of the line # - True is specified with "1" and False with "0" ################################################################################ # GENERAL SETUP AND DATA INPUT ################################################################################ modeltype = speciationextinction # Specify "speciationextinction" or "trait" analysis treefile = %%%% # File name of the phylogenetic tree to be analyzed runInfoFilename = run_info.txt # File name to output general information about this run sampleFromPriorOnly = 0 # Whether to perform analysis sampling from prior only (no likelihoods computed) runMCMC = 1 # Whether to perform the MCMC simulation. If runMCMC = 0, the program will only # check whether the data file can be read and the initial likelihood computed simulatePriorShifts = 1 # Whether to simulate the prior distribution of the number of shift events, # given the hyperprior on the Poisson rate parameter. This is necessary to # compute Bayes factors loadEventData = 0 # Whether to load a previous event data file eventDataInfile = event_data_in.txt # File name of the event data file to load, used only if loadEventData = 1 initializeModel = 1 # Whether to initialize (but not run) the MCMC. If initializeModel = 0, the # program will only ensure that the data files (e.g., treefile) can be read useGlobalSamplingProbability = 1 # Whether to use a "global" sampling probability. If False (0), expects a file # name for species-specific sampling probabilities (see sampleProbsFilename) globalSamplingFraction = 1.0 # The sampling probability. If useGlobalSamplingFraction = 0, this is ignored # and BAMM looks for a file name with species-specific sampling fractions sampleProbsFilename = sample_probs.txt # File name containing species-specific sampling fractions # seed = 12345 # Seed for the random number generator. # If not specified (or is -1), a seed is obtained from the system clock overwrite = 0 # If True (1), the program will overwrite any output files in the current # directory (if present) ################################################################################ # PRIORS ################################################################################ expectedNumberOfShifts = 1.0 # prior on the number of shifts in diversification # Suggested values: # expectedNumberOfShifts = 1.0 for small trees (< 500 tips) # expectedNumberOfShifts = 10 or even 50 for large trees (> 5000 tips) lambdaInitPrior = 1.0 # Prior (rate parameter of exponential) on the initial lambda value for rate # regimes lambdaShiftPrior = 0.05 # Prior (std dev of normal) on lambda shift parameter for rate regimes # You cannot adjust the mean of this distribution (fixed at zero, which is # equal to a constant rate diversification process) muInitPrior = 1.0 # Prior (rate parameter of exponential) on extinction rates lambdaIsTimeVariablePrior = 1 # Prior (probability) of the time mode being time-variable (vs. time-constant) ################################################################################ # MCMC SIMULATION SETTINGS & OUTPUT OPTIONS ################################################################################ numberOfGenerations = %%%% # Number of generations to perform MCMC simulation mcmcOutfile = mcmc_out.txt # File name for the MCMC output, which only includes summary information about # MCMC simulation (e.g., log-likelihoods, log-prior, number of processes) mcmcWriteFreq = %%%% # Frequency in which to write the MCMC output to a file eventDataOutfile = event_data.txt # The raw event data (these are the main results). ALL of the results are # contained in this file, and all branch-specific speciation rates, shift # positions, marginal distributions etc can be reconstructed from this output. # See R package BAMMtools for working with this output eventDataWriteFreq = %%%% # Frequency in which to write the event data to a file printFreq = %%%% # Frequency in which to print MCMC status to the screen acceptanceResetFreq = 1000 # Frequency in which to reset the acceptance rate calculation # The acceptance rate is output to both the MCMC data file and the screen # outName = BAMM # Optional name that will be prefixed on all output files (separated with "_") # If commented out, no prefix will be used ################################################################################ # OPERATORS: MCMC SCALING OPERATORS ################################################################################ updateLambdaInitScale = 2.0 # Scale parameter for updating the initial speciation rate for each process updateLambdaShiftScale = 0.1 # Scale parameter for the exponential change parameter for speciation updateMuInitScale = 2.0 # Scale parameter for updating initial extinction rate for each process updateEventLocationScale = 0.05 # Scale parameter for updating LOCAL moves of events on the tree # This defines the width of the sliding window proposal updateEventRateScale = 4.0 # Scale parameter (proportional shrinking/expanding) for updating # the rate parameter of the Poisson process ################################################################################ # OPERATORS: MCMC MOVE FREQUENCIES ################################################################################ updateRateEventNumber = 0.1 # Relative frequency of MCMC moves that change the number of events updateRateEventPosition = 1 # Relative frequency of MCMC moves that change the location of an event on the # tree updateRateEventRate = 1 # Relative frequency of MCMC moves that change the rate at which events occur updateRateLambda0 = 1 # Relative frequency of MCMC moves that change the initial speciation rate # associated with an event updateRateLambdaShift = 1 # Relative frequency of MCMC moves that change the exponential shift parameter # of the speciation rate associated with an event updateRateMu0 = 1 # Relative frequency of MCMC moves that change the extinction rate for a given # event updateRateLambdaTimeMode = 0 # Relative frequency of MCMC moves that flip the time mode # (time-constant <=> time-variable) localGlobalMoveRatio = 10.0 # Ratio of local to global moves of events ################################################################################ # INITIAL PARAMETER VALUES ################################################################################ lambdaInit0 = 0.032 # Initial speciation rate (at the root of the tree) lambdaShift0 = 0 # Initial shift parameter for the root process muInit0 = 0.005 # Initial value of extinction (at the root) initialNumberEvents = 0 # Initial number of non-root processes ################################################################################ # METROPOLIS COUPLED MCMC ################################################################################ numberOfChains = 4 # Number of Markov chains to run deltaT = 0.01 # Temperature increment parameter. This value should be > 0 # The temperature for the i-th chain is computed as 1 / [1 + deltaT * (i - 1)] swapPeriod = 1000 # Number of generations in which to propose a chain swap chainSwapFileName = chain_swap.txt # File name in which to output data about each chain swap proposal. # The format of each line is [generation],[rank_1],[rank_2],[swap_accepted] # where [generation] is the generation in which the swap proposal was made, # [rank_1] and [rank_2] are the chains that were chosen, and [swap_accepted] is # whether the swap was made. The cold chain has a rank of 1. ################################################################################ # NUMERICAL AND OTHER PARAMETERS ################################################################################ minCladeSizeForShift = 1 # Allows you to constrain location of possible rate-change events to occur # only on branches with at least this many descendant tips. A value of 1 # allows shifts to occur on all branches. segLength = 0.02 # Controls the "grain" of the likelihood calculations. Approximates the # continuous-time change in diversification rates by breaking each branch into # a constant-rate diversification segments, with each segment given a length # determined by segLength. segLength is in units of the root-to-tip distance of # the tree. So, if the segLength parameter is 0.01, and the crown age of your # tree is 50, the "step size" of the constant rate approximation will be 0.5. # If the value is greater than the branch length (e.g., you have a branch of # length < 0.5 in the preceding example) BAMM will not break the branch into # segments but use the mean rate across the entire branch.