# BAMM configuration file for phenotypic 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 = trait # Specify "speciationextinction" or "trait" analysis treefile = %%%% # File name of the phylogenetic tree to be analyzed traitfile = %%%% # File name of the phenotypic traits file 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 # 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) betaInitPrior = 1.0 # Prior (rate parameter of exponential) on the initial # phenotypic evolutionary rate associated with regimes betaShiftPrior = 0.05 # Prior (std dev of normal) on the rate-change parameter # You cannot adjust the mean of this distribution (fixed at zero, which is # equal to a constant rate diversification process) useObservedMinMaxAsTraitPriors = 1 # If True (1), will put a uniform prior density on the distribution # of ancestral character states, with upper and lower bounds determined # by the min and max of the observed data traitPriorMin = 0 # User-defined minimum value for the uniform density on the distribution of # ancestral character states. Only used if useObservedMinMaxAsTraitPriors = 0. traitPriorMax = 0 # User-defined maximum value for the uniform density on the distribution of # ancestral character states. Only used if useObservedMinMaxAsTraitPriors = 0. betaIsTimeVariablePrior = 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 ################################################################################ updateBetaInitScale = 1 # Scale operator for proportional shrinking-expanding move to update # initial phenotypic rate for rate regimes updateBetaShiftScale = 1 # Scale operator for sliding window move to update initial phenotypic rate updateNodeStateScale = 1 # Scale operator for sliding window move to update ancestral states # at internal nodes 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 = 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 updateRateBeta0 = 1 # Relative frequency of MCMC moves that change the initial phenotypic rate # associated with an event updateRateBetaShift = 1 # Relative frequency of MCMC moves that change the exponential shift parameter # of the phenotypic rate associated with an event updateRateNodeState = 25 # Relative frequency of MCMC moves that update the value of ancestral # character states. You have as many ancestral states as you have # internal nodes in your tree, so there are a lot of parameters: # you should update this much more often than you update the event-associated # parameters. updateRateBetaTimeMode = 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 ################################################################################ betaInit = 0.5 # Initial value of the phenotypic evolutionary process at the root of the tree betaShiftInit = 0 # Initial value of the exponential change parameter for the phenotypic # evolutionary process at the root of the tree. A value of zero implies # time-constant rates 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 calculated 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.