# 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 treefile = Herne_partitioned_fixed_nonzero_rho_MCC.tre # MCC tree with original node heights to avoid negative branch lengths runInfoFilename = Herne_part_fixed_nonzero_const_lowShiftProb.txt sampleFromPriorOnly = 0 # Sample from the posterior runMCMC = 1 # Initialize the MCMC loadEventData = 0 # No previous event data file to load initializeModel = 1 # Start the MCMC useGlobalSamplingProbability = 1 # No lineage-specific sampling probabilities globalSamplingFraction = 0.136 # 54 sampled species over 398 total seed = -1 # Seed for the random number generator obtained from the system clock overwrite = 0 ################################################################################ # PRIORS ################################################################################ expectedNumberOfShifts = 0.1 lambdaInitPrior = 6.06036022835445 lambdaShiftPrior = 0.00717778333673413 muInitPrior = 6.06036022835445 lambdaIsTimeVariablePrior = 0 ################################################################################ # MCMC SIMULATION SETTINGS & OUTPUT OPTIONS ################################################################################ numberOfGenerations = 20000000 # Number of generations to perform MCMC simulation # Changed to value used by Mitchell et al. 2018 mcmcOutfile = Herne_part_fixed_nonzero_const_lowShiftProb_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 = 10000 # Frequency in which to write the MCMC output to a file eventDataOutfile = Herne_part_fixed_nonzero_const_lowShiftProb_event_data.txt # The raw event data (main results) from which all branch-specific speciation # rates, shift positions, marginal distributions, etc. can be reconstructed. eventDataWriteFreq = 10000 # Frequency in which to write the event data to a file printFreq = 1000 # 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 = out # Do not prefix output files with an extra string ################################################################################ # OPERATORS: MCMC SCALING OPERATORS ################################################################################ # NOTE: ALL VALUES DEFAULT 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 ################################################################################ # NOTE: ALL VALUES DEFAULT 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 = 0.1 # 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 = Herne_part_fixed_nonzero_const_lowShiftProb_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 # Allow shifts to occur on all branches. checkUltrametric = 0 # Analyzing extinct taxa implies a non-ultrametric tree observationTime = 160.3967 # Height of the tree minus the time by which we are confident all members of # the clade have gone extinct extinctionProbMax = 0.9999999 # Recommended setting from BAMM-fossil-guidelines.txt updateRatePreservationRate = 1 # MCMC operator; should not affect results updatePreservationRateScale = 1.0 # MCMC operator; should not affect results preservationRatePrior = 1.0 # Prior (mean of exponential) on distribution of preservation rates; default # value of 1 said to be OK for many datasets in BAMM-fossil-guidelines.txt preservationRateInit = 0.1 # Initial value of preservation rate; should not affect results preservationModel = one_rate # Single preservation rate used across the tree: no other models currently # available in BAMM numberOccurrences = 265 # Number of stratigraphically unique species-level observations according to # Mitchell et al. 2018 (p. 13 in the corrected proof) 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.