["# BAMM configuration file for speciation/extinction analysis ","# ==========================================================","#","# Source: bamm-2.5.0 ","# References: http://bamm-project.org/; https://github.com/macroevolution/bamm","#","# Authors: Daniel Rabosky (BAMM) & Pascal Title (BAMMtools)","# Modified by Maël Doré for deepSTRAPP","#","# 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)","","validateEventConfiguration = 0","# If 1, rejects proposals that cause a branch and both of its direct descendants to have at least one event. ","# Such an event configuration may cause the parameters of the parent event to change to unrealistic values. ","# If 0, no such proposals are immediately rejected. The default value is 0.","","","################################################################################","# PRIORS","################################################################################","","expectedNumberOfShifts = 1.0","# prior on the number of shifts in diversification","# Suggested values: ","#     expectedNumberOfShifts = 1.0 for small trees (< 500 tips)","#\t  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","","outputAcceptanceInfo = 0","# If 1, outputs whether each proposal was accepted. The number identifying the proposal matches the one in the code.","# The default value is 0 (i.e., do not output this information).","","acceptanceInfoFileName = acceptance_info.txt","# The path of the file to which to write whether each proposal was accepted. outputAcceptedInfo must be set to 1 for this information to be written. ","# The default value is acceptance_info.txt.","","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."]