# 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.