.. highlight:: none Configuration ============= Control File ------------ Configuration options and parameters in BAMM are specified in a *control file*, a plain text file in which each line contains the name of the option or parameter, an equal sign, and the value of the option or parameter:: treefile = whaletree.tre runMCMC = 1 The path of the control file (relative to the current directory) is specified with the flag ``-control`` when running bamm:: ./bamm -control divcontrol.txt Global Options and Parameters ----------------------------- The following describes the configuration options and parameters that are required regardless of the specific model used. For true or false values, 1 is used for true and 0 is used for false. All file paths are relative to the current directory. General ....... treefile The file name of the input tree (in Newick format). sampleFromPriorOnly If true (1), run BAMM by sampling from the prior only (ignoring likelihood contribution to posterior). If false (0), run the full analysis. runMCMC If true (1), run the MCMC sampler. If false (0), just check to see if the data can be loaded correctly. loadEventData *Description not yet available.* eventDataInfile *Description not yet available.* initializeModel Should always be true (1). NumberGenerations Number of MCMC generations to run. MCMC Tuning ........... MeanSpeciationLengthFraction *Description not yet available.* updateEventRateScale *Description not yet available.* localGlobalMoveRatio *Description not yet available.* Priors ...... targetNumber Expeced number of "events" or rate shifts on the tree, if there is no signal in the data. Output ...... mcmcOutfile The file name in which to write the MCMC parameter output. acceptrateOutfile *Description not yet available.* eventDataOutfile *Description not yet available.* treeWriteFreq Frequency (in generations) in which to write speciation/extinction rates. To avoid very large files, use a frequency of at least 10000. mcmcWriteFreq *Description not yet available.* eventDataWriteFreq *Description not yet available.* acceptWriteFreq *Description not yet available.* printFreq Frequency (in generations) in which to write to the screen. Parameter Update Rates ...................... updateRateEventNumber Frequency in which to update the number of events (shifts) on the tree. updateRateEventPosition Frequency in which to move the position of a shift point. updateRateEventRate Frequency in which to update the rate at which events occur. initialNumberEvents *Description not yet available.* Speciation/Extinction Model --------------------------- The following describes the configuration options and parameters for the speciation/extinction model in BAMM. To use this model, run the executable called ``bamm``. General ....... useGlobalSamplingProbability If true (1), use global correction for incomplete taxon sampling in the likelihood calculation. globalSamplingFraction Fraction (0.0 - 1.0) of the total number of species in the clade that are in the tree being analyzed. MCMC Tuning ........... updateLambdaInitScale *Description not yet available.* updateMuInitScale *Description not yet available.* updateLambdaShiftScale *Description not yet available.* updateMuShiftScale *Description not yet available.* minCladeSizeForShift *Description not yet available.* Starting Parameters ................... lambdaInit0 Starting speciation rate. lambdaShift0 Starting rate change parameter for speciation (if 0, speciation rates will not change through time). muInit0 Initial extinction rate. muShift0 *Description not yet available.* Priors ...... lambdaInitPrior Mean of the exponential distribution prior on speciation. lambdaShiftPrior Prior on the speciation rate change parameter. muInitPrior Exponential prior on extinction. muShiftPrior *Description not yet available.* segLength *Description not yet available.* Output ...... lambdaOutfile The file name in which to write branch-specific speciation rates. muOutfile The file name in which to write branch-specific extinction rates. lambdaNodeOutfile *Description not yet available.* Parameter Update Rates ...................... updateRateLambda0 Frequency in which to update the initial speciation rate for an event. updateRateLambdaShift Frequency in which to update how speciation rates change through time. updateRateMu0 Frequency in which to update the initial extinction rate. Phenotypic Evolution Model -------------------------- The following describes the configuration options and parameters for the phenotypic evolution model in BAMM. The parameter "beta" represents the rate of phenotypic evolution at any point in time. To use this model, run the executable called ``bammtrait``. General ....... traitfile The file name the trait data, relative to the current directory. The traits must be continuous characters. Each line must have a species name and the corresponding trait, separated by a tab. No header row is permitted. All species in the trait data file must be in the tree and vice versa. MCMC Tuning ........... updateBetaScale Controls the amount by which to change the value of beta at any step in the MCMC sampling. updateNodeStateScale *Description not yet available.* updateBetaShiftScale *Description not yet available.* Starting Parameters ................... betaInit Initial rate. betaShiftInit Initial time-dependent shift. If negative, it implies a decrease in the rate of phenotypic evolution through time. Priors ...... betaInitPrior *Description not yet available.* betaShiftPrior *Description not yet available.* useObservedMinMaxAsTraitPriors *Description not yet available.* traitPriorMin *Description not yet available.* traitPriorMax *Description not yet available.* Output ...... betaOutfile The file name in which to write the phenotypic rates. nodeStateOutfile *Description not yet available.* Parameter Update Rates ...................... updateRateBeta0 *Description not yet available.* updateRateBetaShift *Description not yet available.* updateRateNodeState Relative rate at which to update individual node state values. This value should, in general, be substantially higher than the other parameter values (recommended 25:1 or 50:1) because there are so many internal nodes states that need to be updated.