Rev Language Reference

setOption - Set a global RevBayes option

Set a global option for RevBayes.

Usage

setOption(String key, String value, Bool save)

Arguments

key : String (pass by value)
The key-identifier for which to set a new value.
value : String (pass by value)
The new value.
save : Bool (pass by const reference)
Save option to file
Default : TRUE

Return Type

void

Details

Runtime options are used to personalize RevBayes and are stored on the local machine. The currently available keys and their associated values are as follows: lineWidth= Screen width when printing (in characters). DEFAULT: 160 outputPrecision= How many significant digits to print for the values of model graph nodes. DEFAULT: 7 printNodeIndex= Print the node indices of a tree as annotations? DEFAULT: true useScaling= Should the partial likelihoods in continuous-time Markov chain (CTMC) models be scaled to avoid underflow? DEFAULT: true scalingDensity= If so, scale CTMC likelihoods every n-th node (min = 1). DEFAULT: 1 tolerance= Tolerance for comparing doubles. DEFAULT: 10e-10 debugMCMC=<0,1> How much work to perform to check MCMC? 0: MCMC run without checks. 1: MCMC run with additional checks at extra CPU time cost. DEFAULT: 0 logMCMC=<0,1,2,3,4> How much logging to perform when checking MCMC? NOTE: This option serves for debugging and should be considered experimental. The exact meaning of individual values may be subject to frequent changes. 0: No information on individual moves written out. 1 or higher: Writes out the generation, within-generation position, and name for each move. 2 or higher: Also writes out posterior, likelihood, prior, and Hastings ratios, and if log likelihood = -Inf or NaN, writes out why this is the case. 3 or higher: Writes out each changed probability density and the name of the corresponding model graph node. 4: Writes out additional details about the mvSlice move (if present). DEFAULT: 0

Example

# compute the absolute value of a real number
getOption("linewidth")

# let us set the linewidth to a new value
setOption("linewidth", 200)

# now let's check what the value is
getOption("linewidth")

See Also

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