A reference class storing the settings for recombination block dating.
MutationRate
Numeric vector of length one. Stores the mutation rate to be used when dating blocks.
PValue
Numeric vector of length one. Stores the critical alpha value for testing the signifcance of recombination regions.
BonfCorrection
Logical vector of length one, stores the option of whether the critical value stored in PValue will be corrected.
DateAnyway
Logical vector of length one, sotres the option of whether blocks will be dated despite failing the critical alpha.
MutationCorrection
Character vector of length 1, can be any of the model supported by the ape package. Default is "JC69".
setBonferonni(newBonf)
Set whether the critical value should be subject to bonferroni correction during block significance testing.
setDateAnyway(newValue)
Set whether blocks should be kept and dated even if they fail the significance test.
setMutationCorrection(model)
Set the model of sequence evolution to correct the distances/number of mutations used in block dating algorithm.
setMutationRate(newRate)
Sets a new mutation rate for the settings.
setPValue(newValue)
Set a new critical value for significance testing of recombinant blocks.
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