BEAST 2 Help Me Choose

BEAST 2 Help Me Choose Exchange operator

Exchange operator

Implements branch exchange operations. There is a NARROW and WIDE variety. The narrow exchange is very similar to a rooted-beast.tree nearest-neighbour interchange but with the restriction that node height must remain consistent.

isNarrow (Boolean)

If true (default) a narrow exchange is performed, otherwise a wide exchange.

markclades (Boolean)

Mark all ancestors of nodes changed by the operator as changed, up to the MRCA of all nodes changed by the operator (optional, default: false). This option is used when a Pruned Tree (BEASTLabs) is included in the analyses, and can be left false for Standard template analyses.

weight (Double)

Weight with which this operator is selected (required). See also operator weight tuning

For narrow exchange, the weight is usually set relatively high, where it proposes only local changes to the tree.

Wide exchange is useful during burn-in, but later on during MCMC tends to have low acceptance rate, so the weight is usually set low.

Bayesian evolutionary analysis by sampling trees

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