Reserved attributes

Reserved elements

run          must be beast.core.Runnable
distribution must be beast.core.Distribution
operator     must be beast.core.Operator
logger       is beast.core.Logger
data         is beast.evolution.alignment.Alignment
sequence     is beast.evolution.alignment.Sequence
state        is beast.core.State
parameter    is beast.core.parameter.RealParameter
tree         is beast.evolution.tree.Tree
input        reserved name
map          maps element name to class name
plate        macro
mergepoint   reserved for BEAUTi templates
mergewith    reserved for BEAUTi templates

Resolving plug-in class

  • specified in spec attribute
  • if not, get from element2class map
  • if not, use element name (and hope it shows up in the namespace somewhere).

Resolving input name

  • specified in name attribute
  • if not, use (non-reserved) attribute name
  • if not, use element name
  • if input, use ’value’ when there is text content, but no element content

Resolving input value

  • if idref is specified, use the referred object
  • specified in value attribute
  • if not, use value of (non-reserved) attribute
  • if not, use text content when there is text content, but

no element content


Parsing rules

Processing non reserved attributes


Processing non reserved element names


unless ’spec’ is a specified attribute, then that overrides, likewise for ’name’ Processing of text content (only when there are no enclosing elements)



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Bayesian evolutionary analysis by sampling trees

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