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lineageSeed

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Tim Vaughan edited this page Jun 6, 2014 · 2 revisions

In inheritance simulations (defined using InheritanceTrajectory and InheritanceEnsemble specifications), lineages descending from separately introduced individuals are simulated in addition to the total population sizes. The <lineageSeed> element is used to specify an individual to seed such a lineage. It takes the following form:

<lineageSeed spec='Individual'
             time='DOUBLE'
             label='STRING'>
  <population>
</lineageSeed>

The population element specifies the population to which the individual belongs. The optional time attribute specifies the time at which the lineage seed is introduced, with the default value being 0.0: the start of the simulation. The optional label attribute specifies that the node generated by this lineageSeed should be labeled with this string in the Newick and Nexus output types.

It is important to understand that the lineage seeds are added to the existing population when they are introduced. (This is necessary, as there is no way to guarantee that a particular population will not have gone extinct by the chosen seed time.) Thus, if an initial state uses a <populationSize> element to specify that population X[0] has an initial size of 100, but a <lineageSeed> element is used to introduce a lineage seed in that same population at t=0, the total size of the starting population will be 100+1=101.

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