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completing_forward_sims.md

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name: python3
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---
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(sec_completing_forwards_simulations)=
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(sec_completing_forward_simulations)=
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# Completing forwards simulations
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# Recapitation: completing a forward simulation
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The ``msprime`` simulator generates tree sequences using the backwards in
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time coalescent model. But it is also possible to output tree sequences
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from [forwards-time](https://doi.org/10.1371/journal.pcbi.1006581)
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The ``msprime`` simulator generates tree sequences using the
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backward-in-time coalescent model. But it is also possible to output tree sequences
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from [forward-time](https://doi.org/10.1371/journal.pcbi.1006581)
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simulators such as [SLiM](https://messerlab.org/slim)
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and [fwdpy11](https://fwdpy11.readthedocs.io/) (see the
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{ref}`sec_tskit_forward_simulations` tutorial).
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There are many advantages to using forward-time simulators, but they
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are usually quite slow compared to similar coalescent simulations. In this
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section we show how to combine the best of both approaches by simulating
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the recent past using a forwards-time simulator and then complete the
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the recent past using a forward-time simulator and then complete the
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simulation of the ancient past using ``msprime``. (We sometimes refer to this
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"recapitation", as we can think of it as adding a "head" onto a tree sequence.)
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coalesced_ts.draw_svg()
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```
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The trees have fully coalesced and we've successfully combined a forwards-time
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The trees have fully coalesced and we've successfully combined a forward-time
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Wright-Fisher simulation with a coalescent simulation: hooray!
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(sec_completing_forward_simulations_input_roots)=
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## Why keep input roots (i.e., the initial generation)?
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## Topology gotchas
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The trees that we output from this combined forwards and backwards simulation
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The trees that we output from this combined forward and backward simulation
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process have some slightly odd properties that are important to be aware of.
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In the example above, we can see that the old roots are still present in both trees,
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even through they have only one child and are clearly redundant.
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2. If you are computing the overall tree "height" by taking the time of the
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root node, you may overestimate the height because there is a unary edge
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above the "real" root (this would happen if one of the trees had already
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coalesced in the forwards-time simulation).
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coalesced in the forward-time simulation).
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For these reasons it may be better to remove this redundancy from your
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computed tree sequence which is easily done using the

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