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Improve two operators, and provide a starting tree generator #19

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Improve two operators, and provide a starting tree generator #19

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Anaphory
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  • Compute logs earlie, to avoid overflow errors
  • Allow sampled ancestors to not sample every leaf (even contemporary leaves!) but only a given list.

Anaphory and others added 3 commits March 23, 2021 16:52
@Anaphory
Move log computation earlier
1b67e9a 
In linguistics, we tend to measure times in years, so heights are in the
order of magnitude of 100s to 1000s, not the 0.1My often found in
biology. In order to avoid overflow errors, the log should be taken
ASAP, and in fact this does not make the computation more expensive.
@Anaphory
Add option to sample a subset of leaves
5295a3a
Fix initialization
c1a3598
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Anaphory commented Mar 25, 2021 •
edited

Currently, this commit fails, because in CompEvol/beast2@e861d5e#diff-83eae796a2334747cb46384b066fe7678ffd80b08c228c6d704041a57a12ac9bL99-L101 the recently introduced method isTreeScaler was renamed to m_bIsTreeScaler, in a commit that otherwise only touches version numbers, years etc.. It looks like a search-and-replace gone awry (@alexeid & @tgvaughan, what do you think?) so I'm hesitant to fix this code to use the new method name.

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alexeid commented Mar 29, 2021 via email

@Anaphory
Modify tree, then set root.
5c93ce3 
This should fix one of the symptoms of CompEvol/beast2#984 and also CompEvol#16
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I have added the suggested small modification I mentioned in #16 to be able to use tree.setRoot() instead of tree.setRootOnly() in the SAWilsonBalding. Do you want to trigger running the workflows, so we see whether I messed with something unpredictably?

@Anaphory Anaphory mentioned this pull request Jul 21, 2021
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Keep Sampled Ancestors as such.
0b2d58e 
The SAWilsonBalding operator was permitted to turn sampled ancestors
into normal tips. For an analysis where certain tips should be kept
sampled ancestors, add a Boolean input (default: false) that aborts the
operator proposal when it is about to do this change.
@Anaphory Anaphory changed the title Improve LeafToSampledAncestorJump operator Improve two operators, and provide a starting tree generator Jul 22, 2021
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Do you still want to merge this, or should I make a separate package for it?

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@Anaphory @alexeid