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Ebola dataset broken #115

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jameshadfield opened this issue Jan 26, 2017 · 4 comments
Closed

Ebola dataset broken #115

jameshadfield opened this issue Jan 26, 2017 · 4 comments
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@jameshadfield
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Possible causes:

  • tree time confidence intervals mis-parsed in Auspice
  • globals are specific to zika
@jameshadfield jameshadfield changed the title Solve ebola Ebola dataset broken Jan 26, 2017
@rneher
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rneher commented Jan 26, 2017

not sure what exactly is the issue, but I suspect the you are referring o confidence intervals not overlapping the actual tree node. this can occur in data sets like ebola with very many zero-length branches. in such a case, the most-likely configuration is a very atypical one. (example: the 5-95% confidence of a draw from an exponential distribution does not contain the most likely values). This should be fixed by assigning the marginal ml positions rather than the global ml positions.

@jameshadfield jameshadfield self-assigned this Jan 28, 2017
@jameshadfield
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Thanks @rneher
I'll look into this ASAP (I think there are more issues than just the CIs)

Current appearance of the ebola tree:
image

Timelines of dataset change (c. 6s):
image

@rneher
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rneher commented Jan 28, 2017

set this to false:

https://github.com/nextstrain/auspice/blob/master/src/components/tree/treeView.js#L194

the confidence stuff was just a first shot, prob shouldn't have made its way into master yet.

@jameshadfield
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Closed in PR #156

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