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Add more information about tree branch-length mode based on fossil calibrations? #1318

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jimallman opened this issue Jun 13, 2023 · 1 comment

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@jimallman
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@LunaSare is interested in a clear indication of whether a tree's branch lengths are based fossil calibration, and whether it's a primary or secondary calibration.

The curation app has several options for a tree’s branch length mode:

  • Expected number of changes per site
  • Expected number of changes
  • Time
  • Bootstrap values
  • Posterior support values
  • Other (describe)
    Screenshot 2023-06-13 at 3 00 58 PM

Time requires ‘Time unit’, so we could add a checkbox: ‘[X] Based on fossil calibration’?

OR add a mode ‘Time based on fossil calibration’, expects ‘Time unit’
...and maybe expects ‘Primary calibration’ vs. ‘Secondary calibration’?

@jimallman
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Related question for @LunaSare: What is your intention for this change? Are we hoping that these settings can be read and used in synthesis? If so, we should use distinct and machine-readable values, as opposed to 'Other (describe)'.

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