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Commits on Jul 7, 2023

• Removed unused files (PhyloDeep clusters)

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• Simulation README update

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• Ebola README updated

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• v0.7

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Commits on Jun 30, 2023

• Allowing for different policies for u estimation (min, max, median, mean times) and estimating it on multiple introductions

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Commits on Jun 29, 2023

• Removed the script to cut a tree into introductions to a country.

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• A script to cut a tree into introductions to a country

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  acdf304

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• Fixed SLE forest extraction: keep all the pending tips

  annazhukova

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• Fixed SLE forest extraction: keep all the pending tips

  annazhukova

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Commits on Jun 28, 2023

• Removed T from the C++ code.

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Commits on Jun 26, 2023

• Estimating u as a median tree time when tree-specific times are used.

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Commits on Jun 22, 2023

• Allowing u to be either fixed or estimated

  annazhukova

  committed
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Commits on Jun 1, 2023

• Rerun times pipeline

  annazhukova

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• v0.5

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  committed
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• Ebola analyses

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• Ebola analyses

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• Ebola analyses: removed unused file production

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• Ebola analyses

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Commits on May 30, 2023

• Removed unused u code

  annazhukova

  committed
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• Estimating u along with other parameters rather than inputting it as a user-defined argument

  annazhukova

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Commits on May 22, 2023

• Testing estimates with different values of u

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Commits on May 16, 2023

• Updated bdei version for likelihood stat calculation

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• pyBDEI v0.4

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Commits on Mar 30, 2023

• Fixed likelihood calculation

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  committed
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Commits on Mar 8, 2023

• removing non-convergent BEAST2 runs from the comparison

  annazhukova

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Commits on Dec 9, 2022

• Fixed Linux install info

  annazhukova

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  934f90b

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• Updated docker info

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• Updated preprint

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  eef0266

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• Added Licence

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• Added Licence

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Commits on Nov 7, 2022

• Updated time counts and added u=0 for Ebola

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• Updated time counts for simulated data

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• Updated Dockerfile

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• Counting CI estimation in time; flexible debug

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Commits on Aug 4, 2022

• SLE data analysis

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