Export clock rate covariance matrix and std dev #1284
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Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## master #1284 +/- ##
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+ Coverage 69.87% 69.92% +0.04%
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Files 67 67
Lines 7158 7161 +3
Branches 1744 1745 +1
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+ Hits 5002 5007 +5
+ Misses 1849 1848 -1
+ Partials 307 306 -1
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Exports the clock rate covariance matrix and std dev from the phylogenetic regression performed by TreeTime in augur refine. This information was already available in a TreeTime data structure and it is useful to users who do not know the std dev of their pathogen's clock rate already. Adds functional tests for behavior when no clock rate is provided by the user and when one is. In the latter case, we shouldn't have a covariance matrix.
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Merged after 👍🏻 from Richard on Slack. |
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Description of proposed changes
Exports the clock rate covariance matrix and std dev from the phylogenetic regression performed by TreeTime in augur refine. This information was already available in a TreeTime data structure and it is useful to users who do not know the std dev of their pathogen's clock rate already.
Testing
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