search

nextstrain / augur

Pipeline components for real-time phylodynamic analysis
https://docs.nextstrain.org/projects/augur/
GNU Affero General Public License v3.0
268 stars 128 forks source link

Frequency estimation fails with missing data. #582

Open rneher opened 4 years ago

rneher commented 4 years ago

Current Behavior
when the metadata can't be parsed into numerical dates, frequencies fail as reported here: https://github.com/nextstrain/ncov/issues/446

We need to make sure that frequency estimation either fails or gracefully handles missing data points.

rneher commented 4 years ago

the problem is here: https://github.com/nextstrain/augur/blob/master/augur/frequencies.py#L97 when numpy attempts to compute a mean of None. None is returned from here: https://github.com/nextstrain/augur/blob/master/augur/utils.py#L132