victorlin
commented
1 month ago This was discussed recently on Slack with some different ideas. I'll plan to work on this soon so I've updated the issue description with latest ideas.
Commenting on some things from the original issue description:
The simplest way to implement this would be to accept the min/max date format that's natively supported by treetime:
[min:max]as in[2022.3452:2022.3649]
On the Slack discussion the existing ISO standard format <start>/<end> was brought up as a 2nd option. But I do think the brackets are nice. I've proposed a 3rd option. While it doesn't follow any standards, it seemed like the best of both worlds: the brackets convey an inclusive range notation, and : could be problematic down the road if supporting ISO dates with a time part. Both added to the new issue description.
A neater solution might be to allow min and max dates to be specified through two columns:
--min-dateand--max-date.
I'll shoot this down as this would be confusing if/when we're to bring this to augur filter which already has --min-date/--max-date. I think it makes more sense to augment the existing handling of ambiguous dates in the date column with added support for precise date ranges.
This change could potentially be made across all date handling: it would be more general than our current x'ing strategy, e.g.
2021-10-XXfor ambiguous date of month. That'd be a lot of work though.
Making this change across all date handling is the best/easiest way to do it since date handling is centralized under augur/dates. Doing it only in one subcommand would require extra work and cause more confusion to users.
trvrb
jameshadfield
tsibley
Context
Currently, date ranges can only be defined by ambiguous/incomplete dates in the format
YYYY-MM-DDwith some characters swapped in with the wildcard characterX¹. This only allows date ranges to be bounded by start/end of a year or month and not a more precise range within or across year/month boundaries.¹ this could be better documented: https://github.com/nextstrain/augur/issues/882
Scope
Anywhere that currently accepts ambiguous/incomplete dates (i.e. uses
AmbiguousDate):augur filteraugur frequenciesaugur refinePotential solutions
--min-date-column/--max-date-columndatecolumn¹[min:max]whereminandmaxare numeric datesmin/maxwhereminandmaxare ISO dates[min/max]whereminandmaxare any scalar date accepted by Augur (ISO or numeric)¹ there is a feature request to make the date column name customizable: https://github.com/nextstrain/augur/issues/1443
original issue description
Context
To ensure patient privacy, Denmark bins SARS-CoV-2 collection dates to the Monday of the week the actual collection date lies in.
Currently, we seem to be unable to specify such ambiguity within
augur refineeven though treetime supports arbitrarily constrained date ranges.The only workaround right now I can think of is to make the date ambiguous, but that throws away information while also not working in situations where the week crosses a month boundary.
The issue has become particularly noticeable when making BA.2.86 trees where Denmark has provided ~30% of global sequences so far. To remove bias, I could add 3/4 days to the dates, but it would be nice if refine just accepted ranges as such.
Description
Make refine support arbitrary min/max input dates.
Possible solution
The simplest way to implement this would be to accept the min/max date format that's natively supported by treetime:
[min:max]as in[2022.3452:2022.3649](opening bracket, min date as year float, colon, max date as year float, closing bracket)A neater solution might be to allow min and max dates to be specified through two columns:
--min-dateand--max-date.This change could potentially be made across all date handling: it would be more general than our current x'ing strategy, e.g.
2021-10-XXfor ambiguous date of month. That'd be a lot of work though.