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Update min_date/max_date descriptions to support relative dates
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victorlin committed Apr 15, 2022
1 parent 58ca2bb commit 3414503
Showing 1 changed file with 30 additions and 5 deletions.
35 changes: 30 additions & 5 deletions docs/src/reference/configuration.rst
Original file line number Diff line number Diff line change
Expand Up @@ -291,7 +291,12 @@ min_date
~~~~~~~~

- type: string
- description: Argument to ``augur filter`` to set the minimum collection date for strains to include in the subsampling set. Dates can be numeric floating point values (e.g., ``2019.74``) or ISO 8601-style strings (e.g., ``2019-10-01``).
- description: Argument to ``augur filter`` to set the minimum collection date for strains to include in the subsampling set. Dates can be:

1. an Augur-style numeric date with the year as the integer part (e.g. 2020.42) or
2. a date in ISO 8601 date format (i.e. YYYY-MM-DD) (e.g. '2020-06-04') or
3. a backwards-looking relative date in ISO 8601 duration format with optional P prefix (e.g. '1W', 'P1W')

- examples:

- ``--min-date 2019-10-01``
Expand All @@ -303,7 +308,12 @@ max_date
~~~~~~~~

- type: string
- description: Argument to ``augur filter`` to set the maximum collection date for strains to include in the subsampling set. Dates can be numeric floating point values (e.g., ``2019.74``) or ISO 8601-style strings (e.g., ``2019-10-01``).
- description: Argument to ``augur filter`` to set the maximum collection date for strains to include in the subsampling set. Dates can be:

1. an Augur-style numeric date with the year as the integer part (e.g. 2020.42) or
2. a date in ISO 8601 date format (i.e. YYYY-MM-DD) (e.g. '2020-06-04') or
3. a backwards-looking relative date in ISO 8601 duration format with optional P prefix (e.g. '1W', 'P1W')

- examples:

- ``--max-date 2021-04-01``
Expand Down Expand Up @@ -779,7 +789,12 @@ min_date
~~~~~~~~

- type: float or string
- description: Minimum collection date for strains to include in the analysis used by ``augur filter --min-date``. Dates can be numeric floating point values (e.g., ``2019.74``) or ISO 8601-style strings (e.g., ``2019-10-01``).
- description: Minimum collection date for strains to include in the analysis used by ``augur filter --min-date``. Dates can be:

1. an Augur-style numeric date with the year as the integer part (e.g. 2020.42) or
2. a date in ISO 8601 date format (i.e. YYYY-MM-DD) (e.g. '2020-06-04') or
3. a backwards-looking relative date in ISO 8601 duration format with optional P prefix (e.g. '1W', 'P1W')

- default: ``2019.74``

skip_diagnostics
Expand Down Expand Up @@ -951,14 +966,24 @@ min_date
~~~~~~~~

- type: float or string
- description: Earliest date to estimate frequencies for. Dates can be numeric floating point values (e.g., ``2019.74``) or ISO 8601-style strings (e.g., ``2019-10-01``).
- description: Earliest date to estimate frequencies for. Dates can be:

1. an Augur-style numeric date with the year as the integer part (e.g. 2020.42) or
2. a date in ISO 8601 date format (i.e. YYYY-MM-DD) (e.g. '2020-06-04') or
3. a backwards-looking relative date in ISO 8601 duration format with optional P prefix (e.g. '1W', 'P1W')

- default: without value supplied, defaults to 1 year before present

max_date
~~~~~~~~

- type: float or string
- description: Earliest date to estimate frequencies for. Dates can be numeric floating point values (e.g., ``2021.5``) or ISO 8601-style strings (e.g., ``2021-07-01``). Specifying ``max_date`` overrides ``recent_days_to_censor``.
- description: Earliest date to estimate frequencies for. Specifying ``max_date`` overrides ``recent_days_to_censor``. Dates can be:

1. an Augur-style numeric date with the year as the integer part (e.g. 2020.42) or
2. a date in ISO 8601 date format (i.e. YYYY-MM-DD) (e.g. '2020-06-04') or
3. a backwards-looking relative date in ISO 8601 duration format with optional P prefix (e.g. '1W', 'P1W')

- default: without value supplied, defaults to today’s date minus ``recent_days_to_censor`` parameter

recent_days_to_censor
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