Update filtering and subsampling docs#222
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joverlee521
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Aug 16, 2024
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joverlee521
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Nice improvement! I only left non-blocking suggestions, but I think all the additions are very helpful.
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significant changes to "Filtering" section added
joverlee521
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Aug 19, 2024
Reword some text and add an example for --query.
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jameshadfield
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Nice additions -- the added "notes" are especially helpful
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victorlin
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Aug 19, 2024
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| Overview | ||
| ======== | ||
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| ``augur filter`` provides the flexibility to choose different subsets of input | ||
| data for various types of analysis. There are several options which can be | ||
| categorized based on the information source and selection method. |
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This new overview portion looks more like reference material that should go on the CLI page. But also, the rest of this page relies heavily on the terminology laid out here. Maybe fine to keep it here and leave the CLI page as a reference for what the options are.
jameshadfield
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Aug 20, 2024
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Looks really good! Thanks for humouring my ideas
genehack
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Aug 20, 2024
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genehack
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some non-blocking suggestions.
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Note that I'm introducing new terminology here: "preliminary" vs. "subsampling" vs. "force-inclusive" filtering options. These are clearly distinct in the order of operations, making these labels helpful for explaining that process. For "preliminary", I had considered a term such as "exclusive" to better contrast with "force-inclusive". However, the expression syntax used for options in this category can be both exclusive (--exclude-where region!=Asia) and inclusive (--min-date 2012). This is also why "inclusive" is not a sufficient name for the "force-inclusive" category. Co-authored-by: James Hadfield <hadfield.james@gmail.com>
Reword the subsampling introduction with *what* it is, followed by examples on *why* paired with *how*. This also allows future sampling methods such as weighted sampling to be added by simply including a new section.
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Description of proposed changes
Prepping for upcoming weighted sampling docs. These changes are applicable to current
augur filterfeatures.Related issue(s)
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