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prevalence-filtering: move Step 2 conditions into Materials and tier them

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2/5
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1-3 hours
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74/100
Issue type
Documentation
Clarity
Clearly specified
Activity status
Active
Domain
documentation

Research direction

Read the Materials and Step 2 sections of the prevalence-filtering protocol, including the ADR 0017 revision. Move the listed input conditions into Materials and tier them, then leave only computation-time checks in Step 2; verify that every condition and the missing-data rule are represented consistently.

Written by the indexing model from the issue text.

Description

protocol-revision

Part of #54. Validates today; this is the ADR 0017 revision.

Untiered in Materials

  • L51 "A feature-by-sample abundance table with unique feature and sample identifiers." Reads as must; Step 2 confirms it.
  • L53 "Sample metadata identifying the prespecified cohort and any study, batch, body site, or other grouping used to define the analysis set." Reads as must under the default prevalence_scope.

Only in Step 2, missing from Materials

  • L76 "The threshold must be between 0 and 1 inclusive." Range on prevalence_threshold; Materials gives only the default. must.
  • L92 "every sample in the selected analysis set has a corresponding abundance column or row." must.
  • L97 "Confirm that abundances are numeric, finite, and non-negative." must.
  • L98 "Do not silently treat missing values as zero" and the "prespecified missing-data rule" it refers to, which is an input Materials does not list.
  • L102 "If a detection floor is used, confirm that all abundance values are on a comparable scale." must, conditional on detection_rule.

Stays where it is

  • L104 zero-total sample handling, and L119 n_samples zero. Both are computation-time checks, and the first is the standard's own example.

Once Materials carries these, Step 2 restates it and can shrink to the computation-time checks. Three of the five existing must lines are "must be recorded" provenance rules rather than input conditions; fine to keep, but they are not the checks an executor runs before Step 1.

🤖 Drafted with Claude Code

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