Skills › Scientific Agent Skills › hypothesis-generation › preregistration_scaffold_template.md
preregistration_scaffold_template.md
137 lines · skills/hypothesis-generation/assets/preregistration_scaffold_template.md at 5f2bc03
1# Preregistration scaffold: {{PROJECT_ID}}
3> **UNREGISTERED DRAFT — NOT AN APPROVAL OR SCIENTIFIC ENDORSEMENT**
4>
5> Generated locally from a structurally validated record last updated {{UPDATED_ON}}. This date is supplied by the record; it is not a generation or registration timestamp. Complete repository-specific fields, obtain required human/ethics/safety/regulatory review, and verify every statement before registration.
Preregistration scaffold: {{PROJECT_ID}}
UNREGISTERED DRAFT — NOT AN APPROVAL OR SCIENTIFIC ENDORSEMENT Generated locally from a structurally validated record last updated {{UPDATED_ON}}. This date is supplied by the record; it is not a generation or registration timestamp. Complete repository-specific fields, obtain required human/ethics/safety/regulatory review, and verify every statement before registration.Raw lines 1 to 6
7## 1. Administrative record
9- Project ID: {{PROJECT_ID}}
10- Accountable human owner: {{HUMAN_OWNER}}
11- Record status: {{RECORD_STATUS}}
12- Record updated: {{UPDATED_ON}}
13- Registration repository and identifier: [TO COMPLETE]
14- Registration timestamp: [TO COMPLETE]
15- Study status and prior access to target data: [TO COMPLETE]
16- Roles, funding, conflicts, sponsor role: [TO COMPLETE]
1. Administrative record
- Project ID: {{PROJECT_ID}}
- Accountable human owner: {{HUMAN_OWNER}}
- Record status: {{RECORD_STATUS}}
- Record updated: {{UPDATED_ON}}
- Registration repository and identifier: [TO COMPLETE]
- Registration timestamp: [TO COMPLETE]
- Study status and prior access to target data: [TO COMPLETE]
- Roles, funding, conflicts, sponsor role: [TO COMPLETE]
18## 2. Authorization and oversight gates
20{{ETHICS_AND_FEASIBILITY}}
22- Human/animal/biosafety/dual-use/data/regulatory determinations and identifiers: [TO COMPLETE]
23- Local policy and jurisdiction checked on: [TO COMPLETE]
24- Unresolved work must not begin until the responsible authority clears it.
2. Authorization and oversight gates
{{ETHICS_AND_FEASIBILITY}}
- Human/animal/biosafety/dual-use/data/regulatory determinations and identifiers: [TO COMPLETE]
- Local policy and jurisdiction checked on: [TO COMPLETE]
- Unresolved work must not begin until the responsible authority clears it.
26## 3. Search boundary and evidence
28{{EVIDENCE_BOUNDARY}}
30- Attach the completed search-boundary record and evidence ledger.
31- “Not located within this boundary” does not establish universal absence or novelty.
32- Verify every citation and claim-to-source link against the primary source.
3. Search boundary and evidence
{{EVIDENCE_BOUNDARY}}
- Attach the completed search-boundary record and evidence ledger.
- “Not located within this boundary” does not establish universal absence or novelty.
- Verify every citation and claim-to-source link against the primary source.
34## 4. Frozen observation
36{{OBSERVATION}}
38- Units, preprocessing, exclusions, missingness, and uncertainty: [TO COMPLETE]
39- Whether expected or selected after inspection: [TO COMPLETE]
4. Frozen observation
{{OBSERVATION}}
- Units, preprocessing, exclusions, missingness, and uncertainty: [TO COMPLETE]
- Whether expected or selected after inspection: [TO COMPLETE]
45## 6. Candidate hypotheses and mechanisms
47{{HYPOTHESES}}
49All listed hypotheses remain candidates. This scaffold does not rank or select one.
6. Candidate hypotheses and mechanisms
{{HYPOTHESES}}
All listed hypotheses remain candidates. This scaffold does not rank or select one.
Raw lines 45 to 5051## 7. Causal estimand(s), if applicable
53{{ESTIMANDS}}
55- Target-trial/design analogue and identification logic: [TO COMPLETE]
56- Confounding, selection, collider, measurement, reverse-causation, positivity, and interference assumptions: [TO COMPLETE]
7. Causal estimand(s), if applicable
{{ESTIMANDS}}
- Target-trial/design analogue and identification logic: [TO COMPLETE]
- Confounding, selection, collider, measurement, reverse-causation, positivity, and interference assumptions: [TO COMPLETE]
58## 8. Predictions, rivals, and falsification
60{{PREDICTIONS}}
62- Indeterminate and mixed-mechanism outcomes: [TO COMPLETE]
63- Assumption/manipulation checks required before interpreting a challenge: [TO COMPLETE]
8. Predictions, rivals, and falsification
{{PREDICTIONS}}
- Indeterminate and mixed-mechanism outcomes: [TO COMPLETE]
- Assumption/manipulation checks required before interpreting a challenge: [TO COMPLETE]
65## 9. Null hypotheses and controls
67{{NULLS_AND_CONTROLS}}
69- Positive/procedural-control details: [TO COMPLETE]
70- Why each negative control cannot operate through the target mechanism and which bias pathways it shares: [TO COMPLETE]
9. Null hypotheses and controls
{{NULLS_AND_CONTROLS}}
- Positive/procedural-control details: [TO COMPLETE]
- Why each negative control cannot operate through the target mechanism and which bias pathways it shares: [TO COMPLETE]
72## 10. Operationalization and measurement validity
74{{OPERATIONALIZATIONS}}
76- Validity applicability, reliability/repeatability, calibration, detection limits, masking, missingness, invariance/comparability, and limitations: [TO COMPLETE]
10. Operationalization and measurement validity
{{OPERATIONALIZATIONS}}
- Validity applicability, reliability/repeatability, calibration, detection limits, masking, missingness, invariance/comparability, and limitations: [TO COMPLETE]
78## 11. Design
80- Target population/system and sampling frame: [TO COMPLETE]
81- Experimental/observational unit and analysis unit: [TO COMPLETE]
82- Eligibility, recruitment/selection, and exclusions: [TO COMPLETE]
83- Intervention/exposure and comparator versions: [TO COMPLETE]
84- Allocation, randomization, concealment, and masking: [TO COMPLETE]
85- Measurement schedule and quality control: [TO COMPLETE]
86- Sample-size, precision, or information rationale with sensitivity to assumptions: [TO COMPLETE]
87- Stopping, attrition, and missing-outcome plan: [TO COMPLETE]
88- Replication, transport, and external-validation plan: [TO COMPLETE]
11. Design
- Target population/system and sampling frame: [TO COMPLETE]
- Experimental/observational unit and analysis unit: [TO COMPLETE]
- Eligibility, recruitment/selection, and exclusions: [TO COMPLETE]
- Intervention/exposure and comparator versions: [TO COMPLETE]
- Allocation, randomization, concealment, and masking: [TO COMPLETE]
- Measurement schedule and quality control: [TO COMPLETE]
- Sample-size, precision, or information rationale with sensitivity to assumptions: [TO COMPLETE]
- Stopping, attrition, and missing-outcome plan: [TO COMPLETE]
- Replication, transport, and external-validation plan: [TO COMPLETE]
90## 12. Analysis plan
92{{ANALYSES}}
94- Software, environment, versions, and seeds where applicable: [TO COMPLETE]
95- Assumption diagnostics and model checks: [TO COMPLETE]
96- Full multiplicity family across hypotheses, outcomes, timepoints, subgroups, models, and looks: [TO COMPLETE]
97- Confirmatory versus exploratory outputs: [TO COMPLETE]
12. Analysis plan
{{ANALYSES}}
- Software, environment, versions, and seeds where applicable: [TO COMPLETE]
- Assumption diagnostics and model checks: [TO COMPLETE]
- Full multiplicity family across hypotheses, outcomes, timepoints, subgroups, models, and looks: [TO COMPLETE]
- Confirmatory versus exploratory outputs: [TO COMPLETE]
99## 13. Data, code, materials, and retention
101- Provenance and versioning: [TO COMPLETE]
102- Data/code/material availability or justified restriction: [TO COMPLETE]
103- Consent, privacy, community governance, intellectual property, export-control, biosafety, and dual-use limits: [TO COMPLETE]
104- Approved storage, access, retention, and deletion: [TO COMPLETE]
13. Data, code, materials, and retention
- Provenance and versioning: [TO COMPLETE]
- Data/code/material availability or justified restriction: [TO COMPLETE]
- Consent, privacy, community governance, intellectual property, export-control, biosafety, and dual-use limits: [TO COMPLETE]
- Approved storage, access, retention, and deletion: [TO COMPLETE]
106## 14. AI and tool assistance
108{{AI_USE}}
110- Named tools/versions and material influence: [TO COMPLETE IF PERMITTED]
111- Verification and disclosure plan: [TO COMPLETE]
112- Sensitive or unpublished information must remain local unless explicitly authorized for a named service and scope.
14. AI and tool assistance
{{AI_USE}}
- Named tools/versions and material influence: [TO COMPLETE IF PERMITTED]
- Verification and disclosure plan: [TO COMPLETE]
- Sensitive or unpublished information must remain local unless explicitly authorized for a named service and scope.
114## 15. Deviations and amendments
116{{DEVIATION_PLAN}}
118For each deviation record:
120- date;
121- affected section and IDs;
122- original plan;
123- change and rationale;
124- decision owner;
125- whether target results were known;
126- expected interpretive impact;
127- whether the original analysis will still be reported.
15. Deviations and amendments
{{DEVIATION_PLAN}}
For each deviation record:
- date;
- affected section and IDs;
- original plan;
- change and rationale;
- decision owner;
- whether target results were known;
- expected interpretive impact;
- whether the original analysis will still be reported.
129## 16. Human sign-off
131- Domain expert: [NAME / DATE / STATUS]
132- Measurement expert: [NAME / DATE / STATUS]
133- Methodologist/statistician: [NAME / DATE / STATUS]
134- Ethics/safety/data/regulatory authorities as applicable: [NAME / DATE / STATUS]
135- Accountable investigator: [NAME / DATE / STATUS]
137No signature turns a hypothesis into fact. Interpret results with uncertainty, rivals, boundary conditions, controls, and replication evidence.
16. Human sign-off
- Domain expert: [NAME / DATE / STATUS]
- Measurement expert: [NAME / DATE / STATUS]
- Methodologist/statistician: [NAME / DATE / STATUS]
- Ethics/safety/data/regulatory authorities as applicable: [NAME / DATE / STATUS]
- Accountable investigator: [NAME / DATE / STATUS]
No signature turns a hypothesis into fact. Interpret results with uncertainty, rivals, boundary conditions, controls, and replication evidence.
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