08 Ethics Compliance

# SKILL 08: Ethics & Compliance

> **Ensure your research meets the highest ethical standards and reporting requirements — because integrity is non-negotiable.**

---

## ACTIVATE: ETHICS

When you input `ACTIVATE: ETHICS`, the system executes a comprehensive ethics audit across five critical sections, each with specific checklist items that must be verified before submission.

---

## SECTION A: HUMAN SUBJECTS RESEARCH

### A1. Institutional Review Board (IRB) / Ethics Committee Approval

- [ ] **IRB/ethics committee approval obtained** before any data collection began
- [ ] Approval number and date documented in the manuscript (typically in Methods section)
- [ ] Approval covers the specific protocol, population, and procedures used
- [ ] If the study was deemed exempt, the exemption category and rationale are documented
- [ ] For multi-site studies: each site has its own approval or a reliance agreement is in place

### A2. Informed Consent

- [ ] **Informed consent obtained** from all participants (or their legal guardians)
- [ ] Consent process documented: written, verbal, or electronic (with justification for non-written)
- [ ] Consent forms included all required elements: purpose, procedures, risks, benefits, alternatives, confidentiality, voluntary participation, right to withdraw, contact information
- [ ] For participants who cannot consent: assent obtained where appropriate, proxy consent documented
- [ ] For retrospective studies: waiver of consent obtained from IRB, with justification
- [ ] For studies using existing datasets: original consent covers secondary use, or waiver obtained

### A3. Vulnerable Populations

- [ ] Special protections implemented for vulnerable populations (children, prisoners, pregnant women, cognitively impaired individuals, economically/educationally disadvantaged persons)
- [ ] Additional safeguards documented: assent procedures for minors, capacity assessments, independent advocates
- [ ] Coercion or undue influence risk assessed and mitigated
- [ ] Compensation is reasonable and not coercive

### A4. Privacy and Confidentiality

- [ ] **De-identification protocol** implemented and documented
- [ ] Direct identifiers removed (name, SSN, medical record number, etc.)
- [ ] Indirect identifiers assessed (combinations of age, location, diagnosis that could enable re-identification)
- [ ] Data storage security measures documented (encryption, access controls, secure servers)
- [ ] Data retention and destruction policy specified
- [ ] If images are used: specific consent for publication of identifying images obtained

### A5. Risk-Benefit Assessment

- [ ] Risks to participants identified and minimized
- [ ] Risk level classified: minimal risk vs. greater than minimal risk
- [ ] Potential benefits to participants and/or society clearly articulated
- [ ] Risk-benefit ratio justified and documented
- [ ] Data safety monitoring plan in place for greater-than-minimal-risk studies

### A6. International and Cultural Considerations

- [ ] Local ethical requirements met in addition to home institution requirements
- [ ] Cultural sensitivity in study design and consent process
- [ ] Community engagement where appropriate (e.g., indigenous populations)
- [ ] Language barriers addressed in consent process and study instruments
- [ ] Compliance with local data protection laws (GDPR, HIPAA, etc.)

---

## SECTION B: DATA INTEGRITY

### B1. Data Collection Standards

- [ ] **Data collection protocol** documented in sufficient detail for replication
- [ ] Standardized instruments and procedures used
- [ ] Inter-rater reliability assessed for subjective measures
- [ ] Data collection forms (paper or electronic) designed to minimize errors
- [ ] Training of data collectors documented

### B2. Data Management

- [ ] **Data management plan** in place before data collection
- [ ] Raw data preserved in original form (never modify raw data files)
- [ ] Version control system used for datasets (dates, version numbers, change logs)
- [ ] Data entry verification: double entry or automated validation checks
- [ ] Missing data tracked and documented (not silently dropped)

### B3. Data Fabrication and Falsification Prevention

- [ ] Audit trail maintained for all data modifications
- [ ] Original raw data preserved alongside processed data
- [ ] Data transformations documented and reversible
- [ ] Outlier handling policy defined a priori (not post hoc)
- [ ] Image integrity verified: no unauthorized manipulation, cropping disclosed

### B4. Data Sharing and Availability

- [ ] Data sharing plan compliant with funder and journal requirements
- [ ] Sensitive data handled appropriately (de-identified, restricted access where needed)
- [ ] Data deposited in appropriate repository with DOI
- [ ] Data dictionary/codebook provided
- [ ] Licensing terms specified for shared data

### B5. Secondary Data Use

- [ ] Original consent covers secondary analysis, or IRB waiver obtained
- [ ] Data provenance documented (source, version, access date)
- [ ] Limitations of secondary data acknowledged (original collection purpose may differ)
- [ ] Data quality assessment performed before analysis

### B6. Qualitative Data Integrity

- [ ] Audio/video recordings stored securely with appropriate consent
- [ ] Transcription accuracy verified (double-checking, member checking)
- [ ] Coding process documented with inter-coder reliability
- [ ] Participant identities protected in quotations (pseudonyms, altered details)
- [ ] Reflexivity statement included for researcher positionality

---

## SECTION C: STATISTICAL INTEGRITY

### C1. Analysis Pre-Registration

- [ ] **Analysis plan pre-registered** (e.g., OSF, AsPredicted, ClinicalTrials.gov) before data analysis
- [ ] Pre-registration includes: hypotheses, variables, exclusion criteria, analysis methods, power analysis
- [ ] Any deviations from pre-registered plan documented and justified
- [ ] Distinction between confirmatory and exploratory analyses clearly stated

### C2. Sample Size Justification

- [ ] **A priori power analysis** conducted and reported
- [ ] Effect size estimate justified (from pilot data, literature, or minimum meaningful effect)
- [ ] Power analysis parameters reported: alpha, desired power, effect size, test type
- [ ] If post-hoc power is reported, labeled as such with appropriate caveats

### C3. Multiple Comparisons

- [ ] Multiple comparison problem acknowledged when applicable
- [ ] Correction method specified and justified (Bonferroni, FDR, Holm, etc.)
- [ ] Both uncorrected and corrected results reported where informative
- [ ] Pre-registered primary outcomes distinguished from secondary/exploratory analyses

### C4. Effect Size Reporting

- [ ] Effect sizes reported for all statistical tests (not just p-values)
- [ ] Appropriate effect size metric chosen: Cohen's d, η², partial η², odds ratio, r, etc.
- [ ] Confidence intervals provided for effect sizes
- [ ] Practical significance discussed alongside statistical significance

### C5. Assumption Checking

- [ ] Statistical test assumptions verified (normality, homogeneity of variance, independence, etc.)
- [ ] Robustness analyses conducted when assumptions are violated
- [ ] Alternative analysis approaches reported when primary assumptions are not met
- [ ] Missing data mechanism assessed and appropriate handling method used (listwise deletion, multiple imputation, etc.)

### C6. P-Hacking Prevention

- [ ] No selective reporting of significant results (file drawer problem assessed)
- [ ] All conducted analyses reported, not just those yielding significant results
- [ ] Optional stopping rules avoided or pre-registered
- [ ] Outlier exclusion criteria defined before analysis
- [ ] Variable transformation decisions made before analysis, not after examining results
- [ ] Researcher degrees of freedom minimized and documented

---

## SECTION D: PUBLICATION ETHICS

### D1. Authorship

- [ ] **Authorship criteria** met for all authors (substantial contribution, drafting/approval, accountability)
- [ ] All contributors who meet authorship criteria are included as authors
- [ ] Contributors who do not meet authorship criteria are acknowledged
- [ ] Author order reflects relative contribution (field-specific conventions followed)
- [ ] Corresponding author responsibilities understood and accepted
- [ ] No ghost authorship (unlisted authors who made substantial contributions)
- [ ] No gift authorship (listed authors who did not make substantial contributions)

### D2. Plagiarism and Self-Plagiarism

- [ ] **Originality verified**: all text is in the authors' own words or properly quoted
- [ ] Self-plagiarism avoided: previously published text not recycled without quotation and citation
- [ ] Paraphrasing is genuine, not cosmetic (changing a few words is insufficient)
- [ ] All sources properly cited
- [ ] Plagiarism detection software run on manuscript (e.g., iThenticate, Turnitin)

### D3. Duplicate Publication

- [ ] Manuscript not published or under review elsewhere
- [ ] Previous publication of any portion disclosed to the editor
- [ ] Conference abstracts, preprints, and theses that contain overlapping content disclosed
- [ ] If expanding a conference paper: new content is ≥ 30% of the journal version, and the conference version is cited
- [ ] No salami slicing: findings not split across multiple papers to inflate publication count

### D4. Image and Figure Integrity

- [ ] No unauthorized image manipulation (no cloning, splicing, selective enhancement)
- [ ] Brightness/contrast adjustments applied uniformly and do not obscure data
- [ ] Cropping disclosed; full uncropped images available in supplementary materials
- [ ] Composite figures clearly labeled with boundaries between panels
- [ ] Microscopy images include scale bars and acquisition parameters

### D5. Peer Review Integrity

- [ ] No fabrication of suggested reviewers (e.g., email addresses that route to the authors)
- [ ] No citation manipulation (adding irrelevant citations to appease editors or reviewers)
- [ ] Confidentiality of the peer review process respected
- [ ] No retaliation against reviewers (identifying and targeting critical reviewers)

### D6. Conflicts of Interest

- [ ] All financial relationships disclosed (consulting, employment, equity, patents, honoraria, grants)
- [ ] All non-financial relationships disclosed (personal, academic, political, religious)
- [ ] Funding sources and their role in the research disclosed
- [ ] Industry sponsorship fully disclosed with details of funder involvement

---

## SECTION E: REPORTING STANDARDS

Use the appropriate reporting checklist based on study design. These are not optional — most top journals require a completed checklist at submission.

### E1. CONSORT — Randomized Controlled Trials

**Key items (37-item checklist):**
- [ ] Title identified as randomized trial
- [ ] Scientific background and rationale
- [ ] Specific objectives and hypotheses
- [ ] Eligibility criteria, settings, and locations
- [ ] Interventions with sufficient detail for replication
- [ ] Primary and secondary outcomes with measurement methods
- [ ] Sample size calculation with assumptions
- [ ] Randomization sequence generation, allocation concealment, implementation
- [ ] Blinding: who was blinded and how
- [ ] Statistical methods for primary and secondary outcomes
- [ ] Flow diagram (enrollment → allocation → follow-up → analysis)
- [ ] Dates of recruitment and follow-up
- [ ] Baseline demographic and clinical characteristics
- [ ] Analysis populations (intention-to-treat, per-protocol)
- [ ] Harms and adverse events

### E2. STROBE — Observational Studies (Cohort, Case-Control, Cross-Sectional)

**Key items (22-item checklist):**
- [ ] Study design in title/abstract
- [ ] Objectives, including specific hypotheses
- [ ] Study design, setting, and dates
- [ ] Eligibility criteria, selection methods, follow-up methods
- [ ] Exposure, outcomes, confounders: definition and measurement
- [ ] Bias assessment
- [ ] Study size rationale
- [ ] Quantitative variables: categories and rationale
- [ ] Statistical methods: confounder adjustment, subgroups, interactions, missing data
- [ ] Flow of participants with reasons for exclusion
- [ ] Descriptive data: characteristics, missing data, follow-up time
- [ ] Main results: estimates, confidence intervals, significance tests
- [ ] Other analyses: sensitivity, subgroup analyses
- [ ] Key results with consideration of objectives and limitations
- [ ] Generalizability (external validity)

### E3. PRISMA — Systematic Reviews and Meta-Analyses

**Key items (27-item checklist):**
- [ ] Title identified as systematic review or meta-analysis
- [ ] Structured summary: background, objectives, data sources, eligibility criteria, participants/interventions, study appraisal/synthesis methods, results, limitations, conclusions
- [ ] Rationale for review
- [ ] Clearly stated research questions (PICOS: Population, Intervention, Comparison, Outcomes, Study design)
- [ ] Protocol registration information
- [ ] Eligibility criteria
- [ ] Information sources with dates of coverage
- [ ] Search strategy for at least one database
- [ ] Study selection process
- [ ] Data collection process
- [ ] Data items and definitions
- [ ] Risk of bias assessment method
- [ ] Effect measures and synthesis methods
- [ ] Additional analyses (meta-regression, sensitivity)
- [ ] PRISMA flow diagram
- [ ] Study characteristics summary
- [ ] Risk of bias within and across studies
- [ ] Results of individual studies and syntheses
- [ ] Certainty of evidence assessment (GRADE)

### E4. COREQ / SRQR — Qualitative Research

**COREQ key items (32-item checklist):**
- [ ] Researcher characteristics and reflexivity
- [ ] Theoretical framework and methodology
- [ ] Participant selection, setting, and data collection
- [ ] Interview guide and pilot testing
- [ ] Recording and transcription methods
- [ ] Data analysis method and software
- [ ] Derivation of themes/codes
- [ ] Techniques to enhance trustworthiness (member checking, triangulation, audit trail)

### E5. STARD — Diagnostic Accuracy Studies

**Key items (30-item checklist):**
- [ ] Index test and reference standard described
- [ ] Flow and timing: order of test administration, interval between tests
- [ ] Blinding of index test interpreters from reference standard results
- [ ] 2×2 contingency table with all four cells populated
- [ ] Sensitivity, specificity with confidence intervals
- [ ] Indeterminate results reported and handled
- [ ] Clinical context and intended use of the test

### E6. CARE — Case Reports

**Key items (13-item checklist):**
- [ ] Patient perspective when appropriate
- [ ] Timeline of events
- [ ] Diagnostic challenges and reasoning
- [ ] Intervention details and outcomes
- [ ] Follow-up and outcomes
- [ ] Informed consent obtained

### E7. ARRIVE — Animal Research

**Key items (21-item checklist):**
- [ ] Ethical approval statement
- [ ] Species, strain, and characteristics
- [ ] Housing and husbandry conditions
- [ ] Sample size justification
- [ ] Allocation and blinding procedures
- [ ] Outcome measures and statistical methods
- [ ] Adverse events and humane endpoints

### E8. MODEL CARDS — AI/ML Model Reporting

**Key items:**
- [ ] Model details (architecture, training data, performance metrics)
- [ ] Intended use and users
- [ ] Factors affecting performance (demographic, environmental, temporal)
- [ ] Metrics and evaluation data
- [ ] Training data description
- [ ] Quantitative analyses (disaggregated by subgroups)
- [ ] Ethical considerations and limitations
- [ ] Caveats and recommendations

---

## Transparency Statement Template

The following statement should appear in all manuscripts, adapted to the specific study:

```
## Transparency Statement

**Data Availability:** [All data / Anonymized data / Summary data] supporting
the findings of this study are available at [repository name and DOI/URL].
[OR: Available from the corresponding author upon reasonable request, due to
(privacy/consent/legal restrictions).]

**Code Availability:** All analysis code is available at [repository URL]
under [license type]. A permanent archived version is available at [DOI].

**Pre-registration:** This study was pre-registered at [registry name]
([registration URL/DOI]). All confirmatory analyses followed the
pre-registered plan. Any deviations are documented in the manuscript.

**AI Disclosure:** [No AI tools were used in the writing or analysis of this
manuscript. / AI-assisted tools (e.g., [tool name]) were used for
[specific purpose: e.g., "grammar checking," "code generation for data
processing," "literature search"]. All AI-generated content was reviewed,
verified, and revised by the authors, who take full responsibility for the
content of this publication.]
```

---

## Ethics Audit Scoring

| Category | Items | Critical Items | Status |
|---|---|---|---|
| A: Human Subjects | 6 | A1, A2, A4 | Must be fully compliant before submission |
| B: Data Integrity | 6 | B1, B3 | Must be fully compliant before submission |
| C: Statistical Integrity | 6 | C1, C3, C6 | Must be fully compliant before submission |
| D: Publication Ethics | 6 | D1, D2, D3 | Must be fully compliant before submission |
| E: Reporting Standards | 8 checklists | Appropriate checklist | Must be completed at submission |

### Status Definitions

- **Compliant**: All items checked and documented
- **Partially Compliant**: Some items addressed; action plan needed for remaining items
- **Non-Compliant**: Critical items not addressed; must be resolved before submission
- **Not Applicable**: Item does not apply to this study type (document the reason)

---

## Integration Notes

This skill integrates with:
- **Skill 01 (Topic Ideation)**: Ethical considerations should inform research questions from the start
- **Skill 03 (Methodology Design)**: Pre-registration and power analysis begin at design stage
- **Skill 05 (Discussion Architecture)**: Limitations should include ethical limitations
- **Skill 07 (Journal Strategy)**: Cover letter must include compliance statements; reporting checklists required at submission
- **Skill 10 (Impact Amplifier)**: Transparency and openness amplify impact through trust

---

*Last updated: 2024 | CRES v2.0*