feat(skills): add deep-research skill
Copy deep-research skill from local Qoder installation to config repo for version control
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skills/deep-research/references/preregistration_guide.md
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skills/deep-research/references/preregistration_guide.md
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# Preregistration Guide — Research Preregistration Guide
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## Purpose
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Decision guide and operational manual for research preregistration. Assists the research_architect_agent in determining whether preregistration is needed during the methodology design stage, and guides researchers through the preregistration process.
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---
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## 1. Preregistration Decision Tree
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```
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Does your research have the following characteristics?
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│
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├── Confirmatory research (hypothesis testing)
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│ └── Strongly recommend preregistration
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│ ├── Has pre-specified statistical hypotheses → Preregister
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│ ├── Will conduct significance testing → Preregister
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│ └── Has primary outcome variables → Preregister
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│
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├── Exploratory research
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│ └── Preregistration not required (but optional)
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│ ├── Qualitative research → Typically not preregistered
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│ ├── Data mining / EDA → Typically not preregistered
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│ └── But you can preregister the research design and analysis process
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│
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├── Systematic review / Meta-analysis
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│ └── Strongly recommend registration (PROSPERO)
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│ └── Many journals require systematic reviews to be pre-registered
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│
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├── Randomized controlled trial (RCT)
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│ └── Must register
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│ ├── ICMJE requires RCTs to be pre-registered
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│ └── Most journals will not accept unregistered RCTs
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│
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├── Replication study
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│ └── Strongly recommend preregistration
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│ └── Preregistration clearly distinguishes original from modified hypotheses
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│
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└── Secondary data analysis
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└── Recommend preregistration
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└── Prevents HARKing (Hypothesizing After Results are Known)
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```
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### When Preregistration Is Not Needed
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- Purely qualitative research (grounded theory, phenomenology)
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- Exploratory data analysis (no pre-specified hypotheses)
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- Theoretical or philosophical research
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- Literature reviews (except systematic reviews)
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- Case reports or case studies
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### When Preregistration Is Strongly Recommended
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- Any research involving hypothesis testing
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- Research involving multiple comparisons
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- Research needing to distinguish confirmatory vs. exploratory analyses
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- Research that may be questioned for p-hacking or HARKing
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- When applying for research funding (demonstrates research rigor)
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- When journals explicitly require or encourage preregistration
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---
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## 2. Preregistration Platform Overview
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| Platform | Applicable Field | Features | Cost |
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|------|---------|------|------|
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| **OSF Registries** | All disciplines | Most widely used, multiple templates, DOI, permanent preservation | Free |
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| **PROSPERO** | Systematic reviews | Dedicated to systematic reviews and meta-analyses | Free |
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| **AEA Registry** | Economics | American Economic Association's RCT registration platform | Free |
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| **AsPredicted** | All disciplines | Simplified preregistration (9 questions), quick to complete | Free |
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| **ClinicalTrials.gov** | Clinical trials | US FDA-required RCT registration | Free |
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| **EGAP** | Political science | Experiments in Governance and Politics | Free |
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| **RIDIE** | Development economics | Registry for International Development Impact Evaluations | Free |
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### Platform Selection Guide
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```
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What is your research?
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│
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├── Systematic review / meta-analysis → PROSPERO
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├── Clinical trial / medical intervention → ClinicalTrials.gov
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├── Economics RCT → AEA Registry
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├── Just need simple preregistration → AsPredicted
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└── All other research → OSF Registries (recommended)
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```
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---
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## 3. 21-Item Core Content Checklist
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Based on the OSF Standard Pre-Data Collection Registration format, the following are the 21 core items:
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### A. Study Information
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| # | Item | Description |
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|---|------|------|
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| 1 | **Study title** | Descriptive title |
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| 2 | **Authors/Research team** | All researchers' names and affiliations |
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| 3 | **Research questions** | Main research questions (clear, specific) |
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| 4 | **Hypotheses** | Pre-specified hypotheses (including directional predictions) |
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### B. Design Plan
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| # | Item | Description |
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|---|------|------|
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| 5 | **Study design** | Experiment/observational, between/within-subjects, factorial design, etc. |
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| 6 | **Randomization** | Randomization method (if applicable) |
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| 7 | **Blinding** | Blinding level and implementation (if applicable) |
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| 8 | **Conditions/manipulations** | Specific description of each experimental condition/group |
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### C. Sampling Plan
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| # | Item | Description |
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|---|------|------|
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| 9 | **Existing data** | Whether existing data is being used; nature and status of data |
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| 10 | **Data collection procedures** | How data will be collected (survey, interview, experiment, archival) |
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| 11 | **Sample size** | Planned sample size and basis for determination |
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| 12 | **Sample size rationale** | Power analysis or other sample size calculation method |
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| 13 | **Stopping rule** | When to stop collecting data (fixed N / target power reached / time cutoff) |
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### D. Variables
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| # | Item | Description |
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|---|------|------|
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| 14 | **Manipulated variables** | Operational definition of independent variables |
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| 15 | **Measured variables** | Operational definition and measurement instruments of dependent variables |
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| 16 | **Indices** | Specific indicators for each variable (scales, items, scoring methods) |
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### E. Analysis Plan
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| # | Item | Description |
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|---|------|------|
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| 17 | **Statistical models** | Primary statistical methods for analysis |
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| 18 | **Transformations** | Data transformation plan (e.g., log transformation, standardization) |
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| 19 | **Inference criteria** | Significance level (alpha), correction methods, effect size reporting |
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| 20 | **Data exclusion** | Exclusion criteria (outlier definition, attention check failure, etc.) |
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| 21 | **Exploratory analyses** | Planned but non-primary hypothesis analyses |
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---
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## 4. Higher Education Research Preregistration Examples
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### Example: Effect of Teaching Strategy on Learning Outcomes
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```
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Title: The Effect of Flipped Classroom on University Students' Critical Thinking
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Skills: A Randomized Controlled Trial
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Hypotheses:
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H1: Students receiving flipped classroom instruction will score significantly
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higher on the CCTST than students receiving traditional lectures
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H2: The benefit of flipped classroom will be greater for students with low
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prior knowledge than for those with high prior knowledge
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Design: Cluster-randomized controlled trial (class as randomization unit)
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Sample: 12 classes (6 experimental / 6 control), approximately 40 students
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per class, total 480
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Power: 80% power to detect d = 0.4, alpha = .05, ICC = 0.05
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Primary outcome: CCTST post-test score (controlling for pre-test)
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Secondary outcomes: Final exam grade, learning motivation scale
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Analysis: Multilevel modeling (students nested in classes)
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Exclusion criteria:
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- Attendance rate < 50%
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- Both pre-test and post-test incomplete
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- Attention check questions answered incorrectly
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Exploratory analyses:
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- Gender × teaching method interaction effect
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- Learning motivation as a mediating variable
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```
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### Example: Systematic Review of University Dropout Factors
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```
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Title: Factors Influencing University Student Dropout Decisions in Taiwan:
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A Systematic Literature Review
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Research question: What factors influence university student dropout decisions
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in Taiwan?
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Databases: Airiti Library, TSSCI, Scopus, Web of Science
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Search strategy: (dropout OR withdrawal OR leave)
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AND (university OR higher education)
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AND (Taiwan)
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Time range: 2010-2025
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Inclusion criteria:
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- Studies with Taiwan university students as research subjects
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- Explore causes or factors of dropout/withdrawal
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- Peer-reviewed journal articles or theses/dissertations
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Exclusion criteria:
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- Research subjects below high school level
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- Pure policy commentary (no empirical data)
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Quality assessment: Mixed Methods Appraisal Tool (MMAT)
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Synthesis method: Thematic synthesis
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Registration platform: PROSPERO
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```
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---
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## 5. Preregistration Disclosure Statement Templates
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### Disclosing Preregistration in a Paper
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#### Standard Statement (Preregistered)
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```
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This study was preregistered on [Platform] prior to data collection
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(registration number: [NUMBER]; URL: [URL]). All hypotheses, sample size
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rationale, and analysis plans were specified before data collection began.
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Deviations from the preregistered plan are noted in [section/supplementary
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materials].
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```
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#### Disclosure of Deviations from Preregistration
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```
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Deviations from preregistered plan:
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1. [Deviation description]: [Reason for deviation]
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2. [Deviation description]: [Reason for deviation]
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These deviations do not affect the confirmatory nature of the primary analyses.
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The preregistered analyses are reported as planned; additional exploratory
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analyses are clearly labeled.
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```
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#### Disclosure When Not Preregistered
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```
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This study was not preregistered. While the hypotheses were formulated before
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data analysis, the distinction between confirmatory and exploratory analyses
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should be interpreted with this limitation in mind.
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```
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---
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## 6. Preregistration vs. Registered Reports
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| Aspect | Preregistration | Registered Reports |
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|------|-------------------------|-------------------------------|
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| **Definition** | Research plan publicly registered in advance | Research plan submitted to a journal for pre-review |
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| **Review** | Does not undergo peer review | Stage 1 peer review (research design) |
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| **Acceptance timing** | Paper submitted only after completion | Receives "In-Principle Acceptance" (IPA) after passing Stage 1 |
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| **Results bias** | Reduced but not eliminated (researchers can still selectively report) | Substantially eliminated (published regardless of results) |
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| **Publication bias** | Cannot solve | Effectively solved (null results also published) |
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| **Applicable journals** | All journals | Only journals accepting Registered Reports |
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| **Difficulty** | Low (just fill in a form) | High (requires complete methodology and passing review) |
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| **Flexibility** | Higher (deviations require disclosure but don't block submission) | Lower (major deviations may affect acceptance) |
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### Registered Reports Process
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```
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Stage 1: Submit research plan
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├── Introduction (theoretical background, literature review)
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├── Methods (complete methodology, analysis plan)
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├── Pilot data (if available)
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└── Interpretation plan for predicted results
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↓
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Stage 1 Review (research design quality)
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├── Accept (In-Principle Acceptance, IPA)
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├── Revise and resubmit
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└── Reject
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↓
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Stage 2: Conduct research, write results
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├── Strictly follow the Stage 1 plan
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├── Report all preregistered analyses (including null results)
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├── Exploratory analyses clearly labeled
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└── Deviations disclosed and explained
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↓
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Stage 2 Review (execution quality)
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├── Was the Stage 1 plan faithfully executed?
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├── Are results reported completely?
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└── Typically not rejected due to null results
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↓
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Publication
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```
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### Selected Higher Education Journals Supporting Registered Reports
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- *Studies in Higher Education*
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- *Higher Education*
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- *Assessment & Evaluation in Higher Education*
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- *Teaching in Higher Education*
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- *Educational Research Review*
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- *Learning and Instruction*
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> Full list: [COS Registered Reports](https://www.cos.io/initiatives/registered-reports)
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---
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## Quick Reference: 3 Steps to Preregistration
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1. **Decide whether to preregister**: Determine if your research involves hypothesis testing
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2. **Choose a platform**: Use PROSPERO for systematic reviews, OSF for everything else
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3. **Fill in the 21-item checklist**: Use the `templates/preregistration_template.md` template
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> Preregistration is not a perfect solution, but it is currently the most practical transparency tool. Even an imperfect preregistration is better than no preregistration at all.
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