scientific-writer 2.1.1__py3-none-any.whl → 2.2.2__py3-none-any.whl

scientific_writer/.claude/skills/literature-review/assets/review_template.md

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+# [Literature Review Title]
+
+**Authors**: [Author Names and Affiliations]
+**Date**: [Date]
+**Review Type**: [Narrative / Systematic / Scoping / Meta-Analysis / Umbrella Review]
+**Review Protocol**: [PROSPERO ID if registered, or state "Not registered"]
+**PRISMA Compliance**: [Yes/No/Partial - specify which guidelines]
+
+---
+
+## Abstract
+
+**Background**: [Context and rationale]  
+**Objectives**: [Primary and secondary objectives]  
+**Methods**: [Databases, dates, selection criteria, quality assessment]  
+**Results**: [n studies included; key findings by theme]  
+**Conclusions**: [Main conclusions and implications]  
+**Registration**: [PROSPERO ID or "Not registered"]  
+**Keywords**: [5-8 keywords]
+
+---
+
+## 1. Introduction
+
+### 1.1 Background and Context
+
+[Provide background information on the topic. Establish why this literature review is important and timely. Discuss the broader context and current state of knowledge.]
+
+### 1.2 Scope and Objectives
+
+[Clearly define the scope of the review and state the specific objectives. What questions will this review address?]
+
+**Primary Research Questions:**
+1. [Research question 1]
+2. [Research question 2]
+3. [Research question 3]
+
+### 1.3 Significance
+
+[Explain the significance of this review. Why is it important to synthesize this literature now? What gaps does it fill?]
+
+---
+
+## 2. Methodology
+
+### 2.1 Protocol and Registration
+
+**Protocol**: [PROSPERO ID / OSF link / Not registered]  
+**Deviations**: [Document any protocol deviations]  
+**PRISMA**: [Checklist in Appendix B]
+
+### 2.2 Search Strategy
+
+**Databases:** [PubMed, Scopus, Web of Science, bioRxiv, etc.]  
+**Supplementary:** [Citation chaining, grey literature, trial registries]
+
+**Search String Example:**
+```
+("CRISPR"[Title/Abstract] OR "Cas9"[Title/Abstract]) AND 
+("disease"[MeSH Terms]) AND ("2015/01/01"[Date] : "2024/12/31"[Date])
+```
+
+**Dates:** [YYYY-MM-DD to YYYY-MM-DD] | **Executed:** [Date]  
+**Validation:** [Key papers used to test search strategy]
+
+### 2.3 Tools and Software
+
+**Screening:** [Rayyan, Covidence, ASReview]  
+**Analysis:** [VOSviewer, R, Python]  
+**Citation Management:** [Zotero, Mendeley, EndNote]  
+**AI Tools:** [Any AI-assisted tools used; document validation approach]
+
+### 2.4 Inclusion and Exclusion Criteria
+
+**Inclusion Criteria:**
+- [Criterion 1: e.g., Published between 2015-2024]
+- [Criterion 2: e.g., Peer-reviewed articles and preprints]
+- [Criterion 3: e.g., English language]
+- [Criterion 4: e.g., Human or animal studies]
+- [Criterion 5: e.g., Original research or systematic reviews]
+
+**Exclusion Criteria:**
+- [Criterion 1: e.g., Case reports with n<5]
+- [Criterion 2: e.g., Conference abstracts without full text]
+- [Criterion 3: e.g., Editorials and commentaries]
+- [Criterion 4: e.g., Duplicate publications]
+- [Criterion 5: e.g., Retracted articles]
+- [Criterion 6: e.g., Studies with unavailable full text after author contact]
+
+### 2.5 Study Selection
+
+**Reviewers:** [n independent reviewers] | **Conflict resolution:** [Method]  
+**Inter-rater reliability:** [Cohen's kappa = X]
+
+**PRISMA Flow:**
+```
+Records identified: n=[X] → Deduplicated: n=[Y] → 
+Title/abstract screened: n=[Y] → Full-text assessed: n=[Z] → Included: n=[N]
+```
+
+**Exclusion reasons:** [List with counts]
+
+### 2.6 Data Extraction
+
+**Method:** [Standardized form (Appendix E); pilot-tested on n studies]  
+**Extractors:** [n independent] | **Verification:** [Double-checked]
+
+**Items:** Study ID, design, population, interventions/exposures, outcomes, statistics, funding, COI, bias domains
+
+**Missing data:** [Author contact protocol]
+
+### 2.7 Quality Assessment
+
+**Tool:** [Cochrane RoB 2.0 / ROBINS-I / Newcastle-Ottawa / AMSTAR 2 / JBI]  
+**Method:** [2 independent reviewers; third for conflicts]  
+**Rating:** [Low/Moderate/High risk of bias]  
+**Publication bias:** [Funnel plots, Egger's test - if meta-analysis]
+
+### 2.8 Synthesis and Analysis
+
+**Approach:** [Narrative / Meta-analysis / Both]  
+**Statistics** (if meta-analysis): Effect measures, heterogeneity (I², τ²), sensitivity analyses, subgroups  
+**Software:** [RevMan, R, Stata]  
+**Certainty:** [GRADE framework; factors: bias, inconsistency, indirectness, imprecision]
+
+---
+
+## 3. Results
+
+### 3.1 Study Selection
+
+**Summary:** [X records → Y deduplicated → Z full-text → N included (M in meta-analysis)]  
+**Study types:** [RCTs: n=X, Observational: n=Y, Reviews: n=Z]  
+**Years:** [Range; peak year]  
+**Geography:** [Countries represented]  
+**Source:** [Peer-reviewed: n=X, Preprints: n=Y]
+
+### 3.2 Bibliometric Overview
+
+[Optional: Trends, journal distribution, author networks, citations, keywords - if analyzed with VOSviewer or similar]
+
+### 3.3 Study Characteristics
+
+| Study | Year | Design | Sample Size | Key Methods | Main Findings | Quality |
+|-------|------|--------|-------------|-------------|---------------|---------|
+| First Author et al. | 2023 | [Type] | n=[X] | [Methods] | [Brief findings] | [Low/Mod/High RoB] |
+
+**Quality:** Low RoB: n=X ([%]); Moderate: n=Y ([%]); High: n=Z ([%])
+
+### 3.4 Thematic Synthesis
+
+[Organize by themes, NOT study-by-study. Synthesize across studies to identify consensus, controversies, and gaps.]
+
+#### 3.4.1 Theme 1: [Title]
+
+**Findings:** [Synthesis of key findings from multiple studies]  
+**Supporting studies:** [X, Y, Z]  
+**Contradictory evidence:** [If any]  
+**Certainty:** [GRADE rating if applicable]
+
+### 3.5 Methodological Approaches
+
+**Common methods:** [Method 1 (n studies), Method 2 (n studies)]  
+**Emerging techniques:** [New approaches observed]  
+**Methodological quality:** [Overall assessment]
+
+### 3.6 Meta-Analysis Results
+
+[Include only if conducting meta-analysis]
+
+**Effect estimates:** [Primary/secondary outcomes with 95% CI, p-values]  
+**Heterogeneity:** [I²=X%, τ²=Y, interpretation]  
+**Subgroups & sensitivity:** [Key findings from analyses]  
+**Publication bias:** [Funnel plot, Egger's p=X]  
+**Forest plots:** [Include for primary outcomes]
+
+### 3.7 Knowledge Gaps
+
+**Knowledge:** [Unanswered research questions]  
+**Methodological:** [Study design/measurement issues]  
+**Translational:** [Research-to-practice gaps]  
+**Populations:** [Underrepresented groups/contexts]
+
+---
+
+## 4. Discussion
+
+### 4.1 Main Findings
+
+[Synthesize key findings by research question]
+
+**Principal findings:** [Top 3-5 takeaways]  
+**Consensus:** [Where studies agree]  
+**Controversy:** [Conflicting results]
+
+### 4.2 Interpretation and Implications
+
+**Context:** [How findings advance/challenge current understanding]  
+**Mechanisms:** [Potential explanations for observed patterns]
+
+**Implications for:**
+- **Practice:** [Actionable recommendations]
+- **Policy:** [If relevant]
+- **Research:** [Theoretical, methodological, priority directions]
+
+### 4.3 Strengths and Limitations
+
+**Strengths:** [Comprehensive search, rigorous methods, large evidence base, transparency]
+
+**Limitations:**
+- Search/selection: [Language bias, database coverage, grey literature, publication bias]
+- Methodological: [Heterogeneity, study quality]
+- Temporal: [Rapid evolution, search cutoff date]
+
+**Impact:** [How limitations affect conclusions]
+
+### 4.4 Comparison with Previous Reviews
+
+[If relevant: How does this review update/differ from prior reviews?]
+
+### 4.5 Future Research
+
+**Priority questions:**
+1. [Question] - Rationale, suggested approach, expected impact
+2. [Question] - Rationale, suggested approach, expected impact
+3. [Question] - Rationale, suggested approach, expected impact
+
+**Recommendations:** [Methodological improvements, understudied populations, emerging technologies]
+
+---
+
+## 5. Conclusions
+
+[Concise conclusions addressing research questions]
+
+1. [Conclusion directly addressing primary research question]
+2. [Key finding conclusion]
+3. [Gap/future direction conclusion]
+
+**Evidence certainty:** [High/Moderate/Low/Very Low]  
+**Translation readiness:** [Ready / Needs more research / Preliminary]
+
+---
+
+## 6. Declarations
+
+### Author Contributions
+[CRediT taxonomy: Author 1 - Conceptualization, Methodology, Writing; Author 2 - Analysis, Review; etc.]
+
+### Funding
+[Grant details with numbers] OR [No funding received]
+
+### Conflicts of Interest
+[Author-specific declarations] OR [None]
+
+### Data Availability
+**Protocol:** [PROSPERO/OSF ID or "Not registered"]  
+**Data/Code:** [Repository URL/DOI or "Available upon request"]  
+**Materials:** [Search strategies (Appendix A), PRISMA checklist (Appendix B), extraction form (Appendix E)]
+
+### Acknowledgments
+[Contributors not meeting authorship criteria, librarians, patient involvement]
+
+---
+
+## 7. References
+
+[Use consistent style: APA / Nature / Vancouver]
+
+**Format examples:**
+
+APA: Author, A. A., & Author, B. B. (Year). Title. *Journal*, *volume*(issue), pages. https://doi.org/xx.xxxx
+
+Nature: Author, A. A. & Author, B. B. Title. *J. Name* **volume**, pages (year).
+
+Vancouver: Author AA, Author BB. Title. J Abbrev. Year;volume(issue):pages. doi:xx.xxxx
+
+1. [First reference]
+2. [Second reference]
+3. [Continue...]
+
+---
+
+## 8. Appendices
+
+### Appendix A: Search Strings
+
+**PubMed** (Date: YYYY-MM-DD; Results: n)
+```
+[Complete search string with operators and MeSH terms]
+```
+
+[Repeat for each database: Scopus, Web of Science, bioRxiv, etc.]
+
+### Appendix B: PRISMA Checklist
+
+| Section | Item | Reported? | Page |
+|---------|------|-----------|------|
+| Title | Identify as systematic review | Yes/No | # |
+| Abstract | Structured summary | Yes/No | # |
+| Methods | Eligibility, sources, search, selection, data, quality | Yes/No | # |
+| Results | Selection, characteristics, risk of bias, syntheses | Yes/No | # |
+| Discussion | Interpretation, limitations, conclusions | Yes/No | # |
+| Other | Registration, support, conflicts, availability | Yes/No | # |
+
+### Appendix C: Excluded Studies
+
+| Study | Year | Reason | Category |
+|-------|------|--------|----------|
+| Author et al. | Year | [Reason] | [Wrong population/outcome/design/etc.] |
+
+**Summary:** Wrong population (n=X), Wrong outcome (n=Y), etc.
+
+### Appendix D: Quality Assessment
+
+**Tool:** [Cochrane RoB 2.0 / ROBINS-I / Newcastle-Ottawa / etc.]
+
+| Study | Domain 1 | Domain 2 | Domain 3 | Overall |
+|-------|----------|----------|----------|---------|
+| Study 1 | Low | Low | Some concerns | Low |
+| Study 2 | [Score] | [Score] | [Score] | [Overall] |
+
+### Appendix E: Data Extraction Form
+
+```
+STUDY: Author______ Year______ DOI______
+DESIGN: □RCT □Cohort □Case-Control □Cross-sectional □Other______
+POPULATION: n=_____ Age_____ Setting_____
+INTERVENTION/EXPOSURE: _____
+OUTCOMES: Primary_____ Secondary_____
+RESULTS: Effect size_____ 95%CI_____ p=_____
+QUALITY: □Low □Moderate □High RoB
+FUNDING/COI: _____
+```
+
+### Appendix F: Meta-Analysis Details
+
+[Only if meta-analysis performed]
+
+**Software:** [R 4.x.x with meta/metafor packages / RevMan / Stata]  
+**Model:** [Random-effects; justification]  
+**Code:** [Link to repository]  
+**Sensitivity analyses:** [Details]
+
+### Appendix G: Author Contacts
+
+| Study | Contact Date | Response | Data Received |
+|-------|--------------|----------|---------------|
+| Author et al. | YYYY-MM-DD | Yes/No | Yes/No/Partial |
+
+---
+
+## 9. Supplementary Materials
+
+[If applicable]
+
+**Tables:** S1 (Full study characteristics), S2 (Quality scores), S3 (Subgroups), S4 (Sensitivity)  
+**Figures:** S1 (PRISMA diagram), S2 (Risk of bias), S3 (Funnel plot), S4 (Forest plots), S5 (Networks)  
+**Data:** S1 (Extraction file), S2 (Search results), S3 (Analysis code), S4 (PRISMA checklist)  
+**Repository:** [OSF/GitHub/Zenodo URL with DOI]
+
+---
+
+## Review Metadata
+
+**Registration:** [Registry] ID: [Number] (Date: YYYY-MM-DD)  
+**Search dates:** Initial: [Date]; Updated: [Date]  
+**Version:** [1.0] | **Last updated:** [Date]
+
+**Quality checks:**
+- [ ] Citations verified with verify_citations.py
+- [ ] PRISMA checklist completed
+- [ ] Search reproducible
+- [ ] Independent data verification
+- [ ] Code peer-reviewed
+- [ ] All authors approved
+
+---
+
+## Usage Notes
+
+**Review type adaptations:**
+- Systematic Review: Use all sections
+- Meta-Analysis: Include sections 3.6, Appendix F
+- Narrative Review: May omit some methodology detail
+- Scoping Review: Follow PRISMA-ScR, may omit quality assessment
+
+**Key principles:**
+1. Remove all [bracketed placeholders]
+2. Follow PRISMA 2020 guidelines
+3. Pre-register when feasible (PROSPERO/OSF)
+4. Use thematic synthesis, not study-by-study
+5. Be transparent and reproducible
+6. Verify all DOIs before submission
+7. Make data/code openly available
+
+**Common pitfalls to avoid:**
+- Don't list studies - synthesize them
+- Don't cherry-pick results
+- Don't ignore limitations
+- Don't overstate conclusions
+- Don't skip publication bias assessment
+
+**Resources:**
+- PRISMA 2020: http://prisma-statement.org/
+- PROSPERO: https://www.crd.york.ac.uk/prospero/
+- Cochrane Handbook: https://training.cochrane.org/handbook
+- GRADE: https://www.gradeworkinggroup.org/
+
+**DELETE THIS SECTION FROM YOUR FINAL REVIEW**
+
+---

scientific_writer/.claude/skills/literature-review/references/citation_styles.md

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+# Citation Styles Reference
+
+This document provides detailed guidelines for formatting citations in various academic styles commonly used in literature reviews.
+
+## APA Style (7th Edition)
+
+### Journal Articles
+
+**Format**: Author, A. A., Author, B. B., & Author, C. C. (Year). Title of article. *Title of Periodical*, *volume*(issue), page range. https://doi.org/xx.xxx/yyyy
+
+**Example**: Smith, J. D., Johnson, M. L., & Williams, K. R. (2023). Machine learning approaches in drug discovery. *Nature Reviews Drug Discovery*, *22*(4), 301-318. https://doi.org/10.1038/nrd.2023.001
+
+### Books
+
+**Format**: Author, A. A. (Year). *Title of work: Capital letter also for subtitle*. Publisher Name. https://doi.org/xxxx
+
+**Example**: Kumar, V., Abbas, A. K., & Aster, J. C. (2021). *Robbins and Cotran pathologic basis of disease* (10th ed.). Elsevier.
+
+### Book Chapters
+
+**Format**: Author, A. A., & Author, B. B. (Year). Title of chapter. In E. E. Editor & F. F. Editor (Eds.), *Title of book* (pp. xx-xx). Publisher.
+
+**Example**: Brown, P. O., & Botstein, D. (2020). Exploring the new world of the genome with DNA microarrays. In M. B. Eisen & P. O. Brown (Eds.), *DNA microarrays: A molecular cloning manual* (pp. 1-45). Cold Spring Harbor Laboratory Press.
+
+### Preprints
+
+**Format**: Author, A. A., & Author, B. B. (Year). Title of preprint. *Repository Name*. https://doi.org/xxxx
+
+**Example**: Zhang, Y., Chen, L., & Wang, H. (2024). Novel therapeutic targets in Alzheimer's disease. *bioRxiv*. https://doi.org/10.1101/2024.01.001
+
+### Conference Papers
+
+**Format**: Author, A. A. (Year, Month day-day). Title of paper. In E. E. Editor (Ed.), *Title of conference proceedings* (pp. xx-xx). Publisher. https://doi.org/xxxx
+
+---
+
+## Nature Style
+
+### Journal Articles
+
+**Format**: Author, A. A., Author, B. B. & Author, C. C. Title of article. *J. Name* **volume**, page range (year).
+
+**Example**: Smith, J. D., Johnson, M. L. & Williams, K. R. Machine learning approaches in drug discovery. *Nat. Rev. Drug Discov.* **22**, 301-318 (2023).
+
+### Books
+
+**Format**: Author, A. A. & Author, B. B. *Book Title* (Publisher, Year).
+
+**Example**: Kumar, V., Abbas, A. K. & Aster, J. C. *Robbins and Cotran Pathologic Basis of Disease* 10th edn (Elsevier, 2021).
+
+### Multiple Authors
+
+- 1-2 authors: List all
+- 3+ authors: List first author followed by "et al."
+
+**Example**: Zhang, Y. et al. Novel therapeutic targets in Alzheimer's disease. *bioRxiv* https://doi.org/10.1101/2024.01.001 (2024).
+
+---
+
+## Chicago Style (Author-Date)
+
+### Journal Articles
+
+**Format**: Author, First Name Middle Initial. Year. "Article Title." *Journal Title* volume, no. issue (Month): page range. https://doi.org/xxxx.
+
+**Example**: Smith, John D., Mary L. Johnson, and Karen R. Williams. 2023. "Machine Learning Approaches in Drug Discovery." *Nature Reviews Drug Discovery* 22, no. 4 (April): 301-318. https://doi.org/10.1038/nrd.2023.001.
+
+### Books
+
+**Format**: Author, First Name Middle Initial. Year. *Book Title: Subtitle*. Edition. Place: Publisher.
+
+**Example**: Kumar, Vinay, Abul K. Abbas, and Jon C. Aster. 2021. *Robbins and Cotran Pathologic Basis of Disease*. 10th ed. Philadelphia: Elsevier.
+
+---
+
+## Vancouver Style (Numbered)
+
+### Journal Articles
+
+**Format**: Author AA, Author BB, Author CC. Title of article. Abbreviated Journal Name. Year;volume(issue):page range.
+
+**Example**: Smith JD, Johnson ML, Williams KR. Machine learning approaches in drug discovery. Nat Rev Drug Discov. 2023;22(4):301-18.
+
+### Books
+
+**Format**: Author AA, Author BB. Title of book. Edition. Place: Publisher; Year.
+
+**Example**: Kumar V, Abbas AK, Aster JC. Robbins and Cotran pathologic basis of disease. 10th ed. Philadelphia: Elsevier; 2021.
+
+### Citation in Text
+
+Use superscript numbers in order of appearance: "Recent studies^1,2^ have shown..."
+
+---
+
+## IEEE Style
+
+### Journal Articles
+
+**Format**: [#] A. A. Author, B. B. Author, and C. C. Author, "Title of article," *Abbreviated Journal Name*, vol. x, no. x, pp. xxx-xxx, Month Year.
+
+**Example**: [1] J. D. Smith, M. L. Johnson, and K. R. Williams, "Machine learning approaches in drug discovery," *Nat. Rev. Drug Discov.*, vol. 22, no. 4, pp. 301-318, Apr. 2023.
+
+### Books
+
+**Format**: [#] A. A. Author, *Title of Book*, xth ed. City, State: Publisher, Year.
+
+**Example**: [2] V. Kumar, A. K. Abbas, and J. C. Aster, *Robbins and Cotran Pathologic Basis of Disease*, 10th ed. Philadelphia, PA: Elsevier, 2021.
+
+---
+
+## Common Abbreviations for Journal Names
+
+- Nature: Nat.
+- Science: Science
+- Cell: Cell
+- Nature Reviews Drug Discovery: Nat. Rev. Drug Discov.
+- Journal of the American Chemical Society: J. Am. Chem. Soc.
+- Proceedings of the National Academy of Sciences: Proc. Natl. Acad. Sci. U.S.A.
+- PLOS ONE: PLoS ONE
+- Bioinformatics: Bioinformatics
+- Nucleic Acids Research: Nucleic Acids Res.
+
+---
+
+## DOI Best Practices
+
+1. **Always verify DOIs**: Use the verify_citations.py script to check all DOIs
+2. **Format as URLs**: https://doi.org/10.xxxx/yyyy (preferred over doi:10.xxxx/yyyy)
+3. **No period after DOI**: DOI should be the last element without trailing punctuation
+4. **Resolve redirects**: Check that DOIs resolve to the correct article
+
+---
+
+## In-Text Citation Guidelines
+
+### APA Style
+- (Smith et al., 2023)
+- Smith et al. (2023) demonstrated...
+- Multiple citations: (Brown, 2022; Smith et al., 2023; Zhang, 2024)
+
+### Nature Style
+- Superscript numbers: Recent studies^1,2^ have shown...
+- Or: Recent studies (refs 1,2) have shown...
+
+### Chicago Style
+- (Smith, Johnson, and Williams 2023)
+- Smith, Johnson, and Williams (2023) found...
+
+---
+
+## Reference List Organization
+
+### By Citation Style
+- **APA, Chicago**: Alphabetical by first author's last name
+- **Nature, Vancouver, IEEE**: Numerical order of first appearance in text
+
+### Hanging Indents
+Most styles use hanging indents where the first line is flush left and subsequent lines are indented.
+
+### Consistency
+Maintain consistent formatting throughout:
+- Capitalization (title case vs. sentence case)
+- Journal name abbreviations
+- DOI presentation
+- Author name format