--- title: "Hypothesis Generation Report - Formatting Quick Reference" description: "This guide provides quick reference for using the hypothesis generation LaTeX template and style package. For complete documentation, see `SKILL.md`." type: tutorial canonical_url: https://claudary.paisolsolutions.com/tutorials/formatting-guide source: "Claudary" difficulty: intermediate author: "Claude Code Knowledge Pack" date: 2026-07-10T11:23:57.351Z license: CC-BY-4.0 attribution: "Hypothesis Generation Report - Formatting Quick Reference — Claudary (https://claudary.paisolsolutions.com/tutorials/formatting-guide)" --- # Hypothesis Generation Report - Formatting Quick Reference This guide provides quick reference for using the hypothesis generation LaTeX template and style package. For complete documentation, see `SKILL.md`. ## Overview # Hypothesis Generation Report - Formatting Quick Reference ## Overview This guide provides quick reference for using the hypothesis generation LaTeX template and style package. For complete documentation, see `SKILL.md`. ## Quick Start ```latex % !TEX program = xelatex \\documentclass[11pt,letterpaper]{article} \\usepackage{hypothesis_generation} \\usepackage{natbib} \\title{Your Phenomenon Name} \\begin{document} \\maketitle % Your content \\end{document} ``` **Compilation:** Use XeLaTeX or LuaLaTeX for best results ```bash xelatex your_document.tex bibtex your_document xelatex your_document.tex xelatex your_document.tex ``` ## Color Scheme Reference ### Hypothesis Colors - **Hypothesis 1**: Deep Blue (RGB: 0, 102, 153) - Use for first hypothesis - **Hypothesis 2**: Forest Green (RGB: 0, 128, 96) - Use for second hypothesis - **Hypothesis 3**: Royal Purple (RGB: 102, 51, 153) - Use for third hypothesis - **Hypothesis 4**: Teal (RGB: 0, 128, 128) - Use for fourth hypothesis (if needed) - **Hypothesis 5**: Burnt Orange (RGB: 204, 85, 0) - Use for fifth hypothesis (if needed) ### Utility Colors - **Predictions**: Amber (RGB: 255, 191, 0) - For testable predictions - **Evidence**: Light Blue (RGB: 102, 178, 204) - For supporting evidence - **Comparisons**: Steel Gray (RGB: 108, 117, 125) - For critical comparisons - **Limitations**: Coral Red (RGB: 220, 53, 69) - For limitations/challenges ## Custom Box Environments ### 1. Executive Summary Box ```latex \\begin{summarybox}[Executive Summary] Content here \\end{summarybox} ``` **Use for:** High-level overview at the beginning of the document --- ### 2. Hypothesis Boxes (5 variants) ```latex \\begin{hypothesisbox1}[Hypothesis 1: Title] \\textbf{Mechanistic Explanation:} [2-3 paragraphs explaining HOW and WHY] \\textbf{Key Supporting Evidence:} \\begin{itemize} \\item Evidence point 1 \\citep{ref1} \\item Evidence point 2 \\citep{ref2} \\end{itemize} \\textbf{Core Assumptions:} \\begin{enumerate} \\item Assumption 1 \\item Assumption 2 \\end{enumerate} \\end{hypothesisbox1} ``` **Available boxes:** `hypothesisbox1`, `hypothesisbox2`, `hypothesisbox3`, `hypothesisbox4`, `hypothesisbox5` **Use for:** Presenting each competing hypothesis with its mechanism, evidence, and assumptions **Best practices for 4-page main text:** - Keep mechanistic explanations to 1-2 brief paragraphs only (6-10 sentences max) - Include 2-3 most essential evidence points with citations - List 1-2 most critical assumptions - Ensure each hypothesis is genuinely distinct - All detailed explanations go to Appendix A - **Use `\\newpage` before each hypothesis box to prevent overflow** - Each complete hypothesis box should be ≤0.6 pages --- ### 3. Prediction Box ```latex \\begin{predictionbox}[Predictions: Hypothesis 1] \\textbf{Prediction 1.1:} [Specific prediction] \\begin{itemize} \\item \\textbf{Conditions:} When/where this applies \\item \\textbf{Expected Outcome:} Specific measurable result \\item \\textbf{Falsification:} What would disprove it \\end{itemize} \\end{predictionbox} ``` **Use for:** Testable predictions derived from each hypothesis **Best practices for 4-page main text:** - Make predictions specific and quantitative when possible - Clearly state conditions under which prediction should hold - Always specify falsification criteria - Include only 1-2 most critical predictions per hypothesis in main text - Additional predictions go to appendices --- ### 4. Evidence Box ```latex \\begin{evidencebox}[Supporting Evidence] Content discussing supporting evidence \\end{evidencebox} ``` **Use for:** Highlighting key supporting evidence or literature synthesis **Best practices:** - Use sparingly in main text (detailed evidence goes in Appendix A) - Include citations for all evidence - Focus on most compelling evidence --- ### 5. Comparison Box ```latex \\begin{comparisonbox}[H1 vs. H2: Key Distinction] \\textbf{Fundamental Difference:} [Description of core difference] \\textbf{Discriminating Experiment:} [Description of experiment] \\textbf{Outcome Interpretation:} \\begin{itemize} \\item \\textbf{If [Result A]:} H1 supported \\item \\textbf{If [Result B]:} H2 supported \\end{itemize} \\end{comparisonbox} ``` **Use for:** Explaining how to distinguish between competing hypotheses **Best practices:** - Focus on fundamental mechanistic differences - Propose clear, feasible discriminating experiments - Specify concrete outcome interpretations - Create comparisons for all major hypothesis pairs --- ### 6. Limitation Box ```latex \\begin{limitationbox}[Limitations \\& Challenges] Discussion of limitations \\end{limitationbox} ``` **Use for:** Highlighting important limitations or challenges **Best practices:** - Use when limitations are particularly important - Be honest about challenges - Suggest how limitations might be addressed --- ## Document Structure ### Main Text (Maximum 4 Pages - Highly Concise) 1. **Executive Summary** (0.5-1 page) - Use `summarybox` - Brief phenomenon overview - List all hypotheses in 1 sentence each - Recommended approach 2. **Competing Hypotheses** (2-2.5 pages) - Use `hypothesisbox1`, `hypothesisbox2`, etc. - One box per hypothesis - Brief mechanistic explanation (1-2 paragraphs) + essential evidence (2-3 points) + key assumptions (1-2) - Target: 3-5 hypotheses - Keep highly concise - details go to appendices 3. **Testable Predictions** (0.5-1 page) - Use `predictionbox` for each hypothesis - 1-2 most critical predictions per hypothesis only - Very brief - full predictions in appendices 4. **Critical Comparisons** (0.5-1 page) - Use `comparisonbox` for highest priority comparison only - Show how to distinguish top hypotheses - Additional comparisons in appendices **Main text total: Maximum 4 pages - be extremely selective about what goes here** ### Appendices (Comprehensive, Detailed) **Appendix A: Comprehensive Literature Review** - Detailed background (extensive citations) - Current understanding - Evidence for each hypothesis (detailed) - Conflicting findings - Knowledge gaps - **Target: 40-60+ citations** **Appendix B: Detailed Experimental Designs** - Full protocols for each hypothesis - Methods, controls, sample sizes - Statistical approaches - Feasibility assessments - Timeline and resource requirements **Appendix C: Quality Assessment** - Detailed evaluation tables - Strengths and weaknesses analysis - Comparative scoring - Recommendations **Appendix D: Supplementary Evidence** - Analogous mechanisms - Preliminary data - Theoretical frameworks - Historical context **References** - **Target: 50+ total references** ## Citation Best Practices ### In Main Text - Cite 15-20 key papers - Use `\\citep{author2023}` for parenthetical citations - Use `\\citet{author2023}` for textual citations - Focus on most important/recent evidence ### In Appendices - Cite 40-60+ papers total - Comprehensive coverage of relevant literature - Include reviews, primary research, theoretical papers - Cite every claim and piece of evidence ### Citation Density Guidelines - Main hypothesis boxes: 2-3 citations per box (most essential only) - Main text total: 10-15 citations maximum (keep concise) - Appendix A literature sections: 8-15 citations per subsection - Experimental designs: 2-5 citations for methods/precedents - Quality assessments: Citations as needed for evaluation criteria - Total document: 50+ citations (vast majority in appendices) ## Tables ### Professional Table Formatting ```latex \\begin{hypotable}{Caption} \\begin{tabular}{|l|l|l|} \\hline \\tableheadercolor \\textcolor{white}{\\textbf{Header 1}} & \\textcolor{white}{\\textbf{Header 2}} \\\\ \\hline Data row 1 & Data \\\\ \\hline \\tablerowcolor % Alternating gray background Data row 2 & Data \\\\ \\hline \\end{tabular} \\caption{Your caption} \\end{hypotable} ``` **Best practices:** - Use `\\tableheadercolor` for header rows - Alternate `\\tablerowcolor` for tables >3 rows - Keep tables readable (not too wide) - Use for quality assessments, comparisons ## Common Formatting Patterns ### Hypothesis Section Pattern ```latex % Use \\newpage before hypothesis box to prevent overflow \\newpage \\subsection*{Hypothesis N: [Concise Title]} \\begin{hypothesisboxN}[Hypothesis N: [Title]] \\textbf{Mechanistic Explanation:} [1-2 brief paragraphs of explanation - 6-10 sentences max] \\vspace{0.3cm} \\textbf{Key Supporting Evidence:} \\begin{itemize} \\item [Evidence 1] \\citep{ref1} \\item [Evidence 2] \\citep{ref2} \\item [Evidence 3] \\citep{ref3} \\end{itemize} \\vspace{0.3cm} \\textbf{Core Assumptions:} \\begin{enumerate} \\item [Assumption 1] \\item [Assumption 2] \\end{enumerate} \\end{hypothesisboxN} \\vspace{0.5cm} ``` **Note:** The `\\newpage` before the hypothesis box ensures it starts on a fresh page, preventing overflow. This is especially important when boxes contain substantial content. ### Prediction Section Pattern ```latex \\subsection*{Predictions from Hypothesis N} \\begin{predictionbox}[Predictions: Hypothesis N] \\textbf{Prediction N.1:} [Statement] \\begin{itemize} \\item \\textbf{Conditions:} [Conditions] \\item \\textbf{Expected Outcome:} [Outcome] \\item \\textbf{Falsification:} [Falsification] \\end{itemize} \\vspace{0.2cm} \\textbf{Prediction N.2:} [Statement] [... continue ...] \\end{predictionbox} ``` ### Comparison Section Pattern ```latex \\subsection*{Distinguishing Hypothesis X vs. Hypothesis Y} \\begin{comparisonbox}[HX vs. HY: Key Distinction] \\textbf{Fundamental Difference:} [Description of core difference] \\vspace{0.3cm} \\textbf{Discriminating Experiment:} [Experiment description] \\vspace{0.3cm} \\textbf{Outcome Interpretation:} \\begin{itemize} \\item \\textbf{If [Result A]:} HX supported \\item \\textbf{If [Result B]:} HY supported \\item \\textbf{If [Result C]:} Both/neither supported \\end{itemize} \\end{comparisonbox} ``` ## Spacing and Layout ### Vertical Spacing - `\\vspace{0.3cm}` - Between elements within boxes - `\\vspace{0.5cm}` - Between major sections or boxes - `\\vspace{1cm}` - After title, before main content ### Page Breaks and Overflow Prevention **CRITICAL: Prevent Content Overflow** LaTeX boxes (tcolorbox environments) do not automatically break across pages. Content that exceeds the remaining page space will overflow and cause formatting issues. Follow these guidelines: 1. **Strategic Page Breaks Before Long Boxes:** ```latex \\newpage % Start on fresh page if box will be long \\begin{hypothesisbox1}[Hypothesis 1: Title] % Substantial content here \\end{hypothesisbox1} ``` 2. **Monitor Box Content Length:** - Each hypothesis box should be ≤0.7 pages maximum - If mechanistic explanation + evidence + assumptions exceeds ~0.6 pages, content is too long - Solution: Move detailed content to appendices, keep only essentials in main text boxes 3. **When to Use `\\newpage`:** - Before any hypothesis box with >3 subsections or >15 lines of content - Before comparison boxes with extensive experimental descriptions - Between major appendix sections - If less than 0.6 pages remain on current page before starting a new box 4. **Content Length Guidelines for Main Text:** - Executive summary box: 0.5-0.8 pages max - Each hypothesis box: 0.4-0.6 pages max - Each prediction box: 0.3-0.5 pages max - Each comparison box: 0.4-0.6 pages max 5. **Breaking Up Long Content:** ```latex % GOOD: Concise main text with page break \\newpage \\begin{hypothesisbox1}[Hypothesis 1: Brief Title] \\textbf{Mechanistic Explanation:} Brief overview in 1-2 paragraphs (6-10 sentences). \\textbf{Key Supporting Evidence:} \\begin{itemize} \\item Evidence 1 \\citep{ref1} \\item Evidence 2 \\citep{ref2} \\end{itemize} \\textbf{Core Assumptions:} \\begin{enumerate} \\item Assumption 1 \\end{enumerate} See Appendix A for detailed mechanism and comprehensive evidence. \\end{hypothesisbox1} ``` ```latex % BAD: Overly long content that will overflow \\begin{hypothesisbox1}[Hypothesis 1] \\subsection{Very Long Section} Multiple paragraphs... \\subsection{Another Long Section} More paragraphs... \\subsection{Even More Content} [Content continues beyond page boundary → OVERFLOW!] \\end{hypothesisbox1} ``` 6. **Page Break Commands:** - `\\newpage` - Force new page (recommended before long boxes) - `\\clearpage` - Force new page and flush floats (use before appendices) ### Section Spacing Already handled by style package, but you can adjust: ```latex \\vspace{0.5cm} % Add extra space if needed ``` ## Troubleshooting ### Common Issues **Issue: "File hypothesis_generation.sty not found"** - Solution: Ensure the .sty file is in the same directory as your .tex file, or in your LaTeX path **Issue: Boxes don't have colors** - Solution: Compile with XeLaTeX or LuaLaTeX, not pdfLaTeX - Command: `xelatex yourfile.tex` **Issue: Citations show as [?]** - Solution: Run bibtex after first xelatex compilation ```bash xelatex yourfile.tex bibtex yourfile xelatex yourfile.tex xelatex yourfile.tex ``` **Issue: Fonts not found** - Solution: Comment out font lines in the .sty file if custom fonts aren't installed - Lines to comment: `\\setmainfont{...}` and `\\setsansfont{...}` **Issue: Box titles overlap with content** - Solution: Add more vertical space with `\\vspace{0.3cm}` after titles **Issue: Tables too wide** - Solution: Use `\\small` or `\\footnotesize` before tabular, or use `p{width}` column specs **Issue: Content overflowing off the page** - **Cause:** Boxes (tcolorbox environments) are too long to fit on remaining page space - **Solution 1:** Add `\\newpage` before the box to start it on a fresh page - **Solution 2:** Reduce box content - move detailed information to appendices - **Solution 3:** Break content into multiple smaller boxes - **Prevention:** Keep each hypothesis box to 0.4-0.6 pages maximum; use `\\newpage` liberally before boxes with substantial content **Issue: Main text exceeds 4 pages** - **Cause:** Boxes contain too much detailed information - **Solution:** Aggressively move content to appendices - main text boxes should contain only: - Brief mechanistic overview (1-2 paragraphs) - 2-3 key evidence bullets - 1-2 core assumptions - All detailed explanations, additional evidence, and comprehensive discussions belong in Appendix A ### Package Requirements Ensure these packages are installed: - `tcolorbox` (with `most` option) - `xcolor` - `fontspec` (for XeLaTeX/LuaLaTeX) - `fancyhdr` - `titlesec` - `enumitem` - `booktabs` - `natbib` Install missing packages: ```bash # For TeX Live tlmgr install tcolorbox xcolor fontspec fancyhdr titlesec enumitem booktabs natbib # For MiKTeX (Windows) # Use MiKTeX Package Manager GUI ``` ## Style Consistency Tips 1. **Color Usage** - Always use the same color for each hypothesis throughout the document - H1 = b --- Source: [Claudary](https://claudary.paisolsolutions.com/tutorials/formatting-guide) · https://claudary.paisolsolutions.com