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Enhance citation management and literature review guidelines
- Updated SKILL.md in citation management to include best practices for identifying seminal and high-impact papers, emphasizing citation count thresholds, venue quality tiers, and author reputation indicators. - Expanded literature review SKILL.md to prioritize high-impact papers, detailing citation metrics, journal tiers, and author reputation assessment. - Added comprehensive evaluation strategies for paper impact and quality in literature_search_strategies.md, including citation count significance and journal impact factor guidance. - Improved research lookup scripts to prioritize results based on citation count, venue prestige, and author reputation, enhancing the quality of research outputs.
This commit is contained in:
Vinayak Agarwal
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# Professional Report Formatting for Scientific Documents
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This reference guide covers professional formatting for scientific reports, technical documents, and white papers. Use the `scientific_report.sty` LaTeX style package for consistent, professional output.
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---
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## When to Use Professional Report Formatting
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### Use This Style For:
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- **Research reports** - Internal and external research summaries
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- **Technical reports** - Detailed technical documentation and analyses
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- **White papers** - Position papers and thought leadership documents
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- **Grant reports** - Progress reports and final grant reports
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- **Policy briefs** - Research-informed policy recommendations
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- **Industry reports** - Technical reports for industry audiences
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- **Internal research summaries** - Team and stakeholder communications
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- **Feasibility studies** - Technical and research feasibility assessments
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- **Project documentation** - Research project deliverables
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### Do NOT Use This Style For:
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- **Journal manuscripts** → Use `venue-templates` skill for journal-specific formatting
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- **Conference papers** → Use `venue-templates` skill for conference requirements
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- **Academic theses/dissertations** → Use institutional templates
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- **Peer-reviewed submissions** → Follow journal author guidelines
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**Key Distinction**: Professional report formatting prioritizes visual appeal and readability for general audiences, while journal manuscripts must follow strict publisher requirements.
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---
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## Overview of scientific_report.sty
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The `scientific_report.sty` package provides:
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| Feature | Description |
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|---------|-------------|
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| Typography | Helvetica font family for modern, professional appearance |
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| Color Scheme | Coordinated blues, greens, oranges, and purples |
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| Box Environments | Colored boxes for organizing content types |
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| Tables | Professional styling with alternating rows |
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| Figures | Consistent caption formatting |
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| Headers/Footers | Professional page headers and footers |
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| Scientific Commands | Shortcuts for p-values, effect sizes, statistics |
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### Basic Document Setup
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```latex
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\documentclass[11pt,letterpaper]{report}
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\usepackage{scientific_report}
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\begin{document}
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% Your content here
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\end{document}
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```
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**Compilation**: Use XeLaTeX or LuaLaTeX for proper Helvetica font rendering:
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```bash
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xelatex document.tex
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```
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---
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## Box Environments for Content Organization
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### Purpose and Usage
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Colored boxes help readers quickly identify different types of content. Use them strategically to highlight important information.
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### Available Box Environments
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| Environment | Color | Purpose |
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|-------------|-------|---------|
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| `keyfindings` | Blue | Major findings, discoveries, key takeaways |
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| `methodology` | Green | Methods, procedures, study design |
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| `resultsbox` | Blue-green | Statistical results, data highlights |
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| `recommendations` | Purple | Recommendations, action items, implications |
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| `limitations` | Orange | Limitations, cautions, caveats |
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| `criticalnotice` | Red | Critical warnings, safety notices |
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| `definition` | Gray | Definitions, notes, supplementary info |
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| `executivesummary` | Blue (shadow) | Executive summaries |
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| `hypothesis` | Light blue | Research hypotheses |
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### Key Findings Box
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Use for major findings and important discoveries:
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```latex
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\begin{keyfindings}[Research Highlights]
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Our analysis revealed three significant findings:
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\begin{enumerate}
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\item Treatment A was 40% more effective than control (\pvalue{0.001})
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\item Effect sizes were clinically meaningful (\effectsize{d}{0.82})
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\item Benefits persisted at 12-month follow-up
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\end{enumerate}
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\end{keyfindings}
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```
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**Best Practices:**
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- Use sparingly (1-3 per chapter maximum)
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- Reserve for genuinely important findings
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- Include specific numbers and statistics
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- Write concisely
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### Methodology Box
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Use for highlighting methods and procedures:
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```latex
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\begin{methodology}[Study Design]
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This double-blind, randomized controlled trial employed a 2×2 factorial
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design. Participants (\samplesize{450}) were randomized to one of four
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conditions: (1) Treatment A, (2) Treatment B, (3) Combined A+B, or
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(4) Placebo control.
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\end{methodology}
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```
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**Best Practices:**
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- Summarize key methodological features
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- Use at the start of methods sections
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- Include sample size and design type
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- Keep technical but accessible
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### Results Box
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Use for highlighting specific statistical results:
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```latex
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\begin{resultsbox}[Primary Outcome Analysis]
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Mixed-effects regression revealed a significant treatment × time
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interaction, \effectsize{F(3, 446)}{8.72}, \psig{< 0.001},
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$\eta^2_p$ = 0.055, indicating differential improvement across
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treatment conditions over the study period.
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\end{resultsbox}
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```
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**Best Practices:**
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- Report complete statistical information
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- Use scientific notation commands
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- Include effect sizes alongside p-values
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- One box per major analysis
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### Recommendations Box
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Use for recommendations and implications:
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```latex
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\begin{recommendations}[Clinical Practice Guidelines]
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Based on our findings, we recommend:
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\begin{enumerate}
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\item \textbf{Primary recommendation:} Implement screening protocol
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for high-risk populations.
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\item \textbf{Secondary recommendation:} Adjust treatment intensity
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based on baseline severity scores.
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\item \textbf{Monitoring:} Reassess at 3-month intervals.
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\end{enumerate}
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\end{recommendations}
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```
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**Best Practices:**
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- Make recommendations specific and actionable
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- Prioritize with clear labels
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- Link to supporting evidence
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- Include implementation guidance
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### Limitations Box
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Use for limitations, caveats, and cautions:
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```latex
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\begin{limitations}[Study Limitations]
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Several limitations should be considered:
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\begin{itemize}
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\item \textbf{Sample:} Participants were recruited from academic
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medical centers, limiting generalizability to community settings.
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\item \textbf{Design:} The observational design precludes causal
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inference about treatment effects.
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\item \textbf{Attrition:} 15% dropout rate may introduce bias.
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\end{itemize}
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\end{limitations}
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```
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**Best Practices:**
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- Be honest and thorough
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- Explain implications of each limitation
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- Suggest how future research could address limitations
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- Don't over-qualify findings
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### Critical Notice Box
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Use for critical warnings or safety information:
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```latex
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\begin{criticalnotice}[Safety Warning]
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\textbf{Contraindication:} This intervention is contraindicated for
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patients with [condition]. Monitor for [adverse effects] and discontinue
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immediately if [symptoms] occur. Report serious adverse events to [contact].
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\end{criticalnotice}
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```
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**Best Practices:**
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- Reserve for genuinely critical information
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- Be clear and direct
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- Include specific actions to take
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- Provide contact information if relevant
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### Definition Box
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Use for definitions and explanatory notes:
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```latex
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\begin{definition}[Effect Size]
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An \textbf{effect size} is a quantitative measure of the magnitude of a
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phenomenon. Unlike significance tests, effect sizes are independent of
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sample size and allow comparison across studies. Common measures include
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Cohen's \textit{d} for mean differences and Pearson's \textit{r} for
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correlations.
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\end{definition}
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```
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**Best Practices:**
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- Define technical terms at first use
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- Keep definitions concise
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- Include practical interpretation guidance
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- Use for audience-appropriate terms
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---
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## Professional Table Formatting
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### Design Principles
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1. **Clean appearance**: Use `booktabs` rules (`\toprule`, `\midrule`, `\bottomrule`)
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2. **Alternating rows**: Apply `\rowcolor{tablealt}` to every other row
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3. **Clear headers**: Bold headers for column identification
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4. **Appropriate precision**: Report statistics to appropriate decimal places
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5. **Complete information**: Include sample sizes, units, and notes
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### Standard Data Table
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```latex
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\begin{table}[htbp]
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\centering
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\caption{Demographic Characteristics by Treatment Group}
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\label{tab:demographics}
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\begin{tabular}{@{}lcc@{}}
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\toprule
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\textbf{Characteristic} & \textbf{Treatment} & \textbf{Control} \\
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& (\samplesize{225}) & (\samplesize{225}) \\
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\midrule
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Age, years, \meansd{M}{SD} & \meansd{42.3}{12.5} & \meansd{43.1}{11.8} \\
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\rowcolor{tablealt} Female, n (\%) & 128 (56.9) & 121 (53.8) \\
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Education, years, \meansd{M}{SD} & \meansd{14.2}{2.8} & \meansd{14.5}{2.6} \\
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\rowcolor{tablealt} Baseline score, \meansd{M}{SD} & \meansd{52.4}{15.3} & \meansd{51.8}{14.9} \\
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\bottomrule
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\end{tabular}
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\figurenote{No significant differences between groups at baseline (all \textit{p} > .10).}
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\end{table}
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```
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### Results Table with Significance Indicators
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```latex
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\begin{table}[htbp]
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\centering
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\caption{Treatment Effects on Primary and Secondary Outcomes}
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\label{tab:results}
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\begin{tabular}{@{}lcccc@{}}
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\toprule
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\textbf{Outcome} & \textbf{Treatment} & \textbf{Control} & \textbf{Effect} & \textbf{p} \\
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& \meansd{M}{SD} & \meansd{M}{SD} & \textbf{(d)} & \\
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\midrule
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Primary outcome & \meansd{68.4}{14.2} & \meansd{54.1}{15.8} & 0.95\sigthree & <.001 \\
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\rowcolor{tablealt} Secondary A & \meansd{4.2}{1.1} & \meansd{3.5}{1.2} & 0.61\sigtwo & .003 \\
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Secondary B & \meansd{22.8}{5.4} & \meansd{21.2}{5.1} & 0.31\sigone & .042 \\
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\rowcolor{tablealt} Secondary C & \meansd{8.9}{2.3} & \meansd{8.5}{2.4} & 0.17\signs & .285 \\
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\bottomrule
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\end{tabular}
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\vspace{0.5em}
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{\small \siglegend}
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\end{table}
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```
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### Comparison Table with Quality Ratings
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```latex
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\begin{table}[htbp]
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\centering
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\caption{Evidence Summary by Study}
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\label{tab:evidence}
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\begin{tabular}{@{}llccc@{}}
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\toprule
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\textbf{Study} & \textbf{Design} & \textbf{N} & \textbf{Quality} & \textbf{Evidence} \\
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\midrule
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Smith et al. (2024) & RCT & 450 & \qualityhigh & \evidencestrong \\
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\rowcolor{tablealt} Jones et al. (2023) & Cohort & 1,250 & \qualitymedium & \evidencemoderate \\
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Chen et al. (2023) & Case-control & 320 & \qualitymedium & \evidencemoderate \\
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\rowcolor{tablealt} Lee et al. (2022) & Cross-sectional & 890 & \qualitylow & \evidenceweak \\
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\bottomrule
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\end{tabular}
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\end{table}
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```
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---
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## Figure and Caption Styling
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### Caption Formatting
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The style package automatically formats captions with:
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- Blue, bold figure labels
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- Gray descriptive text
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- Centered alignment with margins
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### Standard Figure
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```latex
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\begin{figure}[htbp]
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\centering
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\includegraphics[width=0.9\textwidth]{../figures/results_comparison.png}
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\caption{Comparison of Outcome Scores by Treatment Condition and Time Point}
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\label{fig:results}
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\end{figure}
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```
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### Figure with Source Attribution
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```latex
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\begin{figure}[htbp]
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\centering
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\includegraphics[width=0.85\textwidth]{../figures/trend_analysis.png}
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\caption{Trends in Key Metrics Over the Study Period}
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\figuresource{Study data collected January--December 2024}
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\label{fig:trends}
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\end{figure}
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```
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### Figure with Explanatory Note
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```latex
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\begin{figure}[htbp]
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\centering
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\includegraphics[width=0.8\textwidth]{../figures/conceptual_model.png}
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\caption{Conceptual Model of Hypothesized Relationships}
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\figurenote{Solid arrows indicate primary pathways; dashed arrows indicate moderated relationships. Numbers represent standardized coefficients.}
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\label{fig:model}
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\end{figure}
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```
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---
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## Color Palette and Visual Hierarchy
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### Color Usage Guidelines
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| Color | Use For | Avoid Using For |
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|-------|---------|-----------------|
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| Primary Blue | Headers, important findings | Warnings, cautions |
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| Science Green | Methods, positive results | Negative findings |
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| Orange | Cautions, limitations | Positive findings |
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| Red | Critical warnings | Routine content |
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| Purple | Recommendations | Findings, methods |
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| Gray | Definitions, notes | Key findings |
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### Visual Hierarchy
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1. **Executive summary boxes** (shadow effect) - Most prominent
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2. **Colored content boxes** - High prominence for key content
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3. **Tables with color** - Medium prominence for data
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4. **Body text** - Standard prominence
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5. **Definition boxes** - Lower prominence for supplementary info
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### Accessibility Considerations
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- Color palette is designed to be distinguishable for common color vision deficiencies
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- All boxes have both color AND structural indicators (borders, backgrounds)
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- Text maintains sufficient contrast ratios
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- Don't rely solely on color to convey meaning
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---
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## Typography Guidelines
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### Font Specifications
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| Element | Font | Size | Color |
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|---------|------|------|-------|
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| Body text | Helvetica | 11pt | Dark gray (#424242) |
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| Chapter titles | Helvetica Bold | Huge | Primary blue (#003366) |
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| Section headings | Helvetica Bold | Large | Primary blue (#003366) |
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| Subsections | Helvetica Bold | large | Secondary blue (#4A90E2) |
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| Subsubsections | Helvetica Bold | normalsize | Dark gray (#424242) |
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### Spacing
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- Line spacing: 1.15 (for readability)
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- Paragraph spacing: 0.5em between paragraphs
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- Page margins: 1 inch on all sides
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### Best Typography Practices
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1. **Consistency**: Use the same formatting for similar elements
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2. **Hierarchy**: Use visual weight to indicate importance
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3. **Readability**: Adequate spacing and contrast
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4. **Professionalism**: Avoid mixing fonts or excessive formatting
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---
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## Scientific Notation Commands Reference
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### Statistical Reporting
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| Command | Output | When to Use |
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|---------|--------|-------------|
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| `\pvalue{0.023}` | *p* = 0.023 | Report p-values |
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| `\psig{< 0.001}` | ***p*** = < 0.001 | Significant p-values (bold) |
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| `\CI{0.45}{0.72}` | 95% CI [0.45, 0.72] | Confidence intervals |
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| `\effectsize{d}{0.75}` | d = 0.75 | Effect sizes |
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| `\samplesize{250}` | *n* = 250 | Sample sizes |
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| `\meansd{42.5}{8.3}` | 42.5 ± 8.3 | Mean with SD |
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### Significance Indicators
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| Command | Output | Meaning |
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|---------|--------|---------|
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| `\sigone` | * | p < 0.05 |
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| `\sigtwo` | ** | p < 0.01 |
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| `\sigthree` | *** | p < 0.001 |
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| `\signs` | ns | not significant |
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| `\siglegend` | Full legend | For table footnotes |
|
||||
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### Quality and Evidence Ratings
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| Command | Output | Meaning |
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|---------|--------|---------|
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| `\qualityhigh` | **HIGH** (green) | High quality |
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| `\qualitymedium` | **MEDIUM** (orange) | Moderate quality |
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| `\qualitylow` | **LOW** (red) | Low quality |
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| `\evidencestrong` | **Strong** (green) | Strong evidence |
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| `\evidencemoderate` | **Moderate** (orange) | Moderate evidence |
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| `\evidenceweak` | **Weak** (red) | Weak evidence |
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### Trend Indicators
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||||
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| Command | Symbol | Meaning |
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|---------|--------|---------|
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| `\trendup` | ▲ (green) | Increasing trend |
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| `\trenddown` | ▼ (red) | Decreasing trend |
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| `\trendflat` | → (gray) | Stable/no change |
|
||||
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||||
---
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||||
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||||
## Complete LaTeX Examples
|
||||
|
||||
### Executive Summary Example
|
||||
|
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```latex
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\chapter*{Executive Summary}
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\addcontentsline{toc}{chapter}{Executive Summary}
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||||
\begin{executivesummary}[Report Highlights]
|
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This report presents findings from a comprehensive study of [topic]
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involving \samplesize{450} participants across 12 research sites.
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||||
The research addressed [key question] using [methodology].
|
||||
\end{executivesummary}
|
||||
|
||||
\subsection*{Key Findings}
|
||||
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\begin{keyfindings}
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||||
\begin{enumerate}
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||||
\item The primary intervention demonstrated a large effect
|
||||
(\effectsize{d}{0.82}, \psig{< 0.001}).
|
||||
\item Benefits were maintained at 12-month follow-up.
|
||||
\item Cost-effectiveness analysis supports implementation.
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||||
\end{enumerate}
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||||
\end{keyfindings}
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||||
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||||
\subsection*{Recommendations}
|
||||
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||||
\begin{recommendations}
|
||||
Based on these findings, we recommend:
|
||||
\begin{enumerate}
|
||||
\item Implement the intervention in [settings].
|
||||
\item Train practitioners using the standardized protocol.
|
||||
\item Monitor outcomes using the validated measures.
|
||||
\end{enumerate}
|
||||
\end{recommendations}
|
||||
```
|
||||
|
||||
### Methods Section Example
|
||||
|
||||
```latex
|
||||
\chapter{Methods}
|
||||
|
||||
\begin{methodology}[Study Overview]
|
||||
This randomized controlled trial employed a parallel-group design with
|
||||
1:1 allocation to intervention or control conditions. The study was
|
||||
conducted across 12 sites between January 2023 and December 2024.
|
||||
\end{methodology}
|
||||
|
||||
\section{Participants}
|
||||
|
||||
A total of \samplesize{450} participants were enrolled. Eligibility
|
||||
criteria were:
|
||||
|
||||
\begin{itemize}
|
||||
\item Age 18--65 years
|
||||
\item Diagnosis of [condition] per [criteria]
|
||||
\item No contraindications to [intervention]
|
||||
\end{itemize}
|
||||
|
||||
Table~\ref{tab:participants} presents participant characteristics.
|
||||
|
||||
\begin{limitations}[Recruitment Challenges]
|
||||
Recruitment was slower than anticipated due to [reasons]. The final
|
||||
sample was 10% below target, which may affect statistical power for
|
||||
secondary analyses.
|
||||
\end{limitations}
|
||||
```
|
||||
|
||||
### Results Section Example
|
||||
|
||||
```latex
|
||||
\chapter{Results}
|
||||
|
||||
\section{Primary Outcome}
|
||||
|
||||
\begin{resultsbox}[Primary Analysis]
|
||||
Mixed-effects regression revealed a significant treatment effect,
|
||||
\effectsize{F(1, 448)}{42.18}, \psig{< 0.001}, with a large effect
|
||||
size (\effectsize{d}{0.82}). The treatment group showed significantly
|
||||
greater improvement (\meansd{16.4}{5.2} points) compared to control
|
||||
(\meansd{8.1}{4.8} points).
|
||||
\end{resultsbox}
|
||||
|
||||
Figure~\ref{fig:primary} illustrates the treatment effects over time.
|
||||
|
||||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[width=0.9\textwidth]{../figures/primary_outcome.png}
|
||||
\caption{Primary Outcome Scores by Treatment Group and Time Point}
|
||||
\figurenote{Error bars represent 95\% confidence intervals.}
|
||||
\label{fig:primary}
|
||||
\end{figure}
|
||||
|
||||
\section{Secondary Outcomes}
|
||||
|
||||
Results for secondary outcomes are presented in Table~\ref{tab:secondary}.
|
||||
```
|
||||
|
||||
### Discussion Section Example
|
||||
|
||||
```latex
|
||||
\chapter{Discussion}
|
||||
|
||||
\section{Summary of Findings}
|
||||
|
||||
\begin{keyfindings}[Main Conclusions]
|
||||
\begin{enumerate}
|
||||
\item The intervention was highly effective (primary hypothesis
|
||||
\highlight{supported})
|
||||
\item Effects were clinically meaningful and durable
|
||||
\item Evidence strength: \evidencestrong
|
||||
\end{enumerate}
|
||||
\end{keyfindings}
|
||||
|
||||
\section{Limitations}
|
||||
|
||||
\begin{limitations}
|
||||
Several limitations warrant consideration:
|
||||
\begin{itemize}
|
||||
\item The sample was predominantly [demographic], limiting
|
||||
generalizability.
|
||||
\item Attrition was higher in the control group (18\% vs. 12\%).
|
||||
\item Self-report measures may be subject to response bias.
|
||||
\end{itemize}
|
||||
\end{limitations}
|
||||
|
||||
\section{Implications}
|
||||
|
||||
\begin{recommendations}[Research Implications]
|
||||
\begin{enumerate}
|
||||
\item Replicate in diverse populations
|
||||
\item Investigate mechanisms of change
|
||||
\item Test implementation strategies
|
||||
\end{enumerate}
|
||||
\end{recommendations}
|
||||
|
||||
\begin{recommendations}[Practice Implications]
|
||||
\begin{enumerate}
|
||||
\item Adopt the intervention in [settings]
|
||||
\item Train providers using standardized protocols
|
||||
\item Monitor fidelity and outcomes
|
||||
\end{enumerate}
|
||||
\end{recommendations}
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Checklist: Professional Report Quality
|
||||
|
||||
Before finalizing your report, verify:
|
||||
|
||||
### Formatting
|
||||
- [ ] Using `scientific_report.sty` package
|
||||
- [ ] Compiled with XeLaTeX or LuaLaTeX
|
||||
- [ ] Helvetica font rendering correctly
|
||||
- [ ] Colors displaying properly
|
||||
|
||||
### Content Organization
|
||||
- [ ] Executive summary present and complete
|
||||
- [ ] Key findings highlighted in boxes
|
||||
- [ ] Methods clearly described
|
||||
- [ ] Results properly formatted with statistics
|
||||
- [ ] Limitations acknowledged
|
||||
- [ ] Recommendations are specific and actionable
|
||||
|
||||
### Tables
|
||||
- [ ] All tables have captions and labels
|
||||
- [ ] Alternating row colors applied
|
||||
- [ ] Significance indicators explained
|
||||
- [ ] Numbers formatted consistently
|
||||
|
||||
### Figures
|
||||
- [ ] All figures have captions and labels
|
||||
- [ ] Sources attributed where appropriate
|
||||
- [ ] Resolution sufficient for printing (300 DPI)
|
||||
- [ ] Referenced in text
|
||||
|
||||
### Statistical Reporting
|
||||
- [ ] P-values reported appropriately
|
||||
- [ ] Effect sizes included
|
||||
- [ ] Confidence intervals where relevant
|
||||
- [ ] Sample sizes stated
|
||||
|
||||
### Professional Appearance
|
||||
- [ ] Consistent formatting throughout
|
||||
- [ ] No orphaned headers or widows
|
||||
- [ ] Page breaks at appropriate locations
|
||||
- [ ] References complete and formatted
|
||||
|
||||
---
|
||||
|
||||
## Resources
|
||||
|
||||
### Files in This Skill
|
||||
|
||||
- `assets/scientific_report.sty` - The LaTeX style package
|
||||
- `assets/scientific_report_template.tex` - Complete report template
|
||||
- `assets/REPORT_FORMATTING_GUIDE.md` - Quick reference guide
|
||||
|
||||
### Related Skills
|
||||
|
||||
- `venue-templates` - For journal manuscripts and conference papers
|
||||
- `scientific-schematics` - For generating diagrams and figures
|
||||
- `generate-image` - For creating illustrations and graphics
|
||||
|
||||
### External Resources
|
||||
|
||||
- [LaTeX Wikibook](https://en.wikibooks.org/wiki/LaTeX) - General LaTeX reference
|
||||
- [Booktabs Package Documentation](https://ctan.org/pkg/booktabs) - Professional table styling
|
||||
- [tcolorbox Package Documentation](https://ctan.org/pkg/tcolorbox) - Colored box environments
|
||||
|
||||
Reference in New Issue
Block a user