mirror of
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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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# Scientific Report Formatting Guide
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Quick reference for using the `scientific_report.sty` style package.
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## Overview
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The `scientific_report.sty` package provides professional formatting for scientific reports, technical documents, and white papers. It features:
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- **Helvetica font family** for a clean, modern appearance
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- **Professional color scheme** with blues, greens, and accent colors
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- **Colored box environments** for organizing different types of content
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- **Attractive tables** with alternating row colors and professional headers
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- **Scientific notation commands** for p-values, effect sizes, and statistics
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- **Professional headers and footers** with automatic section titles
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---
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## Color Palette
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### Primary Colors (Blues)
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| Color Name | RGB | Hex | Usage |
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|------------|-----|-----|-------|
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| `primaryblue` | (0, 51, 102) | `#003366` | Headers, titles, primary elements |
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| `secondaryblue` | (74, 144, 226) | `#4A90E2` | Subsections, secondary headings |
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| `lightblue` | (220, 235, 252) | `#DCEBFC` | Key findings box backgrounds |
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| `accentblue` | (0, 120, 215) | `#0078D7` | Accent highlights, hypothesis boxes |
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### Scientific Colors (Greens)
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| Color Name | RGB | Hex | Usage |
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|------------|-----|-----|-------|
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| `sciencegreen` | (0, 168, 150) | `#00A896` | Methodology boxes, positive findings |
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| `lightgreen` | (220, 245, 240) | `#DCF5F0` | Methodology box backgrounds |
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| `darkgreen` | (0, 128, 96) | `#008060` | Results boxes, strong evidence |
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### Warning Colors (Orange/Red)
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| Color Name | RGB | Hex | Usage |
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|------------|-----|-----|-------|
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| `cautionorange` | (255, 140, 66) | `#FF8C42` | Limitations, warnings, cautions |
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| `lightorange` | (255, 243, 224) | `#FFF3E0` | Limitations box backgrounds |
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| `criticalred` | (198, 40, 40) | `#C62828` | Critical notices, alerts |
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| `lightred` | (255, 235, 238) | `#FFEBEE` | Critical notice backgrounds |
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### Recommendation Colors
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| Color Name | RGB | Hex | Usage |
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|------------|-----|-----|-------|
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| `recommendpurple` | (103, 58, 183) | `#673AB7` | Recommendations boxes |
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| `lightpurple` | (237, 231, 246) | `#EDE7F6` | Recommendations box backgrounds |
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### Neutral Colors
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| Color Name | RGB | Hex | Usage |
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|------------|-----|-----|-------|
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| `darkgray` | (66, 66, 66) | `#424242` | Body text |
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| `mediumgray` | (117, 117, 117) | `#757575` | Secondary text, definitions |
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| `lightgray` | (245, 245, 245) | `#F5F5F5` | Backgrounds, definition boxes |
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| `tablealt` | (248, 250, 252) | `#F8FAFC` | Alternating table rows |
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---
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## Box Environments
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### Key Findings Box (Blue)
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For major findings, discoveries, and important results.
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```latex
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\begin{keyfindings}[Custom Title]
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This study found that treatment A significantly outperformed
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treatment B (\pvalue{0.001}, \effectsize{d}{0.75}).
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\end{keyfindings}
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```
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### Methodology Box (Green)
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For methods, procedures, and study design highlights.
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```latex
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\begin{methodology}[Study Design]
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This randomized controlled trial employed a 2×2 factorial design
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with pre-post measurements and 6-month follow-up.
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\end{methodology}
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```
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### Results Box (Blue-Green)
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For highlighting specific results and statistical findings.
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```latex
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\begin{resultsbox}[Primary Outcome]
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Analysis revealed a significant main effect, F(2, 147) = 12.45,
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\psig{< 0.001}, $\eta^2$ = 0.145.
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\end{resultsbox}
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```
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### Recommendations Box (Purple)
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For recommendations, implications, and action items.
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```latex
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\begin{recommendations}[Clinical Implications]
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\begin{enumerate}
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\item Implement screening protocol for high-risk patients
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\item Adjust treatment dosage based on biomarker levels
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\item Monitor patients at 3-month intervals
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\end{enumerate}
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\end{recommendations}
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```
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### Limitations Box (Orange)
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For limitations, cautions, and caveats.
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```latex
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\begin{limitations}[Study Limitations]
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\begin{itemize}
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\item Sample limited to urban populations
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\item Cross-sectional design precludes causal inference
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\item Self-report measures may introduce bias
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\end{itemize}
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\end{limitations}
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```
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### Critical Notice Box (Red)
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For critical warnings, important notices, or safety information.
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```latex
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\begin{criticalnotice}[Safety Warning]
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Patients with contraindication X should not receive this treatment.
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Consult specialist before proceeding.
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\end{criticalnotice}
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```
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### Definition Box (Gray)
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For definitions, notes, and supplementary information.
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```latex
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\begin{definition}[Key Term]
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\textbf{Effect size} refers to a quantitative measure of the
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magnitude of a phenomenon, independent of sample size.
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\end{definition}
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```
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### Executive Summary Box (Special)
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For executive summaries with enhanced styling and shadow effect.
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```latex
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\begin{executivesummary}[Report Overview]
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This report presents findings from a comprehensive analysis
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of [topic]. Key findings indicate that...
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\end{executivesummary}
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```
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### Hypothesis Box (Light Blue)
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For stating research hypotheses.
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```latex
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\begin{hypothesis}[Primary Hypothesis]
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We hypothesize that intervention X will significantly improve
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outcome Y compared to control conditions.
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\end{hypothesis}
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```
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---
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## Pull Quotes
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For highlighting important quotes or statements.
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```latex
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\begin{pullquote}
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"These findings represent a paradigm shift in our understanding
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of the underlying mechanisms."
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\end{pullquote}
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```
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---
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## Statistic Boxes
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For highlighting key statistics (use in rows of 3).
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```latex
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\begin{center}
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\statbox{n = 500}{Participants}
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\statbox{p < 0.001}{Significance}
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\statbox{d = 0.75}{Effect Size}
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\end{center}
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```
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---
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## Scientific Notation Commands
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### P-Values
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```latex
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\pvalue{0.023} % Outputs: p = 0.023
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\psig{< 0.001} % Outputs: p = < 0.001 (bold for significant)
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```
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### Confidence Intervals
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```latex
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\CI{0.45}{0.72} % Outputs: 95% CI [0.45, 0.72]
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```
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### Effect Sizes
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```latex
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\effectsize{d}{0.75} % Outputs: d = 0.75
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\effectsize{r}{0.42} % Outputs: r = 0.42
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\effectsize{F(2, 97)}{12.45} % Outputs: F(2, 97) = 12.45
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```
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### Sample Size
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```latex
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\samplesize{250} % Outputs: n = 250
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```
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### Mean with Standard Deviation
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```latex
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\meansd{42.5}{8.3} % Outputs: 42.5 ± 8.3
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```
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### Significance Indicators (for tables)
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```latex
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Result\sigone % * for p < 0.05
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Result\sigtwo % ** for p < 0.01
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Result\sigthree % *** for p < 0.001
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Result\signs % ns for not significant
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% Legend for table footnotes:
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\siglegend % Outputs: *p < 0.05; **p < 0.01; ***p < 0.001; ns not significant
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```
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### Quality/Evidence Indicators
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```latex
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\qualityhigh % HIGH (green)
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\qualitymedium % MEDIUM (orange)
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\qualitylow % LOW (red)
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\evidencestrong % Strong (green)
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\evidencemoderate % Moderate (orange)
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\evidenceweak % Weak (red)
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```
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### Trend Indicators
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```latex
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\trendup % Green up triangle ▲
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\trenddown % Red down triangle ▼
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\trendflat % Gray right arrow →
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```
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### Text Highlighting
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```latex
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\highlight{important text} % Blue bold text
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```
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---
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## Table Formatting
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### Standard Table with Alternating Rows
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```latex
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\begin{table}[htbp]
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\centering
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\caption{Descriptive Statistics by Group}
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\label{tab:descriptives}
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\begin{tabular}{@{}lccc@{}}
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\toprule
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\textbf{Variable} & \textbf{Group A} & \textbf{Group B} & \textbf{p} \\
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\midrule
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Age (years) & \meansd{42.5}{8.3} & \meansd{43.1}{7.9} & .58 \\
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\rowcolor{tablealt} Score 1 & \meansd{15.2}{3.4} & \meansd{18.7}{4.1} & <.001\sigthree \\
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Score 2 & \meansd{22.8}{5.1} & \meansd{23.4}{4.8} & .42 \\
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\rowcolor{tablealt} Score 3 & \meansd{8.9}{2.2} & \meansd{7.2}{2.5} & .003\sigtwo \\
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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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### Table with Quality Indicators
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```latex
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\begin{tabular}{@{}llcc@{}}
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\toprule
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\textbf{Study} & \textbf{Design} & \textbf{Quality} & \textbf{Evidence} \\
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\midrule
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Smith et al. (2023) & RCT & \qualityhigh & \evidencestrong \\
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\rowcolor{tablealt} Jones et al. (2022) & Cohort & \qualitymedium & \evidencemoderate \\
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Lee et al. (2021) & Cross-sectional & \qualitylow & \evidenceweak \\
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\bottomrule
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\end{tabular}
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```
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### Table with Trend Indicators
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```latex
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\begin{tabular}{@{}lrrl@{}}
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\toprule
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\textbf{Metric} & \textbf{Baseline} & \textbf{Follow-up} & \textbf{Change} \\
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\midrule
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Score A & 42.5 & 58.3 & \trendup +37\% \\
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\rowcolor{tablealt} Score B & 18.2 & 15.1 & \trenddown -17\% \\
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Score C & 7.8 & 7.9 & \trendflat +1\% \\
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\bottomrule
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\end{tabular}
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```
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---
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## Figure Formatting
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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_chart.png}
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\caption{Comparison of Outcome Scores Across Treatment Conditions}
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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/data_visualization.png}
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\caption{Distribution of Participant Responses by Category}
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\figuresource{Study data, collected January-March 2024}
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\label{fig:distribution}
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\end{figure}
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```
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### Figure with 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/model_diagram.png}
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\caption{Conceptual Model of Proposed Relationships}
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\figurenote{Solid arrows indicate direct effects; dashed arrows indicate moderated effects.}
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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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## Title Page
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### Standard Title Page
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```latex
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\makereporttitle
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{Research Report Title} % Title
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{A Comprehensive Analysis} % Subtitle
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{Author Name, PhD} % Author(s)
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{Research Institution} % Institution
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{January 2025} % Date
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```
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### Title Page with Cover Image
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```latex
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\makereporttitlewithimage
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{Research Report Title} % Title
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{A Comprehensive Analysis} % Subtitle
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{../figures/cover_image.png} % Image path
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{Author Name, PhD} % Author(s)
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{Research Institution} % Institution
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{January 2025} % Date
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```
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---
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## List Formatting
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Lists automatically use blue bullets/numbers.
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### Bullet Lists
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```latex
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\begin{itemize}
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\item First item with automatic blue bullet
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\item Second item
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\item Third item
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\end{itemize}
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```
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### Numbered Lists
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```latex
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\begin{enumerate}
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\item First item with blue number
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\item Second item
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\item Third item
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\end{enumerate}
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```
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---
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## Appendix Sections
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```latex
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\appendix
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\chapter{Supplementary Materials}
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\appendixsection{Additional Tables}
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% Content appears in table of contents
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\appendixsection{Instruments}
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% Additional appendix content
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```
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---
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## Compilation
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Compile with XeLaTeX or LuaLaTeX for best font rendering:
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```bash
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# Using XeLaTeX
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xelatex report.tex
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bibtex report # If using BibTeX
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xelatex report.tex
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xelatex report.tex
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# Using latexmk (recommended)
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latexmk -xelatex report.tex
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# Using LuaLaTeX
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lualatex report.tex
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```
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---
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## Common Patterns
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### Results Section Example
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|
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```latex
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\section{Primary Outcomes}
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\begin{resultsbox}[Main Finding]
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The intervention group showed significantly higher scores than
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the control group, \effectsize{t(98)}{3.45}, \psig{< 0.001},
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\effectsize{d}{0.69}, \CI{0.42}{0.96}.
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\end{resultsbox}
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Table~\ref{tab:outcomes} presents the complete results for all
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outcome measures.
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\begin{table}[htbp]
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\centering
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\caption{Outcome Measures by Treatment Condition}
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\label{tab:outcomes}
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\begin{tabular}{@{}lcccc@{}}
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\toprule
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\textbf{Measure} & \textbf{Control} & \textbf{Treatment} & \textbf{d} & \textbf{p} \\
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\midrule
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Primary & \meansd{42.1}{8.2} & \meansd{51.3}{9.1} & 0.69\sigthree & <.001 \\
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\rowcolor{tablealt} Secondary & \meansd{3.2}{1.1} & \meansd{4.1}{1.3} & 0.52\sigtwo & .004 \\
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Tertiary & \meansd{18.5}{4.2} & \meansd{19.2}{4.5} & 0.16\signs & .328 \\
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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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### Discussion Section Example
|
||||
|
||||
```latex
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\section{Interpretation of Findings}
|
||||
|
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\begin{keyfindings}[Summary]
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||||
\begin{enumerate}
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||||
\item Primary hypothesis \highlight{supported} with large effect
|
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\item Secondary hypothesis partially supported
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\item Evidence quality: \evidencestrong
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\end{enumerate}
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\end{keyfindings}
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\begin{limitations}
|
||||
This study has several limitations that should be considered...
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||||
\end{limitations}
|
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|
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\begin{recommendations}[Future Research]
|
||||
Future studies should address the following:
|
||||
\begin{enumerate}
|
||||
\item Replicate findings in diverse populations
|
||||
\item Extend follow-up period to assess long-term effects
|
||||
\item Investigate moderating variables
|
||||
\end{enumerate}
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||||
\end{recommendations}
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||||
```
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|
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---
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||||
## Troubleshooting
|
||||
|
||||
### Box Overflow
|
||||
If box content overflows the page:
|
||||
```latex
|
||||
\newpage
|
||||
\begin{keyfindings}[Continued...]
|
||||
```
|
||||
|
||||
### Figure Placement
|
||||
Use `[htbp]` for flexible placement, or `[H]` (requires `float` package) for exact:
|
||||
```latex
|
||||
\usepackage{float}
|
||||
\begin{figure}[H]
|
||||
```
|
||||
|
||||
### Table Too Wide
|
||||
Use `\resizebox` or reduce font size:
|
||||
```latex
|
||||
\resizebox{\textwidth}{!}{
|
||||
\begin{tabular}{...}
|
||||
...
|
||||
\end{tabular}
|
||||
}
|
||||
```
|
||||
|
||||
### Font Issues
|
||||
If Helvetica isn't rendering, ensure you're using XeLaTeX or LuaLaTeX:
|
||||
```bash
|
||||
xelatex report.tex # NOT pdflatex
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Quick Reference Card
|
||||
|
||||
| Purpose | Command/Environment |
|
||||
|---------|---------------------|
|
||||
| Major finding | `\begin{keyfindings}...\end{keyfindings}` |
|
||||
| Methods | `\begin{methodology}...\end{methodology}` |
|
||||
| Results | `\begin{resultsbox}...\end{resultsbox}` |
|
||||
| Recommendation | `\begin{recommendations}...\end{recommendations}` |
|
||||
| Limitation | `\begin{limitations}...\end{limitations}` |
|
||||
| Warning | `\begin{criticalnotice}...\end{criticalnotice}` |
|
||||
| Definition | `\begin{definition}...\end{definition}` |
|
||||
| Executive summary | `\begin{executivesummary}...\end{executivesummary}` |
|
||||
| Hypothesis | `\begin{hypothesis}...\end{hypothesis}` |
|
||||
| P-value | `\pvalue{0.05}` or `\psig{< 0.001}` |
|
||||
| Effect size | `\effectsize{d}{0.75}` |
|
||||
| Sample size | `\samplesize{250}` |
|
||||
| Mean ± SD | `\meansd{42.5}{8.3}` |
|
||||
| CI | `\CI{0.38}{0.72}` |
|
||||
| Highlight | `\highlight{text}` |
|
||||
| Alt row | `\rowcolor{tablealt}` |
|
||||
| Significance | `\sigone`, `\sigtwo`, `\sigthree`, `\signs` |
|
||||
|
||||
Reference in New Issue
Block a user