mirror of
https://github.com/K-Dense-AI/claude-scientific-skills.git
synced 2026-01-26 16:58:56 +08:00
3439a21f57
- 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.
575 lines
14 KiB
Markdown
575 lines
14 KiB
Markdown
# Scientific Report Formatting Guide
|
||
|
||
Quick reference for using the `scientific_report.sty` style package.
|
||
|
||
## Overview
|
||
|
||
The `scientific_report.sty` package provides professional formatting for scientific reports, technical documents, and white papers. It features:
|
||
|
||
- **Helvetica font family** for a clean, modern appearance
|
||
- **Professional color scheme** with blues, greens, and accent colors
|
||
- **Colored box environments** for organizing different types of content
|
||
- **Attractive tables** with alternating row colors and professional headers
|
||
- **Scientific notation commands** for p-values, effect sizes, and statistics
|
||
- **Professional headers and footers** with automatic section titles
|
||
|
||
---
|
||
|
||
## Color Palette
|
||
|
||
### Primary Colors (Blues)
|
||
|
||
| Color Name | RGB | Hex | Usage |
|
||
|------------|-----|-----|-------|
|
||
| `primaryblue` | (0, 51, 102) | `#003366` | Headers, titles, primary elements |
|
||
| `secondaryblue` | (74, 144, 226) | `#4A90E2` | Subsections, secondary headings |
|
||
| `lightblue` | (220, 235, 252) | `#DCEBFC` | Key findings box backgrounds |
|
||
| `accentblue` | (0, 120, 215) | `#0078D7` | Accent highlights, hypothesis boxes |
|
||
|
||
### Scientific Colors (Greens)
|
||
|
||
| Color Name | RGB | Hex | Usage |
|
||
|------------|-----|-----|-------|
|
||
| `sciencegreen` | (0, 168, 150) | `#00A896` | Methodology boxes, positive findings |
|
||
| `lightgreen` | (220, 245, 240) | `#DCF5F0` | Methodology box backgrounds |
|
||
| `darkgreen` | (0, 128, 96) | `#008060` | Results boxes, strong evidence |
|
||
|
||
### Warning Colors (Orange/Red)
|
||
|
||
| Color Name | RGB | Hex | Usage |
|
||
|------------|-----|-----|-------|
|
||
| `cautionorange` | (255, 140, 66) | `#FF8C42` | Limitations, warnings, cautions |
|
||
| `lightorange` | (255, 243, 224) | `#FFF3E0` | Limitations box backgrounds |
|
||
| `criticalred` | (198, 40, 40) | `#C62828` | Critical notices, alerts |
|
||
| `lightred` | (255, 235, 238) | `#FFEBEE` | Critical notice backgrounds |
|
||
|
||
### Recommendation Colors
|
||
|
||
| Color Name | RGB | Hex | Usage |
|
||
|------------|-----|-----|-------|
|
||
| `recommendpurple` | (103, 58, 183) | `#673AB7` | Recommendations boxes |
|
||
| `lightpurple` | (237, 231, 246) | `#EDE7F6` | Recommendations box backgrounds |
|
||
|
||
### Neutral Colors
|
||
|
||
| Color Name | RGB | Hex | Usage |
|
||
|------------|-----|-----|-------|
|
||
| `darkgray` | (66, 66, 66) | `#424242` | Body text |
|
||
| `mediumgray` | (117, 117, 117) | `#757575` | Secondary text, definitions |
|
||
| `lightgray` | (245, 245, 245) | `#F5F5F5` | Backgrounds, definition boxes |
|
||
| `tablealt` | (248, 250, 252) | `#F8FAFC` | Alternating table rows |
|
||
|
||
---
|
||
|
||
## Box Environments
|
||
|
||
### Key Findings Box (Blue)
|
||
|
||
For major findings, discoveries, and important results.
|
||
|
||
```latex
|
||
\begin{keyfindings}[Custom Title]
|
||
This study found that treatment A significantly outperformed
|
||
treatment B (\pvalue{0.001}, \effectsize{d}{0.75}).
|
||
\end{keyfindings}
|
||
```
|
||
|
||
### Methodology Box (Green)
|
||
|
||
For methods, procedures, and study design highlights.
|
||
|
||
```latex
|
||
\begin{methodology}[Study Design]
|
||
This randomized controlled trial employed a 2×2 factorial design
|
||
with pre-post measurements and 6-month follow-up.
|
||
\end{methodology}
|
||
```
|
||
|
||
### Results Box (Blue-Green)
|
||
|
||
For highlighting specific results and statistical findings.
|
||
|
||
```latex
|
||
\begin{resultsbox}[Primary Outcome]
|
||
Analysis revealed a significant main effect, F(2, 147) = 12.45,
|
||
\psig{< 0.001}, $\eta^2$ = 0.145.
|
||
\end{resultsbox}
|
||
```
|
||
|
||
### Recommendations Box (Purple)
|
||
|
||
For recommendations, implications, and action items.
|
||
|
||
```latex
|
||
\begin{recommendations}[Clinical Implications]
|
||
\begin{enumerate}
|
||
\item Implement screening protocol for high-risk patients
|
||
\item Adjust treatment dosage based on biomarker levels
|
||
\item Monitor patients at 3-month intervals
|
||
\end{enumerate}
|
||
\end{recommendations}
|
||
```
|
||
|
||
### Limitations Box (Orange)
|
||
|
||
For limitations, cautions, and caveats.
|
||
|
||
```latex
|
||
\begin{limitations}[Study Limitations]
|
||
\begin{itemize}
|
||
\item Sample limited to urban populations
|
||
\item Cross-sectional design precludes causal inference
|
||
\item Self-report measures may introduce bias
|
||
\end{itemize}
|
||
\end{limitations}
|
||
```
|
||
|
||
### Critical Notice Box (Red)
|
||
|
||
For critical warnings, important notices, or safety information.
|
||
|
||
```latex
|
||
\begin{criticalnotice}[Safety Warning]
|
||
Patients with contraindication X should not receive this treatment.
|
||
Consult specialist before proceeding.
|
||
\end{criticalnotice}
|
||
```
|
||
|
||
### Definition Box (Gray)
|
||
|
||
For definitions, notes, and supplementary information.
|
||
|
||
```latex
|
||
\begin{definition}[Key Term]
|
||
\textbf{Effect size} refers to a quantitative measure of the
|
||
magnitude of a phenomenon, independent of sample size.
|
||
\end{definition}
|
||
```
|
||
|
||
### Executive Summary Box (Special)
|
||
|
||
For executive summaries with enhanced styling and shadow effect.
|
||
|
||
```latex
|
||
\begin{executivesummary}[Report Overview]
|
||
This report presents findings from a comprehensive analysis
|
||
of [topic]. Key findings indicate that...
|
||
\end{executivesummary}
|
||
```
|
||
|
||
### Hypothesis Box (Light Blue)
|
||
|
||
For stating research hypotheses.
|
||
|
||
```latex
|
||
\begin{hypothesis}[Primary Hypothesis]
|
||
We hypothesize that intervention X will significantly improve
|
||
outcome Y compared to control conditions.
|
||
\end{hypothesis}
|
||
```
|
||
|
||
---
|
||
|
||
## Pull Quotes
|
||
|
||
For highlighting important quotes or statements.
|
||
|
||
```latex
|
||
\begin{pullquote}
|
||
"These findings represent a paradigm shift in our understanding
|
||
of the underlying mechanisms."
|
||
\end{pullquote}
|
||
```
|
||
|
||
---
|
||
|
||
## Statistic Boxes
|
||
|
||
For highlighting key statistics (use in rows of 3).
|
||
|
||
```latex
|
||
\begin{center}
|
||
\statbox{n = 500}{Participants}
|
||
\statbox{p < 0.001}{Significance}
|
||
\statbox{d = 0.75}{Effect Size}
|
||
\end{center}
|
||
```
|
||
|
||
---
|
||
|
||
## Scientific Notation Commands
|
||
|
||
### P-Values
|
||
|
||
```latex
|
||
\pvalue{0.023} % Outputs: p = 0.023
|
||
\psig{< 0.001} % Outputs: p = < 0.001 (bold for significant)
|
||
```
|
||
|
||
### Confidence Intervals
|
||
|
||
```latex
|
||
\CI{0.45}{0.72} % Outputs: 95% CI [0.45, 0.72]
|
||
```
|
||
|
||
### Effect Sizes
|
||
|
||
```latex
|
||
\effectsize{d}{0.75} % Outputs: d = 0.75
|
||
\effectsize{r}{0.42} % Outputs: r = 0.42
|
||
\effectsize{F(2, 97)}{12.45} % Outputs: F(2, 97) = 12.45
|
||
```
|
||
|
||
### Sample Size
|
||
|
||
```latex
|
||
\samplesize{250} % Outputs: n = 250
|
||
```
|
||
|
||
### Mean with Standard Deviation
|
||
|
||
```latex
|
||
\meansd{42.5}{8.3} % Outputs: 42.5 ± 8.3
|
||
```
|
||
|
||
### Significance Indicators (for tables)
|
||
|
||
```latex
|
||
Result\sigone % * for p < 0.05
|
||
Result\sigtwo % ** for p < 0.01
|
||
Result\sigthree % *** for p < 0.001
|
||
Result\signs % ns for not significant
|
||
|
||
% Legend for table footnotes:
|
||
\siglegend % Outputs: *p < 0.05; **p < 0.01; ***p < 0.001; ns not significant
|
||
```
|
||
|
||
### Quality/Evidence Indicators
|
||
|
||
```latex
|
||
\qualityhigh % HIGH (green)
|
||
\qualitymedium % MEDIUM (orange)
|
||
\qualitylow % LOW (red)
|
||
|
||
\evidencestrong % Strong (green)
|
||
\evidencemoderate % Moderate (orange)
|
||
\evidenceweak % Weak (red)
|
||
```
|
||
|
||
### Trend Indicators
|
||
|
||
```latex
|
||
\trendup % Green up triangle ▲
|
||
\trenddown % Red down triangle ▼
|
||
\trendflat % Gray right arrow →
|
||
```
|
||
|
||
### Text Highlighting
|
||
|
||
```latex
|
||
\highlight{important text} % Blue bold text
|
||
```
|
||
|
||
---
|
||
|
||
## Table Formatting
|
||
|
||
### Standard Table with Alternating Rows
|
||
|
||
```latex
|
||
\begin{table}[htbp]
|
||
\centering
|
||
\caption{Descriptive Statistics by Group}
|
||
\label{tab:descriptives}
|
||
\begin{tabular}{@{}lccc@{}}
|
||
\toprule
|
||
\textbf{Variable} & \textbf{Group A} & \textbf{Group B} & \textbf{p} \\
|
||
\midrule
|
||
Age (years) & \meansd{42.5}{8.3} & \meansd{43.1}{7.9} & .58 \\
|
||
\rowcolor{tablealt} Score 1 & \meansd{15.2}{3.4} & \meansd{18.7}{4.1} & <.001\sigthree \\
|
||
Score 2 & \meansd{22.8}{5.1} & \meansd{23.4}{4.8} & .42 \\
|
||
\rowcolor{tablealt} Score 3 & \meansd{8.9}{2.2} & \meansd{7.2}{2.5} & .003\sigtwo \\
|
||
\bottomrule
|
||
\end{tabular}
|
||
|
||
\vspace{0.5em}
|
||
{\small \siglegend}
|
||
\end{table}
|
||
```
|
||
|
||
### Table with Quality Indicators
|
||
|
||
```latex
|
||
\begin{tabular}{@{}llcc@{}}
|
||
\toprule
|
||
\textbf{Study} & \textbf{Design} & \textbf{Quality} & \textbf{Evidence} \\
|
||
\midrule
|
||
Smith et al. (2023) & RCT & \qualityhigh & \evidencestrong \\
|
||
\rowcolor{tablealt} Jones et al. (2022) & Cohort & \qualitymedium & \evidencemoderate \\
|
||
Lee et al. (2021) & Cross-sectional & \qualitylow & \evidenceweak \\
|
||
\bottomrule
|
||
\end{tabular}
|
||
```
|
||
|
||
### Table with Trend Indicators
|
||
|
||
```latex
|
||
\begin{tabular}{@{}lrrl@{}}
|
||
\toprule
|
||
\textbf{Metric} & \textbf{Baseline} & \textbf{Follow-up} & \textbf{Change} \\
|
||
\midrule
|
||
Score A & 42.5 & 58.3 & \trendup +37\% \\
|
||
\rowcolor{tablealt} Score B & 18.2 & 15.1 & \trenddown -17\% \\
|
||
Score C & 7.8 & 7.9 & \trendflat +1\% \\
|
||
\bottomrule
|
||
\end{tabular}
|
||
```
|
||
|
||
---
|
||
|
||
## Figure Formatting
|
||
|
||
### Standard Figure
|
||
|
||
```latex
|
||
\begin{figure}[htbp]
|
||
\centering
|
||
\includegraphics[width=0.9\textwidth]{../figures/results_chart.png}
|
||
\caption{Comparison of Outcome Scores Across Treatment Conditions}
|
||
\label{fig:results}
|
||
\end{figure}
|
||
```
|
||
|
||
### Figure with Source Attribution
|
||
|
||
```latex
|
||
\begin{figure}[htbp]
|
||
\centering
|
||
\includegraphics[width=0.85\textwidth]{../figures/data_visualization.png}
|
||
\caption{Distribution of Participant Responses by Category}
|
||
\figuresource{Study data, collected January-March 2024}
|
||
\label{fig:distribution}
|
||
\end{figure}
|
||
```
|
||
|
||
### Figure with Note
|
||
|
||
```latex
|
||
\begin{figure}[htbp]
|
||
\centering
|
||
\includegraphics[width=0.8\textwidth]{../figures/model_diagram.png}
|
||
\caption{Conceptual Model of Proposed Relationships}
|
||
\figurenote{Solid arrows indicate direct effects; dashed arrows indicate moderated effects.}
|
||
\label{fig:model}
|
||
\end{figure}
|
||
```
|
||
|
||
---
|
||
|
||
## Title Page
|
||
|
||
### Standard Title Page
|
||
|
||
```latex
|
||
\makereporttitle
|
||
{Research Report Title} % Title
|
||
{A Comprehensive Analysis} % Subtitle
|
||
{Author Name, PhD} % Author(s)
|
||
{Research Institution} % Institution
|
||
{January 2025} % Date
|
||
```
|
||
|
||
### Title Page with Cover Image
|
||
|
||
```latex
|
||
\makereporttitlewithimage
|
||
{Research Report Title} % Title
|
||
{A Comprehensive Analysis} % Subtitle
|
||
{../figures/cover_image.png} % Image path
|
||
{Author Name, PhD} % Author(s)
|
||
{Research Institution} % Institution
|
||
{January 2025} % Date
|
||
```
|
||
|
||
---
|
||
|
||
## List Formatting
|
||
|
||
Lists automatically use blue bullets/numbers.
|
||
|
||
### Bullet Lists
|
||
|
||
```latex
|
||
\begin{itemize}
|
||
\item First item with automatic blue bullet
|
||
\item Second item
|
||
\item Third item
|
||
\end{itemize}
|
||
```
|
||
|
||
### Numbered Lists
|
||
|
||
```latex
|
||
\begin{enumerate}
|
||
\item First item with blue number
|
||
\item Second item
|
||
\item Third item
|
||
\end{enumerate}
|
||
```
|
||
|
||
---
|
||
|
||
## Appendix Sections
|
||
|
||
```latex
|
||
\appendix
|
||
|
||
\chapter{Supplementary Materials}
|
||
|
||
\appendixsection{Additional Tables}
|
||
% Content appears in table of contents
|
||
|
||
\appendixsection{Instruments}
|
||
% Additional appendix content
|
||
```
|
||
|
||
---
|
||
|
||
## Compilation
|
||
|
||
Compile with XeLaTeX or LuaLaTeX for best font rendering:
|
||
|
||
```bash
|
||
# Using XeLaTeX
|
||
xelatex report.tex
|
||
bibtex report # If using BibTeX
|
||
xelatex report.tex
|
||
xelatex report.tex
|
||
|
||
# Using latexmk (recommended)
|
||
latexmk -xelatex report.tex
|
||
|
||
# Using LuaLaTeX
|
||
lualatex report.tex
|
||
```
|
||
|
||
---
|
||
|
||
## Common Patterns
|
||
|
||
### Results Section Example
|
||
|
||
```latex
|
||
\section{Primary Outcomes}
|
||
|
||
\begin{resultsbox}[Main Finding]
|
||
The intervention group showed significantly higher scores than
|
||
the control group, \effectsize{t(98)}{3.45}, \psig{< 0.001},
|
||
\effectsize{d}{0.69}, \CI{0.42}{0.96}.
|
||
\end{resultsbox}
|
||
|
||
Table~\ref{tab:outcomes} presents the complete results for all
|
||
outcome measures.
|
||
|
||
\begin{table}[htbp]
|
||
\centering
|
||
\caption{Outcome Measures by Treatment Condition}
|
||
\label{tab:outcomes}
|
||
\begin{tabular}{@{}lcccc@{}}
|
||
\toprule
|
||
\textbf{Measure} & \textbf{Control} & \textbf{Treatment} & \textbf{d} & \textbf{p} \\
|
||
\midrule
|
||
Primary & \meansd{42.1}{8.2} & \meansd{51.3}{9.1} & 0.69\sigthree & <.001 \\
|
||
\rowcolor{tablealt} Secondary & \meansd{3.2}{1.1} & \meansd{4.1}{1.3} & 0.52\sigtwo & .004 \\
|
||
Tertiary & \meansd{18.5}{4.2} & \meansd{19.2}{4.5} & 0.16\signs & .328 \\
|
||
\bottomrule
|
||
\end{tabular}
|
||
\end{table}
|
||
```
|
||
|
||
### Discussion Section Example
|
||
|
||
```latex
|
||
\section{Interpretation of Findings}
|
||
|
||
\begin{keyfindings}[Summary]
|
||
\begin{enumerate}
|
||
\item Primary hypothesis \highlight{supported} with large effect
|
||
\item Secondary hypothesis partially supported
|
||
\item Evidence quality: \evidencestrong
|
||
\end{enumerate}
|
||
\end{keyfindings}
|
||
|
||
\begin{limitations}
|
||
This study has several limitations that should be considered...
|
||
\end{limitations}
|
||
|
||
\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}
|
||
\end{recommendations}
|
||
```
|
||
|
||
---
|
||
|
||
## 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` |
|
||
|