claude-scientific-skills/scientific-skills/scientific-writing/assets/REPORT_FORMATTING_GUIDE.md

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.

\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.

\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.

\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.

\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.

\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.

\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.

\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.

\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.

\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.

\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).

\begin{center}
\statbox{n = 500}{Participants}
\statbox{p < 0.001}{Significance}
\statbox{d = 0.75}{Effect Size}
\end{center}

---

Scientific Notation Commands

P-Values

\pvalue{0.023}          % Outputs: p = 0.023
\psig{< 0.001}          % Outputs: p = < 0.001 (bold for significant)

Confidence Intervals

\CI{0.45}{0.72}         % Outputs: 95% CI [0.45, 0.72]

Effect Sizes

\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

\samplesize{250}        % Outputs: n = 250

Mean with Standard Deviation

\meansd{42.5}{8.3}      % Outputs: 42.5 ± 8.3

Significance Indicators (for tables)

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

\qualityhigh            % HIGH (green)
\qualitymedium          % MEDIUM (orange)
\qualitylow             % LOW (red)

\evidencestrong         % Strong (green)
\evidencemoderate       % Moderate (orange)
\evidenceweak           % Weak (red)

Trend Indicators

\trendup                % Green up triangle ▲
\trenddown              % Red down triangle ▼
\trendflat              % Gray right arrow →

Text Highlighting

\highlight{important text}  % Blue bold text

---

Table Formatting

Standard Table with Alternating Rows

\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

\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

\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

\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

\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

\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

\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

\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

\begin{itemize}
    \item First item with automatic blue bullet
    \item Second item
    \item Third item
\end{itemize}

Numbered Lists

\begin{enumerate}
    \item First item with blue number
    \item Second item
    \item Third item
\end{enumerate}

---

Appendix Sections

\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:

# 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

\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

\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:

\newpage
\begin{keyfindings}[Continued...]

Figure Placement

Use [htbp] for flexible placement, or [H] (requires float package) for exact:

\usepackage{float}
\begin{figure}[H]

Table Too Wide

Use \resizebox or reduce font size:

\resizebox{\textwidth}{!}{
\begin{tabular}{...}
...
\end{tabular}
}

Font Issues

If Helvetica isn't rendering, ensure you're using XeLaTeX or LuaLaTeX:

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