Write Methods Section

I'll help you write a comprehensive methods section for your statistical manuscript.

Usage: /research:manuscript:methods or /research:manuscript:methods <topic>

Examples:

• /research:manuscript:methods
• /research:manuscript:methods "bootstrap mediation analysis"

Let's write your methods section

I'll guide you through writing a rigorous statistical methods section.

<system> This command helps write methods sections for statistical manuscripts. It activates specialized skills and guides the user through the process.

Process

1. Understand the Study

   • What statistical method(s) are you using?
   • What is the research question?
   • What data do you have?

2. Structure Outline Create structured methods with:

   • Data description
   • Statistical model
   • Estimation procedure
   • Software and implementation
   • Inference approach

3. Activate Skills Automatically engages:

   • methods-paper-writer skill (writing/methods-paper-writer.md)
   • methods-communicator skill (writing/methods-communicator.md)
   • Relevant mathematical skills if needed

4. Generate Content Write each section with:

   • Clear mathematical notation
   • Proper citations
   • Reproducibility details
   • Assumptions and limitations

Key Sections

Data and Study Design

• Sample size and characteristics
• Variables and measurement
• Study design (cross-sectional, longitudinal, experimental)

Statistical Model

• Model specification with equations
• Parameters and interpretation
• Assumptions

Estimation

• Estimation method (ML, Bayesian, bootstrap, etc.)
• Software and packages
• Convergence criteria
• Sample size determination

Inference

• Hypothesis tests
• Confidence intervals
• Model comparison
• Sensitivity analyses

Best Practices

1. Mathematical Notation

   • Define all notation clearly
   • Use consistent symbols
   • Number equations for reference

2. Reproducibility

   • Specify software versions
   • Include random seeds if applicable
   • Note computational environment

3. Assumptions

   • State all assumptions explicitly
   • Justify why they're reasonable
   • Describe robustness checks

4. Citations

   • Cite methods papers
   • Cite software packages
   • Use /research:bib:search to find references

Example Interaction

User: /research:manuscript:methods "bootstrap mediation analysis"