Research Agents for Public Health & Epidemiology

🔬 Specialized AI Agents for R-based Public Health Research

A curated collection of Claude Code plugins designed specifically for public health data science, spatial epidemiology, reproducible research, and academic writing. These agents are optimized for R workflows (tidyverse, sf, targets, quarto) and Personal Knowledge Management (Obsidian/Zotero).

🚀 Quick Start

1. Add the Marketplace

Add this repository to your Claude Code configuration:

/plugin marketplace add drarunmitra/research-agents

2. Install Research Plugins

Install the specialized plugins you need:

# 📊 Data Science & Epidemiology
/plugin install public-health-data       # Outbreak detection, epi curves, biostats
/plugin install spatial-epidemiology     # GIS, disease mapping, spatial regression

# 🧪 Research Workflow
/plugin install reproducible-research    # targets pipelines, renv, Docker
/plugin install academic-writing         # Grant proposals, Quarto manuscripts
/plugin install knowledge-management     # Obsidian & Zotero integration

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📦 Available Plugins

1. Public Health Data Science (public-health-data)

Focus: Epidemiological analysis, surveillance, and biostatistics using R.

• Agent: public-health-analyst
  • Capabilities: Incidence/prevalence calc, outbreak detection (surveillance), standardization.
  • Stack: tidyverse, epikit, epitools, incidence.
• Command: epidemic-surveillance
  • Automates the generation of epi curves and situation reports.

2. Spatial Epidemiology (spatial-epidemiology)

Focus: GIS, disease mapping, and spatial statistics.

• Agent: spatial-epidemiologist
  • Capabilities: Choropleth mapping, cluster detection (Moran's I), spatial regression.
  • Stack: sf, terra, tmap, spdep.
• Command: spatial-analysis
  • Workflows for cleaning spatial data and generating publication-quality maps.

3. Reproducible Research (reproducible-research)

Focus: Open science, computational reproducibility, and pipeline management.

• Agent: reproducibility-expert
  • Capabilities: Setting up targets pipelines, locking dependencies with renv, Dockerizing projects.
  • Stack: targets, renv, here, testthat.
• Command: reproducibility-check
  • Audits projects for absolute paths, missing seeds, and dependency issues.

4. Academic Writing (academic-writing)

Focus: Grant proposals, protocols, and reproducible manuscripts.

• Agent: public-health-writer
  • Capabilities: Drafting NIH/CDC proposals, writing IMRAD sections, editing for clarity.
  • Stack: R Markdown, Quarto, BibTeX.
• Command: academic-workflow
  • Scaffolds Quarto manuscripts with proper CSL formatting and citation management.

5. Research Knowledge Management (knowledge-management)

Focus: Personal Knowledge Management (PKM) for researchers.

• Agent: knowledge-architect
  • Capabilities: Designing Obsidian vaults, Zotero integration, Dataview dashboards.
  • Stack: Obsidian, Zotero, Dataview, Templater.
• Command: vault-setup
  • Creates a research-optimized Obsidian vault structure with templates.

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🛠️ Usage Examples

Analyze an Outbreak:

"Analyze the weekly_cases.csv file for potential outbreaks using the Farrington algorithm and plot the epi curve." (Activates public-health-analyst)

Map Disease Risk:

"Create a choropleth map of malaria incidence by district using the shapefile in data/shp. Adjust for spatial autocorrelation." (Activates spatial-epidemiologist)

Ensure Reproducibility:

"Audit this project for reproducibility. Set up a targets pipeline and lock the environment with renv." (Activates reproducibility-expert)

Draft a Proposal:

"Draft the Specific Aims section for an NIH R01 proposal on the spatial determinants of dengue fever." (Activates public-health-writer)

Organize Literature:

"Help me set up an Obsidian template for processing Zotero exports with tags and reading status." (Activates knowledge-architect)

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📄 License

MIT License