@wentorai/research-plugins 1.0.0 → 1.2.0

package/skills/research/automation/claude-academic-workflow-guide/SKILL.md

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+---
+name: claude-academic-workflow-guide
+description: "Claude Code template for LaTeX, Beamer, and R research workflows"
+metadata:
+  openclaw:
+    emoji: "📚"
+    category: "research"
+    subcategory: "automation"
+    keywords: ["Claude Code", "academic workflow", "LaTeX", "Beamer", "R", "multi-agent review"]
+    source: "https://github.com/pedrohcgs/claude-code-my-workflow"
+---
+
+# Claude Code Academic Workflow Guide
+
+## Overview
+
+A template and workflow guide for using Claude Code in academic research — managing LaTeX papers, Beamer presentations, R analysis scripts, and multi-agent peer review. Provides structured CLAUDE.md configurations, project templates, and automation patterns for common academic tasks. Designed for economists, social scientists, and quantitative researchers.
+
+## Project Structure
+
+```
+research-project/
+├── CLAUDE.md              # Claude Code instructions
+├── paper/
+│   ├── main.tex           # Main LaTeX document
+│   ├── references.bib     # Bibliography
+│   ├── sections/          # LaTeX sections
+│   └── figures/           # Generated figures
+├── slides/
+│   ├── presentation.tex   # Beamer slides
+│   └── figures/
+├── code/
+│   ├── analysis.R         # Main analysis
+│   ├── data_clean.R       # Data preparation
+│   └── figures.R          # Figure generation
+├── data/
+│   ├── raw/               # Original data
+│   └── processed/         # Cleaned data
+└── output/
+    ├── tables/            # LaTeX tables
+    └── figures/           # PDF/PNG figures
+```
+
+## CLAUDE.md Configuration
+
+```markdown
+# Project: [Your Paper Title]
+
+## Instructions
+- This is an academic research project in economics
+- LaTeX compiler: pdflatex (paper) or xelatex (if CJK)
+- R version: 4.3+ with tidyverse, fixest, ggplot2
+- Citation style: natbib, authoryear
+- Always compile paper after LaTeX changes
+- Run R scripts from project root
+
+## Paper Conventions
+- Use \input{sections/intro} for section includes
+- Tables: booktabs package, generated from R
+- Figures: PDF format, width=\textwidth
+- Cross-refs: \label{sec:}, \label{tab:}, \label{fig:}
+
+## R Conventions
+- Style: tidyverse style guide
+- Data: read from data/processed/
+- Output: tables/ (LaTeX), figures/ (PDF)
+- Reproducibility: set.seed(42) for all random ops
+
+## Build Commands
+- Paper: `cd paper && pdflatex main && bibtex main && pdflatex main && pdflatex main`
+- Slides: `cd slides && pdflatex presentation`
+- Analysis: `cd code && Rscript analysis.R`
+```
+
+## LaTeX Paper Workflow
+
+```bash
+# Claude Code can manage the full LaTeX workflow:
+
+# 1. Draft a section
+# "Write the methodology section for our diff-in-diff analysis"
+
+# 2. Generate tables from R output
+# "Create a LaTeX table from the regression results in output/tables/"
+
+# 3. Fix compilation errors
+# "The paper won't compile — fix the LaTeX errors"
+
+# 4. Update bibliography
+# "Add the Callaway & Sant'Anna (2021) reference"
+
+# 5. Format for submission
+# "Format the paper for AER submission guidelines"
+```
+
+## Beamer Presentations
+
+```latex
+% Template for academic presentations
+\documentclass[aspectratio=169]{beamer}
+\usetheme{metropolis}
+
+\title{Your Presentation Title}
+\subtitle{Conference/Seminar Name}
+\author{Author Name}
+\institute{University}
+\date{\today}
+
+\begin{document}
+\maketitle
+
+\begin{frame}{Motivation}
+\begin{itemize}
+    \item Research question
+    \item Why it matters
+    \item What we do
+\end{itemize}
+\end{frame}
+
+\begin{frame}{Data}
+\input{figures/summary_stats_table}
+\end{frame}
+
+\begin{frame}{Results}
+\centering
+\includegraphics[width=0.8\textwidth]{figures/main_result.pdf}
+\end{frame}
+\end{document}
+```
+
+## R Analysis Integration
+
+```r
+# analysis.R — Main analysis script
+library(tidyverse)
+library(fixest)
+library(modelsummary)
+
+# Load cleaned data
+df <- read_csv("data/processed/analysis_data.csv")
+
+# Main regression
+model1 <- feols(outcome ~ treatment | year + state, data = df)
+model2 <- feols(outcome ~ treatment + controls | year + state,
+                data = df, cluster = ~state)
+
+# Export table for LaTeX
+modelsummary(
+  list("(1)" = model1, "(2)" = model2),
+  output = "output/tables/main_results.tex",
+  stars = c("*" = 0.1, "**" = 0.05, "***" = 0.01),
+  gof_map = c("nobs", "r.squared", "FE: year", "FE: state"),
+)
+
+# Export figure
+ggplot(df, aes(x = year, y = outcome, color = treated)) +
+  geom_point(alpha = 0.3) +
+  geom_smooth(method = "loess") +
+  theme_minimal() +
+  labs(x = "Year", y = "Outcome", color = "Treatment Group")
+ggsave("output/figures/treatment_trends.pdf", width = 8, height = 5)
+```
+
+## Multi-Agent Review
+
+```markdown
+### Self-Review Workflow
+Use Claude Code to simulate peer review:
+
+1. "Review this paper as a critical referee for AER"
+2. "Check all mathematical derivations in section 3"
+3. "Verify that all tables match the R code output"
+4. "Check for consistency between text claims and results"
+5. "List potential referee objections and how to address them"
+```
+
+## Common Tasks
+
+```markdown
+### Things to ask Claude Code:
+- "Compile the paper and fix any errors"
+- "Add robustness check using propensity score matching"
+- "Create a Beamer slide summarizing Table 2"
+- "Generate event study plot from the regression results"
+- "Convert this Word draft to LaTeX format"
+- "Check all cross-references are correct"
+- "Format references in AEA style"
+```
+
+## Use Cases
+
+1. **Paper writing**: LaTeX drafting and compilation workflow
+2. **Data analysis**: R script development and debugging
+3. **Presentations**: Beamer slide creation from paper content
+4. **Self-review**: Multi-agent review simulation
+5. **Submission prep**: Format conversion for journal submission
+
+## References
+
+- [claude-code-my-workflow](https://github.com/pedrohcgs/claude-code-my-workflow)
+- [Metropolis Beamer Theme](https://github.com/matze/mtheme)
+- [modelsummary](https://modelsummary.com/)

package/skills/research/automation/coexist-ai-guide/SKILL.md

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+---
+name: coexist-ai-guide
+description: "Modular MCP-based research assistant framework"
+metadata:
+  openclaw:
+    emoji: "🧩"
+    category: "research"
+    subcategory: "automation"
+    keywords: ["CoexistAI", "MCP", "research assistant", "modular agents", "academic workflow", "framework"]
+    source: "https://github.com/SPThole/CoexistAI"
+---
+
+# CoexistAI Research Assistant Guide
+
+## Overview
+
+CoexistAI is a modular research assistant framework built on MCP (Model Context Protocol) that provides composable academic research capabilities. It offers MCP servers for paper search, citation management, data analysis, and writing assistance that can be mixed and matched with any MCP-compatible LLM client. Designed for researchers who want customizable, extensible AI research tooling.
+
+## Architecture
+
+```
+LLM Client (Claude Code / Open WebUI / etc.)
+      ↓ MCP Protocol
+  CoexistAI MCP Servers
+  ├── paper-search     (arXiv, S2, PubMed)
+  ├── citation-manager (BibTeX, formatting)
+  ├── data-analysis    (Python execution)
+  ├── writing-assist   (drafting, revision)
+  ├── note-taker       (structured notes)
+  └── custom modules   (extend as needed)
+```
+
+## Installation
+
+```bash
+# Install CoexistAI
+npm install -g @coexistai/mcp-servers
+
+# Or individual modules
+npm install -g @coexistai/paper-search
+npm install -g @coexistai/citation-manager
+npm install -g @coexistai/data-analysis
+```
+
+## MCP Configuration
+
+```json
+{
+  "mcpServers": {
+    "coexist-paper-search": {
+      "command": "npx",
+      "args": ["@coexistai/paper-search"],
+      "env": {}
+    },
+    "coexist-citation": {
+      "command": "npx",
+      "args": ["@coexistai/citation-manager"],
+      "env": {
+        "BIB_FILE": "./references.bib"
+      }
+    },
+    "coexist-analysis": {
+      "command": "npx",
+      "args": ["@coexistai/data-analysis"],
+      "env": {
+        "SANDBOX": "true"
+      }
+    }
+  }
+}
+```
+
+## Module: Paper Search
+
+```markdown
+### Available Tools
+- `search_papers(query, source, limit)` — Search academic DBs
+- `get_paper_details(id)` — Fetch full metadata
+- `find_related(id, limit)` — Find related papers
+- `get_citations(id)` — List citing papers
+- `get_references(id)` — List referenced papers
+
+### Example Usage
+"Search for papers on contrastive learning in NLP from 2023"
+→ Returns top results with title, authors, abstract, DOI
+```
+
+## Module: Citation Manager
+
+```markdown
+### Available Tools
+- `add_citation(doi)` — Add to .bib file from DOI
+- `format_citation(id, style)` — Format in APA/MLA/etc
+- `search_bib(query)` — Search existing bibliography
+- `check_duplicates()` — Find duplicate entries
+- `export_bib(format)` — Export in various formats
+
+### Example Usage
+"Add the BERT paper to my bibliography"
+→ Fetches metadata, generates BibTeX, appends to refs.bib
+```
+
+## Module: Data Analysis
+
+```markdown
+### Available Tools
+- `run_python(code)` — Execute Python in sandbox
+- `analyze_csv(path, task)` — Auto-analyze data file
+- `generate_plot(data, type)` — Create visualizations
+- `run_statistics(data, test)` — Statistical tests
+
+### Example Usage
+"Run a t-test comparing groups A and B in experiment.csv"
+→ Loads data, runs scipy.stats.ttest_ind, returns results
+```
+
+## Custom Module Development
+
+```typescript
+// Create a custom MCP module
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+
+const server = new McpServer({
+  name: "my-research-tool",
+  version: "1.0.0",
+});
+
+server.tool(
+  "custom_analysis",
+  { description: "Run custom research analysis" },
+  async (args) => {
+    // Your custom logic
+    return { result: "Analysis complete" };
+  }
+);
+```
+
+## Use Cases
+
+1. **Modular research**: Pick-and-choose research capabilities
+2. **Custom pipelines**: Build tailored research workflows
+3. **Tool integration**: Connect to existing research infrastructure
+4. **Team standardization**: Shared MCP modules across lab
+5. **Extension**: Add domain-specific research tools
+
+## References
+
+- [CoexistAI GitHub](https://github.com/SPThole/CoexistAI)
+- [MCP Specification](https://modelcontextprotocol.io/)

package/skills/research/automation/datagen-research-guide/SKILL.md

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+---
+name: datagen-research-guide
+description: "AI-driven multi-agent research assistant for end-to-end studies"
+version: 1.0.0
+author: wentor-community
+source: https://github.com/DATAGEN-AI/DATAGEN
+metadata:
+  openclaw:
+    category: "research"
+    subcategory: "automation"
+    keywords:
+      - multi-agent
+      - research-assistant
+      - data-generation
+      - study-automation
+      - pipeline-orchestration
+      - ai-research
+---
+
+# DATAGEN Research Guide
+
+A skill for orchestrating AI-driven multi-agent research workflows that handle literature review, hypothesis generation, experiment design, data analysis, and report writing. Based on the DATAGEN project (2K stars), this skill provides structured guidance on building automated research pipelines using collaborative agent architectures.
+
+## Overview
+
+Modern research increasingly benefits from AI assistance at every stage. DATAGEN's approach uses multiple specialized agents that collaborate on a research task, each handling a different aspect of the workflow. This skill teaches the agent how to coordinate such multi-agent pipelines, ensuring quality control at each handoff point and maintaining scientific rigor throughout.
+
+The multi-agent paradigm is particularly powerful for research tasks that span multiple competencies: a literature agent gathers relevant prior work, a methodology agent designs appropriate experiments, a data agent handles collection and cleaning, an analysis agent runs statistical tests, and a writing agent produces publication-ready text.
+
+## Multi-Agent Architecture
+
+The research pipeline employs these specialized agent roles:
+
+**Literature Agent**
+- Conducts systematic literature searches across academic databases
+- Filters results by relevance, recency, and citation impact
+- Extracts key findings and methodological details from selected papers
+- Identifies research gaps that motivate the current study
+- Produces structured literature summaries with citation metadata
+
+**Hypothesis Agent**
+- Generates testable hypotheses based on literature gaps
+- Evaluates feasibility of proposed hypotheses given available resources
+- Ranks hypotheses by potential impact and testability
+- Defines operationalizations for abstract constructs
+- Produces formal hypothesis statements with predicted effect directions
+
+**Experiment Agent**
+- Designs experimental protocols appropriate to the hypotheses
+- Selects control conditions and randomization strategies
+- Calculates sample size requirements and power estimates
+- Identifies potential confounds and proposes mitigation strategies
+- Generates detailed protocol documents suitable for pre-registration
+
+**Analysis Agent**
+- Selects statistical methods aligned with the experimental design
+- Implements analysis pipelines with documented parameters
+- Runs assumption checks before applying parametric tests
+- Produces visualization of results with appropriate uncertainty measures
+- Generates analysis reports with effect sizes and confidence intervals
+
+**Writing Agent**
+- Drafts sections following target journal formatting guidelines
+- Integrates results from analysis into coherent narratives
+- Ensures claims are proportional to the evidence strength
+- Manages references and in-text citations consistently
+- Produces abstracts, summaries, and highlight points
+
+## Pipeline Orchestration
+
+Coordinating multiple agents requires careful orchestration:
+
+**Task Decomposition**
+- Break the overall research question into sub-tasks aligned with agent capabilities
+- Define clear input-output contracts between agents
+- Establish quality gates at each pipeline stage
+- Allow for iterative refinement when downstream agents identify issues
+- Maintain a shared context document accessible to all agents
+
+**Quality Control**
+- Each agent output passes through a validation checkpoint
+- Cross-reference literature findings with known databases
+- Verify statistical analyses meet the assumptions of chosen tests
+- Check written outputs against reporting guidelines (APA, CONSORT, etc.)
+- Flag inconsistencies between sections for human review
+
+**Error Recovery**
+- Define fallback strategies when an agent cannot complete its task
+- Allow agents to request clarification from upstream agents
+- Implement retry logic with modified parameters for failed steps
+- Escalate to human oversight when confidence is below threshold
+- Log all decisions and their rationale for audit trails
+
+## Data Generation Workflows
+
+The DATAGEN approach excels at synthetic data generation for research:
+
+- Generate synthetic datasets matching real-world statistical properties
+- Create simulation-based datasets for power analysis and method testing
+- Produce augmented training data for machine learning experiments
+- Build synthetic control groups when ethical constraints limit real data
+- Validate analysis pipelines on known ground truth before applying to real data
+
+## Research Domain Applications
+
+This skill adapts to multiple research contexts:
+
+**Social Sciences** - Survey design, factor analysis, structural equation modeling
+**Natural Sciences** - Experimental protocols, measurement validation, replication studies
+**Computer Science** - Benchmark design, ablation studies, performance evaluation
+**Health Sciences** - Clinical trial design, meta-analysis, systematic reviews
+**Engineering** - Design of experiments, optimization, reliability testing
+
+## Integration with Research-Claw
+
+This skill coordinates with other Research-Claw capabilities:
+
+- Literature search skills feed the Literature Agent
+- Statistical analysis skills power the Analysis Agent
+- Writing and citation skills support the Writing Agent
+- Domain-specific skills provide specialized knowledge to all agents
+- The orchestration layer uses Research-Claw's task management for pipeline control
+
+## Best Practices
+
+- Always maintain human oversight at critical decision points
+- Document every automated decision with its reasoning
+- Validate automated outputs against domain expert judgment periodically
+- Start with simpler single-agent workflows before scaling to multi-agent pipelines
+- Use version control for all generated artifacts (data, analyses, drafts)
+- Ensure reproducibility by logging all random seeds and model versions

package/skills/research/automation/foam-agent-guide/SKILL.md

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+---
+name: foam-agent-guide
+description: "Agent for automated knowledge graph building from research notes"
+metadata:
+  openclaw:
+    emoji: "🫧"
+    category: "research"
+    subcategory: "automation"
+    keywords: ["Foam", "knowledge graph", "Zettelkasten", "research notes", "linked notes", "PKM agent"]
+    source: "https://github.com/foambubble/foam"
+---
+
+# Foam Agent Guide
+
+## Overview
+
+Foam is a personal knowledge management and note-sharing system built on VS Code, inspired by Roam Research. This guide covers using AI agents to automate Foam-based research workflows — extracting concepts from papers, building knowledge graphs, discovering connections between notes, and maintaining a Zettelkasten-style research knowledge base. Particularly useful for researchers managing large literature collections.
+
+## Foam Basics
+
+### Workspace Structure
+
+```
+research-foam/
+├── .foam/
+│   └── config.json          # Foam configuration
+├── .vscode/
+│   └── settings.json        # VS Code settings
+├── inbox/                   # Unprocessed notes
+├── literature/              # Paper notes (one per paper)
+├── concepts/                # Concept/topic notes
+├── projects/                # Project-specific notes
+├── daily/                   # Daily research journal
+└── README.md                # Graph entry point
+```
+
+### Note Format
+
+```markdown
+# Attention Mechanism
+
+Tags: #transformer #nlp #deep-learning
+
+## Summary
+The attention mechanism allows models to focus on relevant parts
+of the input sequence when producing output.
+
+## Key Concepts
+- [[self-attention]] computes relationships within a sequence
+- [[cross-attention]] relates two different sequences
+- [[multi-head-attention]] runs parallel attention functions
+
+## References
+- [[vaswani-2017-attention]] — original Transformer paper
+- [[bahdanau-2015-attention]] — attention for NMT
+
+## Related
+- [[transformer-architecture]]
+- [[positional-encoding]]
+```
+
+## Automated Note Generation
+
+```python
+from foam_agent import FoamAgent
+
+agent = FoamAgent(
+    workspace="./research-foam",
+    llm_provider="anthropic",
+)
+
+# Generate literature note from PDF
+note = agent.process_paper(
+    pdf_path="papers/vaswani2017attention.pdf",
+    template="literature",
+)
+# Creates: literature/vaswani-2017-attention.md
+# - Extracts title, authors, year, venue
+# - Summarizes key contributions
+# - Identifies main concepts → [[wikilinks]]
+# - Adds BibTeX reference
+
+# Batch process papers directory
+agent.process_papers_batch(
+    input_dir="papers/",
+    output_dir="literature/",
+    skip_existing=True,
+)
+```
+
+## Knowledge Graph Building
+
+```python
+# Discover connections between notes
+connections = agent.discover_connections(
+    scope="literature/",
+    min_similarity=0.7,
+)
+
+for conn in connections:
+    print(f"{conn.source} ↔ {conn.target}")
+    print(f"  Reason: {conn.reason}")
+    print(f"  Similarity: {conn.score:.2f}")
+
+# Auto-insert wikilinks for discovered connections
+agent.link_notes(connections, mode="suggest")
+# Adds [[suggested-link]] with <!-- foam:auto --> comment
+
+# Build concept map from literature notes
+concept_map = agent.build_concept_map(
+    scope="literature/",
+    min_mentions=3,
+)
+for concept in concept_map.nodes:
+    print(f"{concept.name}: mentioned in {concept.count} papers")
+```
+
+## Daily Research Journal
+
+```python
+# Generate daily note with research context
+agent.create_daily_note(
+    include=[
+        "recent_papers",        # Papers read recently
+        "open_questions",       # Unresolved questions from notes
+        "stale_notes",          # Notes not updated in 30+ days
+        "orphan_notes",         # Notes with no incoming links
+        "suggested_reading",    # Papers related to recent work
+    ],
+)
+
+# Output: daily/2025-03-10.md
+# ## Recently Added
+# - [[vaswani-2017-attention]] (added yesterday)
+#
+# ## Open Questions
+# - How does [[rotary-position-embedding]] compare to [[alibi]]?
+#
+# ## Suggested Reading
+# Based on recent notes on [[flash-attention]], consider:
+# - "FlashAttention-2: Faster Attention" (Dao, 2023)
+```
+
+## Graph Analysis
+
+```python
+# Analyze knowledge graph structure
+stats = agent.analyze_graph()
+
+print(f"Total notes: {stats.total_notes}")
+print(f"Total links: {stats.total_links}")
+print(f"Orphan notes: {stats.orphan_count}")
+print(f"Most connected: {stats.top_nodes[:5]}")
+print(f"Clusters: {stats.cluster_count}")
+
+# Identify research gaps
+gaps = agent.find_gaps()
+for gap in gaps:
+    print(f"Gap: {gap.description}")
+    print(f"  Between clusters: {gap.cluster_a} ↔ {gap.cluster_b}")
+    print(f"  Suggested topics: {gap.suggested_topics}")
+```
+
+## Configuration
+
+```json
+{
+  "foam.agent": {
+    "llm_provider": "anthropic",
+    "templates": {
+      "literature": "templates/literature.md",
+      "concept": "templates/concept.md",
+      "daily": "templates/daily.md"
+    },
+    "auto_link": {
+      "enabled": true,
+      "min_similarity": 0.75,
+      "max_suggestions_per_note": 5
+    },
+    "graph": {
+      "exclude_patterns": ["daily/*", "templates/*"],
+      "tag_colors": {
+        "transformer": "#3B82F6",
+        "nlp": "#10B981"
+      }
+    }
+  }
+}
+```
+
+## Use Cases
+
+1. **Literature management**: Auto-generate linked notes from papers
+2. **Concept mapping**: Build and visualize research concept graphs
+3. **Research journaling**: AI-assisted daily research summaries
+4. **Gap discovery**: Find under-explored connections between topics
+5. **Collaborative wikis**: Shared team research knowledge bases
+
+## References
+
+- [Foam GitHub](https://github.com/foambubble/foam)
+- [Foam Documentation](https://foambubble.github.io/foam/)
+- [Zettelkasten Method](https://zettelkasten.de/introduction/)