@wentorai/research-plugins 1.0.0 → 1.2.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (415) hide show
  1. package/README.md +22 -22
  2. package/curated/analysis/README.md +82 -56
  3. package/curated/domains/README.md +225 -69
  4. package/curated/literature/README.md +115 -46
  5. package/curated/research/README.md +106 -58
  6. package/curated/tools/README.md +107 -87
  7. package/curated/writing/README.md +92 -45
  8. package/mcp-configs/academic-db/alphafold-mcp.json +20 -0
  9. package/mcp-configs/academic-db/brightspace-mcp.json +21 -0
  10. package/mcp-configs/academic-db/climatiq-mcp.json +20 -0
  11. package/mcp-configs/academic-db/gibs-mcp.json +20 -0
  12. package/mcp-configs/academic-db/gis-mcp-server.json +22 -0
  13. package/mcp-configs/academic-db/google-earth-engine-mcp.json +21 -0
  14. package/mcp-configs/academic-db/m4-clinical-mcp.json +21 -0
  15. package/mcp-configs/academic-db/medical-mcp.json +21 -0
  16. package/mcp-configs/academic-db/nexonco-mcp.json +20 -0
  17. package/mcp-configs/academic-db/omop-mcp.json +20 -0
  18. package/mcp-configs/academic-db/onekgpd-mcp.json +20 -0
  19. package/mcp-configs/academic-db/openedu-mcp.json +20 -0
  20. package/mcp-configs/academic-db/opengenes-mcp.json +20 -0
  21. package/mcp-configs/academic-db/openstax-mcp.json +21 -0
  22. package/mcp-configs/academic-db/openstreetmap-mcp.json +21 -0
  23. package/mcp-configs/academic-db/opentargets-mcp.json +21 -0
  24. package/mcp-configs/academic-db/pdb-mcp.json +21 -0
  25. package/mcp-configs/academic-db/smithsonian-mcp.json +20 -0
  26. package/mcp-configs/ai-platform/magi-researchers.json +21 -0
  27. package/mcp-configs/ai-platform/mcp-academic-researcher.json +22 -0
  28. package/mcp-configs/ai-platform/open-paper-machine.json +21 -0
  29. package/mcp-configs/ai-platform/paper-intelligence.json +21 -0
  30. package/mcp-configs/ai-platform/paper-reader.json +21 -0
  31. package/mcp-configs/ai-platform/paperdebugger.json +21 -0
  32. package/mcp-configs/browser/exa-mcp.json +20 -0
  33. package/mcp-configs/browser/mcp-searxng.json +21 -0
  34. package/mcp-configs/browser/mcp-webresearch.json +20 -0
  35. package/mcp-configs/cloud-docs/confluence-mcp.json +37 -0
  36. package/mcp-configs/cloud-docs/google-drive-mcp.json +35 -0
  37. package/mcp-configs/cloud-docs/notion-mcp.json +29 -0
  38. package/mcp-configs/communication/discord-mcp.json +29 -0
  39. package/mcp-configs/communication/discourse-mcp.json +21 -0
  40. package/mcp-configs/communication/slack-mcp.json +29 -0
  41. package/mcp-configs/communication/telegram-mcp.json +28 -0
  42. package/mcp-configs/data-platform/automl-stat-mcp.json +21 -0
  43. package/mcp-configs/data-platform/jefferson-stats-mcp.json +22 -0
  44. package/mcp-configs/data-platform/mcp-excel-server.json +21 -0
  45. package/mcp-configs/data-platform/mcp-stata.json +21 -0
  46. package/mcp-configs/data-platform/mcpstack-jupyter.json +21 -0
  47. package/mcp-configs/data-platform/ml-mcp.json +21 -0
  48. package/mcp-configs/data-platform/nasdaq-data-link-mcp.json +20 -0
  49. package/mcp-configs/data-platform/numpy-mcp.json +21 -0
  50. package/mcp-configs/database/neo4j-mcp.json +37 -0
  51. package/mcp-configs/database/postgres-mcp.json +28 -0
  52. package/mcp-configs/database/sqlite-mcp.json +29 -0
  53. package/mcp-configs/dev-platform/geogebra-mcp.json +21 -0
  54. package/mcp-configs/dev-platform/github-mcp.json +31 -0
  55. package/mcp-configs/dev-platform/gitlab-mcp.json +34 -0
  56. package/mcp-configs/dev-platform/latex-mcp-server.json +21 -0
  57. package/mcp-configs/dev-platform/manim-mcp.json +20 -0
  58. package/mcp-configs/dev-platform/mcp-echarts.json +20 -0
  59. package/mcp-configs/dev-platform/panel-viz-mcp.json +20 -0
  60. package/mcp-configs/dev-platform/paperbanana.json +20 -0
  61. package/mcp-configs/dev-platform/texflow-mcp.json +20 -0
  62. package/mcp-configs/dev-platform/texmcp.json +20 -0
  63. package/mcp-configs/dev-platform/typst-mcp.json +21 -0
  64. package/mcp-configs/dev-platform/vizro-mcp.json +20 -0
  65. package/mcp-configs/email/email-mcp.json +40 -0
  66. package/mcp-configs/email/gmail-mcp.json +37 -0
  67. package/mcp-configs/note-knowledge/local-faiss-mcp.json +21 -0
  68. package/mcp-configs/note-knowledge/mcp-memory-service.json +21 -0
  69. package/mcp-configs/note-knowledge/mcp-obsidian.json +23 -0
  70. package/mcp-configs/note-knowledge/mcp-ragdocs.json +20 -0
  71. package/mcp-configs/note-knowledge/mcp-summarizer.json +21 -0
  72. package/mcp-configs/note-knowledge/mediawiki-mcp.json +21 -0
  73. package/mcp-configs/note-knowledge/openzim-mcp.json +20 -0
  74. package/mcp-configs/note-knowledge/zettelkasten-mcp.json +21 -0
  75. package/mcp-configs/reference-mgr/academic-paper-mcp-http.json +20 -0
  76. package/mcp-configs/reference-mgr/academix.json +20 -0
  77. package/mcp-configs/reference-mgr/arxiv-research-mcp.json +21 -0
  78. package/mcp-configs/reference-mgr/google-scholar-abstract-mcp.json +19 -0
  79. package/mcp-configs/reference-mgr/google-scholar-mcp.json +20 -0
  80. package/mcp-configs/reference-mgr/mcp-paperswithcode.json +21 -0
  81. package/mcp-configs/reference-mgr/mcp-scholarly.json +20 -0
  82. package/mcp-configs/reference-mgr/mcp-simple-arxiv.json +20 -0
  83. package/mcp-configs/reference-mgr/mcp-simple-pubmed.json +20 -0
  84. package/mcp-configs/reference-mgr/mcp-zotero.json +21 -0
  85. package/mcp-configs/reference-mgr/mendeley-mcp.json +20 -0
  86. package/mcp-configs/reference-mgr/ncbi-mcp-server.json +22 -0
  87. package/mcp-configs/reference-mgr/onecite.json +21 -0
  88. package/mcp-configs/reference-mgr/paper-search-mcp.json +21 -0
  89. package/mcp-configs/reference-mgr/pubmed-search-mcp.json +21 -0
  90. package/mcp-configs/reference-mgr/scholar-mcp.json +21 -0
  91. package/mcp-configs/reference-mgr/scholar-multi-mcp.json +21 -0
  92. package/mcp-configs/reference-mgr/seerai.json +21 -0
  93. package/mcp-configs/reference-mgr/semantic-scholar-fastmcp.json +21 -0
  94. package/mcp-configs/reference-mgr/sourcelibrary.json +20 -0
  95. package/mcp-configs/registry.json +178 -149
  96. package/mcp-configs/repository/dataverse-mcp.json +33 -0
  97. package/mcp-configs/repository/huggingface-mcp.json +29 -0
  98. package/openclaw.plugin.json +2 -2
  99. package/package.json +2 -2
  100. package/skills/analysis/dataviz/algorithm-visualizer-guide/SKILL.md +259 -0
  101. package/skills/analysis/dataviz/bokeh-visualization-guide/SKILL.md +270 -0
  102. package/skills/analysis/dataviz/chart-image-generator/SKILL.md +229 -0
  103. package/skills/analysis/dataviz/citation-map-guide/SKILL.md +184 -0
  104. package/skills/analysis/dataviz/d3-visualization-guide/SKILL.md +281 -0
  105. package/skills/analysis/dataviz/data-visualization-principles/SKILL.md +171 -0
  106. package/skills/analysis/dataviz/echarts-visualization-guide/SKILL.md +250 -0
  107. package/skills/analysis/dataviz/metabase-analytics-guide/SKILL.md +242 -0
  108. package/skills/analysis/dataviz/plotly-interactive-guide/SKILL.md +266 -0
  109. package/skills/analysis/dataviz/redash-analytics-guide/SKILL.md +284 -0
  110. package/skills/analysis/econometrics/econml-causal-guide/SKILL.md +163 -0
  111. package/skills/analysis/econometrics/empirical-paper-analysis/SKILL.md +192 -0
  112. package/skills/analysis/econometrics/mostly-harmless-guide/SKILL.md +139 -0
  113. package/skills/analysis/econometrics/panel-data-analyst/SKILL.md +259 -0
  114. package/skills/analysis/econometrics/panel-data-regression-workflow/SKILL.md +267 -0
  115. package/skills/analysis/econometrics/python-causality-guide/SKILL.md +134 -0
  116. package/skills/analysis/econometrics/stata-accounting-guide/SKILL.md +269 -0
  117. package/skills/analysis/econometrics/stata-analyst-guide/SKILL.md +245 -0
  118. package/skills/analysis/econometrics/stata-reference-guide/SKILL.md +293 -0
  119. package/skills/analysis/statistics/data-anomaly-detection/SKILL.md +157 -0
  120. package/skills/analysis/statistics/general-statistics-guide/SKILL.md +226 -0
  121. package/skills/analysis/statistics/infiagent-benchmark-guide/SKILL.md +106 -0
  122. package/skills/analysis/statistics/ml-experiment-tracker/SKILL.md +212 -0
  123. package/skills/analysis/statistics/pywayne-statistics-guide/SKILL.md +192 -0
  124. package/skills/analysis/statistics/quantitative-methods-guide/SKILL.md +193 -0
  125. package/skills/analysis/statistics/senior-data-scientist-guide/SKILL.md +223 -0
  126. package/skills/analysis/wrangling/claude-data-analysis-guide/SKILL.md +100 -0
  127. package/skills/analysis/wrangling/csv-data-analyzer/SKILL.md +170 -0
  128. package/skills/analysis/wrangling/data-cleaning-pipeline/SKILL.md +266 -0
  129. package/skills/analysis/wrangling/data-cog-guide/SKILL.md +178 -0
  130. package/skills/analysis/wrangling/open-data-scientist-guide/SKILL.md +197 -0
  131. package/skills/analysis/wrangling/stata-data-cleaning/SKILL.md +276 -0
  132. package/skills/analysis/wrangling/streamline-analyst-guide/SKILL.md +119 -0
  133. package/skills/analysis/wrangling/survey-data-processing/SKILL.md +298 -0
  134. package/skills/domains/ai-ml/ai-agent-papers-guide/SKILL.md +146 -0
  135. package/skills/domains/ai-ml/ai-model-benchmarking/SKILL.md +209 -0
  136. package/skills/domains/ai-ml/annotated-dl-papers-guide/SKILL.md +159 -0
  137. package/skills/domains/ai-ml/anomaly-detection-papers-guide/SKILL.md +167 -0
  138. package/skills/domains/ai-ml/autonomous-agents-papers-guide/SKILL.md +178 -0
  139. package/skills/domains/ai-ml/dl-transformer-finetune/SKILL.md +239 -0
  140. package/skills/domains/ai-ml/domain-adaptation-papers-guide/SKILL.md +173 -0
  141. package/skills/domains/ai-ml/generative-ai-guide/SKILL.md +146 -0
  142. package/skills/domains/ai-ml/graph-learning-papers-guide/SKILL.md +125 -0
  143. package/skills/domains/ai-ml/huggingface-inference-guide/SKILL.md +196 -0
  144. package/skills/domains/ai-ml/keras-deep-learning/SKILL.md +210 -0
  145. package/skills/domains/ai-ml/kolmogorov-arnold-networks-guide/SKILL.md +185 -0
  146. package/skills/domains/ai-ml/llm-from-scratch-guide/SKILL.md +124 -0
  147. package/skills/domains/ai-ml/ml-pipeline-guide/SKILL.md +295 -0
  148. package/skills/domains/ai-ml/nlp-toolkit-guide/SKILL.md +247 -0
  149. package/skills/domains/ai-ml/npcpy-research-guide/SKILL.md +137 -0
  150. package/skills/domains/ai-ml/pytorch-guide/SKILL.md +281 -0
  151. package/skills/domains/ai-ml/pytorch-lightning-guide/SKILL.md +244 -0
  152. package/skills/domains/ai-ml/responsible-ai-guide/SKILL.md +126 -0
  153. package/skills/domains/ai-ml/tensorflow-guide/SKILL.md +241 -0
  154. package/skills/domains/ai-ml/vmas-simulator-guide/SKILL.md +129 -0
  155. package/skills/domains/biomedical/bioagents-guide/SKILL.md +308 -0
  156. package/skills/domains/biomedical/clawbio-guide/SKILL.md +167 -0
  157. package/skills/domains/biomedical/clinical-dialogue-agents-guide/SKILL.md +145 -0
  158. package/skills/domains/biomedical/ena-sequence-api/SKILL.md +175 -0
  159. package/skills/domains/biomedical/genomas-guide/SKILL.md +126 -0
  160. package/skills/domains/biomedical/genotex-benchmark-guide/SKILL.md +125 -0
  161. package/skills/domains/biomedical/med-researcher-guide/SKILL.md +161 -0
  162. package/skills/domains/biomedical/med-researcher-r1-guide/SKILL.md +146 -0
  163. package/skills/domains/biomedical/medgeclaw-guide/SKILL.md +345 -0
  164. package/skills/domains/biomedical/medical-imaging-guide/SKILL.md +305 -0
  165. package/skills/domains/biomedical/ncbi-blast-api/SKILL.md +195 -0
  166. package/skills/domains/biomedical/ncbi-datasets-api/SKILL.md +220 -0
  167. package/skills/domains/biomedical/quickgo-api/SKILL.md +181 -0
  168. package/skills/domains/business/architecture-design-guide/SKILL.md +279 -0
  169. package/skills/domains/business/innovation-management-guide/SKILL.md +257 -0
  170. package/skills/domains/business/operations-research-guide/SKILL.md +258 -0
  171. package/skills/domains/business/xpert-bi-guide/SKILL.md +84 -0
  172. package/skills/domains/chemistry/cactus-cheminformatics-guide/SKILL.md +89 -0
  173. package/skills/domains/chemistry/chemeagle-guide/SKILL.md +147 -0
  174. package/skills/domains/chemistry/chemgraph-agent-guide/SKILL.md +120 -0
  175. package/skills/domains/chemistry/molecular-dynamics-guide/SKILL.md +237 -0
  176. package/skills/domains/chemistry/pubchem-api-guide/SKILL.md +180 -0
  177. package/skills/domains/chemistry/spectroscopy-analysis-guide/SKILL.md +290 -0
  178. package/skills/domains/cs/ai-security-papers-guide/SKILL.md +103 -0
  179. package/skills/domains/cs/code-llm-papers-guide/SKILL.md +131 -0
  180. package/skills/domains/cs/distributed-systems-guide/SKILL.md +268 -0
  181. package/skills/domains/cs/formal-verification-guide/SKILL.md +298 -0
  182. package/skills/domains/cs/gaussian-splatting-papers-guide/SKILL.md +158 -0
  183. package/skills/domains/cs/llm-aiops-guide/SKILL.md +70 -0
  184. package/skills/domains/cs/software-heritage-api/SKILL.md +200 -0
  185. package/skills/domains/ecology/species-distribution-guide/SKILL.md +343 -0
  186. package/skills/domains/economics/imf-data-api-guide/SKILL.md +174 -0
  187. package/skills/domains/economics/nber-working-papers-api/SKILL.md +177 -0
  188. package/skills/domains/economics/post-labor-economics/SKILL.md +254 -0
  189. package/skills/domains/economics/pricing-psychology-guide/SKILL.md +273 -0
  190. package/skills/domains/economics/repec-economics-api/SKILL.md +188 -0
  191. package/skills/domains/economics/world-bank-data-guide/SKILL.md +179 -0
  192. package/skills/domains/education/academic-study-methods/SKILL.md +228 -0
  193. package/skills/domains/education/assessment-design-guide/SKILL.md +213 -0
  194. package/skills/domains/education/educational-research-methods/SKILL.md +179 -0
  195. package/skills/domains/education/edumcp-guide/SKILL.md +74 -0
  196. package/skills/domains/education/mooc-analytics-guide/SKILL.md +206 -0
  197. package/skills/domains/education/open-syllabus-api/SKILL.md +171 -0
  198. package/skills/domains/finance/akshare-finance-data/SKILL.md +207 -0
  199. package/skills/domains/finance/finsight-research-guide/SKILL.md +113 -0
  200. package/skills/domains/finance/options-analytics-agent-guide/SKILL.md +117 -0
  201. package/skills/domains/finance/portfolio-optimization-guide/SKILL.md +279 -0
  202. package/skills/domains/finance/risk-modeling-guide/SKILL.md +260 -0
  203. package/skills/domains/finance/stata-accounting-research/SKILL.md +372 -0
  204. package/skills/domains/geoscience/climate-modeling-guide/SKILL.md +215 -0
  205. package/skills/domains/geoscience/pangaea-data-api/SKILL.md +197 -0
  206. package/skills/domains/geoscience/satellite-remote-sensing/SKILL.md +193 -0
  207. package/skills/domains/geoscience/seismology-data-guide/SKILL.md +208 -0
  208. package/skills/domains/humanities/digital-humanities-methods/SKILL.md +232 -0
  209. package/skills/domains/humanities/ethical-philosophy-guide/SKILL.md +244 -0
  210. package/skills/domains/humanities/history-research-guide/SKILL.md +260 -0
  211. package/skills/domains/humanities/political-history-guide/SKILL.md +241 -0
  212. package/skills/domains/law/caselaw-access-api/SKILL.md +149 -0
  213. package/skills/domains/law/legal-agent-skills-guide/SKILL.md +132 -0
  214. package/skills/domains/law/legal-nlp-guide/SKILL.md +236 -0
  215. package/skills/domains/law/legal-research-methods/SKILL.md +190 -0
  216. package/skills/domains/law/opencontracts-guide/SKILL.md +168 -0
  217. package/skills/domains/law/patent-analysis-guide/SKILL.md +257 -0
  218. package/skills/domains/law/regulatory-compliance-guide/SKILL.md +267 -0
  219. package/skills/domains/math/lean-theorem-proving-guide/SKILL.md +140 -0
  220. package/skills/domains/math/symbolic-computation-guide/SKILL.md +263 -0
  221. package/skills/domains/math/topology-data-analysis/SKILL.md +305 -0
  222. package/skills/domains/pharma/clinical-trial-design-guide/SKILL.md +271 -0
  223. package/skills/domains/pharma/drug-target-interaction/SKILL.md +242 -0
  224. package/skills/domains/pharma/madd-drug-discovery-guide/SKILL.md +153 -0
  225. package/skills/domains/pharma/pharmacovigilance-guide/SKILL.md +216 -0
  226. package/skills/domains/physics/astrophysics-data-guide/SKILL.md +305 -0
  227. package/skills/domains/physics/particle-physics-guide/SKILL.md +287 -0
  228. package/skills/domains/social-science/ipums-microdata-api/SKILL.md +211 -0
  229. package/skills/domains/social-science/network-analysis-guide/SKILL.md +310 -0
  230. package/skills/domains/social-science/psychology-research-guide/SKILL.md +270 -0
  231. package/skills/domains/social-science/sociology-research-guide/SKILL.md +238 -0
  232. package/skills/domains/social-science/sociology-research-methods/SKILL.md +181 -0
  233. package/skills/literature/discovery/arxiv-paper-monitoring/SKILL.md +233 -0
  234. package/skills/literature/discovery/paper-recommendation-guide/SKILL.md +120 -0
  235. package/skills/literature/discovery/papers-we-love-guide/SKILL.md +169 -0
  236. package/skills/literature/discovery/semantic-paper-radar/SKILL.md +144 -0
  237. package/skills/literature/discovery/zotero-arxiv-daily-guide/SKILL.md +94 -0
  238. package/skills/literature/fulltext/bioc-pmc-api/SKILL.md +146 -0
  239. package/skills/literature/fulltext/core-api-guide/SKILL.md +144 -0
  240. package/skills/literature/fulltext/dataverse-api/SKILL.md +215 -0
  241. package/skills/literature/fulltext/hal-archive-api/SKILL.md +218 -0
  242. package/skills/literature/fulltext/institutional-repository-guide/SKILL.md +212 -0
  243. package/skills/literature/fulltext/open-access-mining-guide/SKILL.md +341 -0
  244. package/skills/literature/fulltext/osf-api/SKILL.md +212 -0
  245. package/skills/literature/fulltext/pmc-ftp-bulk-download/SKILL.md +182 -0
  246. package/skills/literature/fulltext/zotero-ai-butler-guide/SKILL.md +166 -0
  247. package/skills/literature/fulltext/zotero-scihub-guide/SKILL.md +168 -0
  248. package/skills/literature/metadata/academic-paper-summarizer/SKILL.md +101 -0
  249. package/skills/literature/metadata/bibliometrix-guide/SKILL.md +164 -0
  250. package/skills/literature/metadata/crossref-event-data-api/SKILL.md +183 -0
  251. package/skills/literature/metadata/doi-content-negotiation/SKILL.md +202 -0
  252. package/skills/literature/metadata/orkg-api/SKILL.md +153 -0
  253. package/skills/literature/metadata/plumx-metrics-api/SKILL.md +188 -0
  254. package/skills/literature/metadata/ror-organization-api/SKILL.md +208 -0
  255. package/skills/literature/metadata/sophosia-reference-guide/SKILL.md +110 -0
  256. package/skills/literature/metadata/viaf-authority-api/SKILL.md +209 -0
  257. package/skills/literature/metadata/wikidata-api-guide/SKILL.md +156 -0
  258. package/skills/literature/metadata/zoplicate-dedup-guide/SKILL.md +147 -0
  259. package/skills/literature/metadata/zotero-actions-tags-guide/SKILL.md +212 -0
  260. package/skills/literature/metadata/zotmoov-guide/SKILL.md +120 -0
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  262. package/skills/literature/search/arxiv-batch-reporting/SKILL.md +133 -0
  263. package/skills/literature/search/arxiv-cli-tools/SKILL.md +172 -0
  264. package/skills/literature/search/arxiv-osiris/SKILL.md +199 -0
  265. package/skills/literature/search/arxiv-paper-processor/SKILL.md +141 -0
  266. package/skills/literature/search/baidu-scholar-guide/SKILL.md +110 -0
  267. package/skills/literature/search/base-academic-search/SKILL.md +196 -0
  268. package/skills/literature/search/chatpaper-guide/SKILL.md +122 -0
  269. package/skills/literature/search/citeseerx-api/SKILL.md +183 -0
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1
+ ---
2
+ name: rd-agent-guide
3
+ description: "Microsoft AI-driven R&D agent for automated data and model development"
4
+ metadata:
5
+ openclaw:
6
+ emoji: "🤖"
7
+ category: "research"
8
+ subcategory: "automation"
9
+ keywords: ["r-and-d", "microsoft", "automation", "model-development", "data-science", "experiment-automation"]
10
+ source: "https://github.com/microsoft/RD-Agent"
11
+ ---
12
+
13
+ # RD-Agent Guide
14
+
15
+ ## Overview
16
+
17
+ RD-Agent is an open-source AI-powered research and development automation framework developed by Microsoft Research, with over 12,000 stars on GitHub. It automates key steps in the R&D lifecycle -- including hypothesis generation, experiment design, code implementation, and result analysis -- enabling researchers and data scientists to accelerate their development cycles significantly.
18
+
19
+ The framework implements a closed-loop R&D automation pipeline where an AI agent iteratively proposes hypotheses, implements experiments, evaluates results, and refines its approach based on feedback. This mirrors the scientific method but operates at machine speed, allowing researchers to explore a much larger space of ideas and configurations than would be feasible manually.
20
+
21
+ RD-Agent is particularly valuable for researchers working in quantitative finance, data science, and machine learning, where the development process involves iterating on feature engineering, model architectures, and hyperparameter configurations. The framework has demonstrated the ability to autonomously develop competitive machine learning models and trading strategies, achieving results comparable to experienced human practitioners.
22
+
23
+ ## Installation and Setup
24
+
25
+ ```bash
26
+ # Clone the repository
27
+ git clone https://github.com/microsoft/RD-Agent.git
28
+ cd RD-Agent
29
+
30
+ # Install dependencies
31
+ pip install -e .
32
+
33
+ # Or install from PyPI
34
+ pip install rdagent
35
+ ```
36
+
37
+ ### Environment Configuration
38
+
39
+ ```bash
40
+ # LLM configuration (required)
41
+ export OPENAI_API_KEY=$OPENAI_API_KEY
42
+ export CHAT_MODEL=gpt-4o
43
+
44
+ # Or use Azure OpenAI
45
+ export AZURE_OPENAI_API_KEY=$AZURE_OPENAI_API_KEY
46
+ export AZURE_OPENAI_ENDPOINT=$AZURE_OPENAI_ENDPOINT
47
+ export AZURE_OPENAI_DEPLOYMENT=$AZURE_OPENAI_DEPLOYMENT
48
+
49
+ # Docker is required for sandboxed code execution
50
+ # Ensure Docker is installed and running
51
+ docker --version
52
+ ```
53
+
54
+ RD-Agent uses Docker containers to execute generated code safely, ensuring that automatically generated experiments cannot affect the host system. This sandboxed execution is critical for an autonomous agent that writes and runs arbitrary code.
55
+
56
+ ## Core Concepts
57
+
58
+ ### The R&D Loop
59
+
60
+ RD-Agent implements a continuous improvement loop with four phases:
61
+
62
+ 1. **Proposal**: The agent analyzes the current state and proposes new hypotheses or improvements
63
+ 2. **Implementation**: Hypotheses are translated into executable code (feature engineering, model changes, etc.)
64
+ 3. **Evaluation**: The implemented changes are executed in a sandbox and results are measured against defined metrics
65
+ 4. **Feedback**: Results are analyzed and used to inform the next round of proposals
66
+
67
+ ```python
68
+ from rdagent.core.runner import RDRunner
69
+ from rdagent.scenarios.data_science import DataScienceScenario
70
+
71
+ # Define the research scenario
72
+ scenario = DataScienceScenario(
73
+ task="tabular_classification",
74
+ dataset_path="path/to/dataset.csv",
75
+ target_column="label",
76
+ metric="auc",
77
+ )
78
+
79
+ # Create and run the R&D agent
80
+ runner = RDRunner(
81
+ scenario=scenario,
82
+ max_iterations=50,
83
+ llm_model="gpt-4o",
84
+ )
85
+
86
+ # Start the autonomous R&D loop
87
+ results = runner.run()
88
+
89
+ # Review the best solution found
90
+ print(f"Best metric: {results.best_score}")
91
+ print(f"Iterations: {results.total_iterations}")
92
+ print(f"Solutions explored: {results.num_solutions}")
93
+ ```
94
+
95
+ ### Scenario Types
96
+
97
+ RD-Agent supports multiple R&D scenarios out of the box:
98
+
99
+ #### Data Science / Kaggle Competitions
100
+
101
+ Automatically engineer features, select models, and tune hyperparameters for tabular data tasks:
102
+
103
+ ```python
104
+ from rdagent.scenarios.data_science import DataScienceScenario
105
+
106
+ scenario = DataScienceScenario(
107
+ task="tabular_regression",
108
+ dataset_path="data/housing.csv",
109
+ target_column="price",
110
+ metric="rmse",
111
+ time_budget_hours=4,
112
+ )
113
+ ```
114
+
115
+ #### Quantitative Finance
116
+
117
+ Develop and backtest trading factors and strategies:
118
+
119
+ ```python
120
+ from rdagent.scenarios.qlib import QlibScenario
121
+
122
+ scenario = QlibScenario(
123
+ market="csi300",
124
+ task="alpha_factor_mining",
125
+ backtest_start="2020-01-01",
126
+ backtest_end="2024-12-31",
127
+ metric="information_coefficient",
128
+ )
129
+ ```
130
+
131
+ #### Model Development
132
+
133
+ Iterate on model architectures and training procedures:
134
+
135
+ ```python
136
+ from rdagent.scenarios.model_dev import ModelDevScenario
137
+
138
+ scenario = ModelDevScenario(
139
+ task="image_classification",
140
+ base_model="resnet50",
141
+ dataset="cifar100",
142
+ optimization_target="accuracy",
143
+ )
144
+ ```
145
+
146
+ ## Advanced Features
147
+
148
+ ### Experiment Tracking and Analysis
149
+
150
+ RD-Agent maintains detailed logs of all experiments, enabling post-hoc analysis of the R&D process:
151
+
152
+ ```python
153
+ # Access experiment history
154
+ for experiment in results.history:
155
+ print(f"Iteration {experiment.iteration}:")
156
+ print(f" Hypothesis: {experiment.hypothesis}")
157
+ print(f" Changes: {experiment.code_changes}")
158
+ print(f" Metric: {experiment.score}")
159
+ print(f" Analysis: {experiment.feedback}")
160
+ ```
161
+
162
+ ### Custom Evaluation Functions
163
+
164
+ Define custom evaluation metrics for domain-specific research:
165
+
166
+ ```python
167
+ from rdagent.core.evaluation import EvaluationFunction
168
+
169
+ class CustomMetric(EvaluationFunction):
170
+ def evaluate(self, predictions, ground_truth, **kwargs):
171
+ # Your custom metric computation
172
+ score = compute_domain_specific_metric(predictions, ground_truth)
173
+ return {
174
+ "primary_metric": score,
175
+ "secondary_metrics": {
176
+ "precision": compute_precision(predictions, ground_truth),
177
+ "recall": compute_recall(predictions, ground_truth),
178
+ }
179
+ }
180
+
181
+ scenario = DataScienceScenario(
182
+ evaluation_function=CustomMetric(),
183
+ # ... other config
184
+ )
185
+ ```
186
+
187
+ ### Human-in-the-Loop Mode
188
+
189
+ Guide the agent with human feedback at key decision points:
190
+
191
+ ```python
192
+ runner = RDRunner(
193
+ scenario=scenario,
194
+ human_in_the_loop=True,
195
+ review_frequency=5, # Review every 5 iterations
196
+ )
197
+
198
+ # The agent will pause for human review at specified intervals
199
+ # You can approve, reject, or modify proposed experiments
200
+ ```
201
+
202
+ ## Research Applications
203
+
204
+ ### Ablation Studies at Scale
205
+
206
+ Use RD-Agent to systematically explore which components contribute most to model performance:
207
+
208
+ ```python
209
+ # Define ablation study
210
+ ablation_config = {
211
+ "base_model": "your_full_model",
212
+ "components_to_ablate": [
213
+ "attention_mechanism",
214
+ "residual_connections",
215
+ "layer_normalization",
216
+ "data_augmentation",
217
+ ],
218
+ "metric": "accuracy",
219
+ "num_seeds": 5, # Run each configuration with 5 seeds
220
+ }
221
+ ```
222
+
223
+ ### Automated Feature Engineering
224
+
225
+ Let the agent discover and implement novel features for your dataset:
226
+
227
+ ```python
228
+ scenario = DataScienceScenario(
229
+ task="feature_engineering",
230
+ dataset_path="data/research_data.csv",
231
+ existing_features=["feature_a", "feature_b", "feature_c"],
232
+ target="outcome",
233
+ max_new_features=20,
234
+ )
235
+ ```
236
+
237
+ ### Reproducibility
238
+
239
+ Every experiment run by RD-Agent is fully reproducible. The framework saves the complete experiment specification including code, data transformations, random seeds, and environment details, enabling other researchers to reproduce and build upon the results.
240
+
241
+ ## References
242
+
243
+ - Repository: https://github.com/microsoft/RD-Agent
244
+ - Microsoft Research blog post: https://www.microsoft.com/en-us/research/project/rd-agent/
245
+ - Qlib quantitative platform: https://github.com/microsoft/qlib
246
+ - Documentation: https://microsoft.github.io/RD-Agent/
@@ -0,0 +1,254 @@
1
+ ---
2
+ name: research-paper-orchestrator
3
+ description: "Master orchestrator coordinating 10 specialized subagents for papers"
4
+ metadata:
5
+ openclaw:
6
+ emoji: "🎼"
7
+ category: "research"
8
+ subcategory: "automation"
9
+ keywords: ["research orchestration", "multi-agent", "automated research", "paper production", "workflow automation", "agent coordination"]
10
+ source: "https://github.com/AcademicSkills/research-paper-orchestrator"
11
+ ---
12
+
13
+ # Research Paper Orchestrator
14
+
15
+ A master orchestrator skill that coordinates up to 10 specialized subagents to produce comprehensive research outputs. Each subagent handles a distinct phase of the research pipeline -- from literature search through data analysis to manuscript drafting -- while the orchestrator manages sequencing, data flow, quality gates, and synthesis across all components.
16
+
17
+ ## Overview
18
+
19
+ Producing a research paper involves many distinct tasks: searching literature, reading and summarizing papers, analyzing data, generating figures, writing sections, formatting citations, and checking consistency. Each task requires different expertise and tools. The Research Paper Orchestrator decomposes the full research workflow into specialized roles, assigns each to a dedicated subagent, and coordinates their execution through a defined pipeline with quality checkpoints.
20
+
21
+ This approach mirrors how research teams operate in practice: a PI sets the direction and checks quality, a literature specialist handles the review, a statistician runs the analysis, a writer drafts the prose, and reviewers provide feedback. The orchestrator plays the PI role, ensuring all components align and meet quality standards before advancing to the next phase.
22
+
23
+ ## Orchestrator Architecture
24
+
25
+ ### The 10 Subagent Roles
26
+
27
+ ```yaml
28
+ subagents:
29
+ 1_planner:
30
+ role: "Research Planner"
31
+ responsibility: "Define research question, scope, methodology, and timeline"
32
+ inputs: ["user topic", "constraints"]
33
+ outputs: ["research_plan.yaml"]
34
+
35
+ 2_literature_scout:
36
+ role: "Literature Scout"
37
+ responsibility: "Search databases, identify relevant papers, build bibliography"
38
+ inputs: ["research_plan", "search_queries"]
39
+ outputs: ["candidate_papers.json", "search_log.md"]
40
+
41
+ 3_paper_reader:
42
+ role: "Paper Reader"
43
+ responsibility: "Read and extract structured summaries from selected papers"
44
+ inputs: ["candidate_papers"]
45
+ outputs: ["paper_summaries.json", "evidence_matrix.csv"]
46
+
47
+ 4_gap_analyzer:
48
+ role: "Gap Analyzer"
49
+ responsibility: "Identify research gaps, contradictions, and opportunities"
50
+ inputs: ["paper_summaries", "evidence_matrix"]
51
+ outputs: ["gap_analysis.md", "positioning_statement.md"]
52
+
53
+ 5_data_analyst:
54
+ role: "Data Analyst"
55
+ responsibility: "Clean, analyze, and model the research data"
56
+ inputs: ["research_data", "analysis_plan"]
57
+ outputs: ["results.json", "statistical_tests.md"]
58
+
59
+ 6_figure_generator:
60
+ role: "Figure Generator"
61
+ responsibility: "Create publication-quality figures and tables"
62
+ inputs: ["results", "figure_specifications"]
63
+ outputs: ["figures/", "tables/"]
64
+
65
+ 7_section_writer:
66
+ role: "Section Writer"
67
+ responsibility: "Draft each manuscript section following academic conventions"
68
+ inputs: ["research_plan", "paper_summaries", "results", "figures"]
69
+ outputs: ["draft_sections/"]
70
+
71
+ 8_citation_manager:
72
+ role: "Citation Manager"
73
+ responsibility: "Format citations, build bibliography, check reference consistency"
74
+ inputs: ["draft_sections", "paper_summaries"]
75
+ outputs: ["references.bib", "citation_report.md"]
76
+
77
+ 9_consistency_checker:
78
+ role: "Consistency Checker"
79
+ responsibility: "Verify internal consistency across sections, figures, and claims"
80
+ inputs: ["full_draft"]
81
+ outputs: ["consistency_report.md", "issues.json"]
82
+
83
+ 10_quality_reviewer:
84
+ role: "Quality Reviewer"
85
+ responsibility: "Final quality assessment against journal standards"
86
+ inputs: ["full_draft", "consistency_report"]
87
+ outputs: ["review_comments.md", "quality_score"]
88
+ ```
89
+
90
+ ### Pipeline Execution Flow
91
+
92
+ ```
93
+ Phase 1: PLANNING
94
+ [1_planner] → research_plan
95
+ Quality Gate: Is the plan specific, feasible, and novel?
96
+
97
+ Phase 2: LITERATURE
98
+ [2_literature_scout] → candidate_papers
99
+ [3_paper_reader] → paper_summaries, evidence_matrix
100
+ [4_gap_analyzer] → gap_analysis, positioning
101
+ Quality Gate: Is the literature coverage sufficient? Is the gap real?
102
+
103
+ Phase 3: ANALYSIS
104
+ [5_data_analyst] → results
105
+ [6_figure_generator] → figures, tables
106
+ Quality Gate: Are results statistically sound? Do figures accurately represent data?
107
+
108
+ Phase 4: WRITING
109
+ [7_section_writer] → draft_sections
110
+ [8_citation_manager] → formatted_references
111
+ Quality Gate: Does each section follow conventions? Are all claims cited?
112
+
113
+ Phase 5: REVIEW
114
+ [9_consistency_checker] → consistency_report
115
+ [10_quality_reviewer] → review_comments
116
+ Quality Gate: Overall quality score >= threshold?
117
+
118
+ If any quality gate fails → loop back to the relevant phase.
119
+ ```
120
+
121
+ ## Quality Gates
122
+
123
+ ### Gate Definitions
124
+
125
+ ```python
126
+ QUALITY_GATES = {
127
+ 'planning': {
128
+ 'checks': [
129
+ 'Research question is specific and testable',
130
+ 'Scope is achievable within stated constraints',
131
+ 'Methodology matches the research question',
132
+ 'Timeline is realistic'
133
+ ],
134
+ 'threshold': 4, # All checks must pass
135
+ 'fallback': 'Return to planner with feedback'
136
+ },
137
+ 'literature': {
138
+ 'checks': [
139
+ 'Minimum 20 relevant papers identified',
140
+ 'Coverage spans last 5 years',
141
+ 'Multiple databases searched',
142
+ 'Gap analysis identifies a clear contribution',
143
+ 'No critical papers obviously missing'
144
+ ],
145
+ 'threshold': 4, # At least 4 of 5 must pass
146
+ 'fallback': 'Expand search with additional queries'
147
+ },
148
+ 'analysis': {
149
+ 'checks': [
150
+ 'Statistical assumptions verified',
151
+ 'Results are reproducible (seed set)',
152
+ 'Effect sizes reported alongside p-values',
153
+ 'Figures match reported statistics',
154
+ 'Sensitivity analysis performed'
155
+ ],
156
+ 'threshold': 5, # All must pass
157
+ 'fallback': 'Data analyst revises analysis'
158
+ },
159
+ 'writing': {
160
+ 'checks': [
161
+ 'All sections present and complete',
162
+ 'Every factual claim has a citation',
163
+ 'No plagiarized passages',
164
+ 'Consistent terminology throughout',
165
+ 'Abstract accurately reflects content'
166
+ ],
167
+ 'threshold': 5,
168
+ 'fallback': 'Section writer revises with specific feedback'
169
+ },
170
+ 'review': {
171
+ 'checks': [
172
+ 'No internal contradictions found',
173
+ 'Figures referenced correctly in text',
174
+ 'References complete and formatted',
175
+ 'Meets target journal formatting requirements',
176
+ 'Overall quality score >= 7/10'
177
+ ],
178
+ 'threshold': 5,
179
+ 'fallback': 'Loop back to relevant earlier phase'
180
+ }
181
+ }
182
+ ```
183
+
184
+ ## Coordination Protocol
185
+
186
+ ### Inter-Agent Communication
187
+
188
+ ```python
189
+ class OrchestratorMessage:
190
+ """
191
+ Standard message format for communication between orchestrator and subagents.
192
+ """
193
+ def __init__(self, sender: str, receiver: str, msg_type: str, payload: dict):
194
+ self.sender = sender # e.g., "orchestrator", "data_analyst"
195
+ self.receiver = receiver # e.g., "figure_generator"
196
+ self.msg_type = msg_type # "task", "result", "feedback", "query"
197
+ self.payload = payload # task-specific data
198
+ self.timestamp = None
199
+ self.status = "pending" # pending, in_progress, completed, failed
200
+
201
+ # Example: Orchestrator assigns task to data analyst
202
+ msg = OrchestratorMessage(
203
+ sender="orchestrator",
204
+ receiver="data_analyst",
205
+ msg_type="task",
206
+ payload={
207
+ "action": "run_analysis",
208
+ "data_path": "data/experiment_results.csv",
209
+ "analysis_plan": "analysis_plan.yaml",
210
+ "output_format": "json",
211
+ "deadline": "phase_3_end"
212
+ }
213
+ )
214
+ ```
215
+
216
+ ### Progress Tracking Dashboard
217
+
218
+ | Phase | Subagent | Status | Output | Quality Gate |
219
+ |-------|----------|--------|--------|-------------|
220
+ | Planning | Planner | Completed | research_plan.yaml | PASSED |
221
+ | Literature | Scout | Completed | 45 papers found | - |
222
+ | Literature | Reader | Completed | 28 papers summarized | - |
223
+ | Literature | Gap Analyzer | Completed | gap_analysis.md | PASSED |
224
+ | Analysis | Data Analyst | In Progress | 60% complete | - |
225
+ | Analysis | Figure Gen | Pending | waiting for results | - |
226
+ | Writing | Section Writer | Pending | - | - |
227
+ | Writing | Citation Mgr | Pending | - | - |
228
+ | Review | Consistency | Pending | - | - |
229
+ | Review | Quality Rev | Pending | - | - |
230
+
231
+ ## Error Handling and Recovery
232
+
233
+ When a subagent fails or a quality gate is not met:
234
+
235
+ 1. **Isolate the failure**: Determine which specific check failed and why.
236
+ 2. **Provide targeted feedback**: Send the subagent specific, actionable instructions for revision.
237
+ 3. **Limit retries**: Maximum 3 attempts per subagent before escalating to user.
238
+ 4. **Preserve progress**: Never discard completed upstream work when re-running a downstream phase.
239
+ 5. **Log everything**: Record all attempts, feedback, and revisions for debugging and improvement.
240
+
241
+ ## Best Practices
242
+
243
+ - Run the pipeline end-to-end on a small scope first (e.g., 5 papers, 1 analysis) before scaling up.
244
+ - Human-in-the-loop at quality gates produces much better results than fully automated runs.
245
+ - The planner subagent is the most critical; invest extra time in the research plan.
246
+ - Allow the consistency checker to flag issues even if the quality reviewer has not yet run.
247
+ - Save intermediate outputs at each phase for debugging and incremental refinement.
248
+ - The orchestrator should not perform research tasks itself; its role is coordination and quality control.
249
+
250
+ ## References
251
+
252
+ - Gu, J., et al. (2024). Agent Workflow Memory for Multi-Agent Systems. *arXiv:2409.07429*.
253
+ - Wu, Q., et al. (2023). AutoGen: Enabling Next-Gen LLM Applications via Multi-Agent Conversation. *arXiv:2308.08155*.
254
+ - Hong, S., et al. (2023). MetaGPT: Meta Programming for Multi-Agent Collaborative Framework. *ICLR 2024*.
@@ -0,0 +1,190 @@
1
+ ---
2
+ name: academic-deep-research
3
+ description: "Multi-cycle exhaustive investigation framework for academic topics"
4
+ metadata:
5
+ openclaw:
6
+ emoji: "🔬"
7
+ category: "research"
8
+ subcategory: "deep-research"
9
+ keywords: ["deep research", "exhaustive search", "multi-cycle investigation", "literature synthesis", "comprehensive review"]
10
+ source: "https://github.com/AcademicSkills/academic-deep-research"
11
+ ---
12
+
13
+ # Academic Deep Research
14
+
15
+ A structured multi-cycle investigation framework designed for exhaustive academic research. Unlike single-pass literature searches, this skill implements iterative deepening: each cycle expands the search scope, refines the query based on discovered themes, and synthesizes findings into an increasingly comprehensive knowledge map.
16
+
17
+ ## Overview
18
+
19
+ Traditional literature searches follow a linear process: define keywords, search databases, screen results, extract data, synthesize. This approach works well for scoping reviews but often misses important connections across subfields, fails to surface grey literature, and stops too early when the obvious sources have been found. Academic Deep Research addresses these limitations through a multi-cycle approach where each cycle builds on the findings of the previous one, progressively expanding the search frontier.
20
+
21
+ The framework is inspired by systematic review methodology but optimized for speed and breadth rather than exhaustive recall within a single database. It is particularly useful for interdisciplinary research questions, emerging fields where terminology is not yet standardized, and complex topics where important insights may be scattered across diverse literatures.
22
+
23
+ ## The Multi-Cycle Framework
24
+
25
+ ### Cycle Architecture
26
+
27
+ ```
28
+ Cycle 1: BREADTH (Survey Phase)
29
+ Purpose: Map the landscape, identify major themes and key authors
30
+ Sources: Google Scholar, Semantic Scholar, review articles
31
+ Output: Theme taxonomy, key author list, terminology inventory
32
+ Duration: 2-4 hours
33
+
34
+ Cycle 2: DEPTH (Focused Phase)
35
+ Purpose: Deep-dive into each identified theme
36
+ Sources: Discipline-specific databases (PubMed, IEEE, SSRN, etc.)
37
+ Output: Annotated bibliography, evidence matrix, gap identification
38
+ Duration: 4-8 hours
39
+
40
+ Cycle 3: CONNECTIONS (Synthesis Phase)
41
+ Purpose: Find cross-theme relationships, contradictions, and gaps
42
+ Sources: Citation networks, author collaboration networks
43
+ Output: Conceptual framework, research gap map, contradiction log
44
+ Duration: 2-4 hours
45
+
46
+ Cycle 4: FRONTIERS (Currency Phase)
47
+ Purpose: Capture the latest work and preprints
48
+ Sources: arXiv, bioRxiv, conference proceedings, working papers
49
+ Output: Trend analysis, emerging methods, future directions
50
+ Duration: 1-2 hours
51
+ ```
52
+
53
+ ### Cycle Execution Protocol
54
+
55
+ ```python
56
+ class ResearchCycle:
57
+ """
58
+ Execute a single cycle of the deep research framework.
59
+ """
60
+ def __init__(self, cycle_number: int, focus: str, prior_findings: dict = None):
61
+ self.cycle = cycle_number
62
+ self.focus = focus # 'breadth', 'depth', 'connections', 'frontiers'
63
+ self.prior = prior_findings or {}
64
+ self.findings = []
65
+ self.new_queries = []
66
+ self.gaps = []
67
+
68
+ def generate_queries(self, base_topic: str) -> list:
69
+ """
70
+ Generate search queries adapted to the cycle's focus.
71
+ """
72
+ if self.focus == 'breadth':
73
+ return [
74
+ f'"{base_topic}" review',
75
+ f'"{base_topic}" survey',
76
+ f'"{base_topic}" systematic review',
77
+ f'"{base_topic}" meta-analysis',
78
+ f'"{base_topic}" overview OR tutorial',
79
+ ]
80
+ elif self.focus == 'depth':
81
+ # Use themes discovered in Cycle 1
82
+ themes = self.prior.get('themes', [])
83
+ return [f'"{base_topic}" AND "{theme}"' for theme in themes]
84
+ elif self.focus == 'connections':
85
+ # Cross-theme queries
86
+ themes = self.prior.get('themes', [])
87
+ queries = []
88
+ for i, t1 in enumerate(themes):
89
+ for t2 in themes[i+1:]:
90
+ queries.append(f'"{t1}" AND "{t2}"')
91
+ return queries
92
+ elif self.focus == 'frontiers':
93
+ return [
94
+ f'"{base_topic}" 2025 OR 2026',
95
+ f'"{base_topic}" preprint',
96
+ f'"{base_topic}" forthcoming OR "in press"',
97
+ ]
98
+ return []
99
+
100
+ def evaluate_saturation(self) -> bool:
101
+ """
102
+ Determine if additional searching is likely to yield new information.
103
+ Saturation is reached when >80% of new results are already in the corpus.
104
+ """
105
+ if not self.findings:
106
+ return False
107
+ new_unique = sum(1 for f in self.findings if not f.get('seen_before'))
108
+ total = len(self.findings)
109
+ novelty_rate = new_unique / total if total > 0 else 1.0
110
+ return novelty_rate < 0.20 # Saturated when <20% new
111
+ ```
112
+
113
+ ## Evidence Matrix Construction
114
+
115
+ ### Structuring Findings Across Studies
116
+
117
+ | Study | Method | Sample | Key Finding | Effect Size | Relevance |
118
+ |-------|--------|--------|-------------|-------------|-----------|
119
+ | Author (Year) | RCT | n=200 | Treatment improved X by 15% | d=0.45 | High |
120
+ | Author (Year) | Survey | n=1500 | Factor Y predicts Z (beta=0.3) | R2=0.12 | Medium |
121
+ | Author (Year) | Qualitative | n=30 | Three themes emerged | N/A | High |
122
+
123
+ ### Tracking Contradictions
124
+
125
+ ```
126
+ Contradiction Log:
127
+ 1. Study A (2023) finds positive effect of X on Y (d=0.4, n=200)
128
+ Study B (2024) finds null effect (d=0.02, n=500)
129
+ Possible explanations:
130
+ - Different populations (students vs. professionals)
131
+ - Different operationalization of X
132
+ - Study A may have publication bias
133
+ Resolution needed: moderator analysis or direct replication
134
+ ```
135
+
136
+ ## Knowledge Map Generation
137
+
138
+ ### From Findings to Conceptual Framework
139
+
140
+ After completing all cycles, synthesize findings into a knowledge map:
141
+
142
+ 1. **Core concepts**: The fundamental constructs in the field.
143
+ 2. **Established relationships**: Well-replicated findings supported by multiple studies.
144
+ 3. **Contested relationships**: Findings with conflicting evidence.
145
+ 4. **Unexplored areas**: Logical research questions that no study has addressed.
146
+ 5. **Methodological gaps**: Approaches not yet applied to the topic.
147
+
148
+ ```
149
+ Knowledge Map: [Topic]
150
+
151
+ Established:
152
+ A → B (strong evidence, 12 studies, meta-analytic d=0.5)
153
+ C moderates A → B (4 studies)
154
+
155
+ Contested:
156
+ D → E (3 positive, 2 null, 1 negative; likely moderator)
157
+
158
+ Unexplored:
159
+ F → B (theoretically plausible, no empirical studies)
160
+ A → B in context G (only studied in context H)
161
+
162
+ Methodological Gaps:
163
+ No longitudinal studies of A → B
164
+ No experimental manipulation of C
165
+ ```
166
+
167
+ ## Output Deliverables
168
+
169
+ Each deep research session produces:
170
+
171
+ 1. **Executive summary** (500 words): Key findings, gaps, and recommended next steps.
172
+ 2. **Annotated bibliography** (20-100 entries): Each source with a 2-3 sentence summary and relevance rating.
173
+ 3. **Evidence matrix**: Tabular comparison of studies on key dimensions.
174
+ 4. **Knowledge map**: Visual or structured representation of the field's state.
175
+ 5. **Research gap inventory**: Prioritized list of unanswered questions.
176
+ 6. **Search audit trail**: All queries, databases, dates, and result counts for reproducibility.
177
+
178
+ ## Best Practices
179
+
180
+ - Start with Cycle 1 even if you think you know the field well. Survey-level searching often reveals adjacent literatures you did not know existed.
181
+ - Keep a running terminology inventory. The same concept may be called different things across subfields.
182
+ - Do not skip the contradiction log. Contested findings often point to the most productive research opportunities.
183
+ - Set a time budget for each cycle. Diminishing returns set in; use the saturation check to know when to move on.
184
+ - Save all search results with timestamps for PRISMA-style reporting if needed later.
185
+
186
+ ## References
187
+
188
+ - Arksey, H. & O'Malley, L. (2005). Scoping Studies: Towards a Methodological Framework. *International Journal of Social Research Methodology*, 8(1), 19-32.
189
+ - Greenhalgh, T. & Peacock, R. (2005). Effectiveness and Efficiency of Search Methods in Systematic Reviews. *BMJ*, 331(7524), 1064-1065.
190
+ - Wohlin, C. (2014). Guidelines for Snowballing in Systematic Literature Studies. *EASE 2014*.