psyclaw 0.27.23 → 0.28.1

package/vendor/ars/deep-research/references/literature_monitoring_strategies.md

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+# Literature Monitoring Strategies — Reference Guide
+
+## Purpose
+
+Comprehensive reference for setting up post-research literature monitoring across major academic databases and platforms. Used by the `monitoring_agent` to configure monitoring strategies tailored to the user's research field and publication velocity.
+
+---
+
+## 1. Google Scholar Alerts
+
+### Setup
+
+1. Go to [Google Scholar](https://scholar.google.com)
+2. Enter your search query (use the same keywords from your systematic search)
+3. Click the envelope icon (📧) in the left sidebar, or go to scholar.google.com/scholar_alerts
+4. Set email address and frequency
+
+### Best Practices
+
+- Create separate alerts for each major keyword cluster (not one giant query)
+- Use quotes for exact phrases: `"quality assurance" "higher education"`
+- Use OR for synonyms: `"quality assurance" OR "quality evaluation"`
+- Limit to 10-15 active alerts to avoid email overload
+- Review alerts monthly and deactivate stale ones
+
+### Limitations
+
+- No Boolean NOT support in alerts
+- Cannot filter by date, journal, or document type
+- May include non-peer-reviewed sources (theses, reports, patents)
+- Coverage varies by discipline (strong in STEM, weaker in humanities)
+
+---
+
+## 2. PubMed Email Alerts
+
+### Setup
+
+1. Go to [PubMed](https://pubmed.ncbi.nlm.nih.gov)
+2. Run your search using MeSH terms and filters
+3. Click "Save" below the search box
+4. Log in to My NCBI account (free)
+5. Set email alert frequency: daily, weekly, or monthly
+
+### Best Practices
+
+- Use MeSH terms for precise matching (e.g., `"Quality Assurance, Health Care"[MeSH]`)
+- Combine with free-text search for newer terms not yet in MeSH
+- Set weekly frequency for active research areas, monthly for stable fields
+- Use the "Sort by: Most Recent" option to prioritize new publications
+- Save your search strategy for reproducibility
+
+### Advanced Features
+
+- **MyNCBI Collections**: Organize saved articles into folders
+- **Filters**: Limit by date, article type, language, species
+- **RSS feed**: Available for any saved search (click RSS icon)
+
+### Limitations
+
+- Biomedical focus — limited coverage of social sciences, education, humanities
+- Indexing lag: 1-4 weeks for new articles to appear
+- No citation tracking built in
+
+---
+
+## 3. RSS Feeds for Major Databases
+
+### What is RSS?
+
+RSS (Really Simple Syndication) allows you to subscribe to content updates from websites without checking each site manually. Use an RSS reader (e.g., Feedly, Inoreader, NewsBlur) to aggregate feeds.
+
+### Recommended Feeds
+
+| Source | Feed URL Pattern | Content |
+|--------|-----------------|---------|
+| **PubMed** | Saved search → RSS icon | New articles matching your search |
+| **arXiv** | `arxiv.org/rss/[category]` (e.g., `cs.AI`, `cs.CL`) | Preprints by category |
+| **bioRxiv** | `connect.biorxiv.org/biorxiv_xml.php?subject=[subject]` | Biology preprints |
+| **medRxiv** | `connect.medrxiv.org/medrxiv_xml.php?subject=[subject]` | Medical preprints |
+| **SSRN** | Subscribe to specific research networks | Social science preprints |
+| **Journal TOC** | Most journals offer RSS on their homepage | New issues of specific journals |
+| **Retraction Watch** | `retractionwatch.com/feed/` | Retraction news and updates |
+
+### RSS Reader Recommendations
+
+| Reader | Platform | Cost | Best For |
+|--------|----------|------|----------|
+| **Feedly** | Web, iOS, Android | Free (basic) / $6/mo (Pro) | Organized categorization, AI features |
+| **Inoreader** | Web, iOS, Android | Free (basic) / $5/mo (Pro) | Power users, rules/filters |
+| **NewsBlur** | Web, iOS, Android | Free (limited) / $36/yr | Open source option |
+| **Zotero RSS** | Desktop | Free | Integrates with reference manager |
+
+---
+
+## 4. Retraction Watch Integration
+
+### Retraction Watch Database
+
+- **URL**: [retractiondatabase.org](http://retractiondatabase.org)
+- **Coverage**: 40,000+ retracted or corrected papers
+- **Searchable by**: author, journal, subject, reason, date
+
+### Monitoring Workflow
+
+1. **Baseline check**: Search all cited authors and paper titles in the Retraction Watch Database
+2. **Ongoing monitoring**: Subscribe to Retraction Watch blog RSS feed
+3. **Periodic re-check**: Every 3-6 months, re-run the baseline check for cited sources
+
+### Retraction Reasons to Watch For
+
+| Reason | Severity | Action Required |
+|--------|----------|-----------------|
+| Data fabrication/falsification | Critical | Remove citation; add note explaining removal |
+| Plagiarism | High | Replace with original source |
+| Duplicate publication | Moderate | Keep the primary publication; remove duplicate |
+| Honest error | Moderate | Check whether the error affects cited findings |
+| Author dispute | Low | Usually no impact on findings |
+| Publisher error | Low | Update citation to corrected version |
+
+---
+
+## 5. Preprint Server Monitoring
+
+### arXiv
+
+- **Coverage**: Physics, mathematics, computer science, statistics, quantitative biology, economics
+- **Monitoring**: Subscribe to RSS feeds by category and cross-list
+- **Alert service**: [arxiv-sanity](http://arxiv-sanity-lite.com/) for AI-curated recommendations
+- **Update frequency**: Daily (new submissions posted ~8 PM ET)
+
+### SSRN
+
+- **Coverage**: Social sciences, humanities, law, economics, management
+- **Monitoring**: Subscribe to eJournal alerts by research network
+- **Alert service**: Email notifications for new papers in subscribed networks
+- **Note**: Now owned by Elsevier; some content behind paywall
+
+### bioRxiv / medRxiv
+
+- **Coverage**: Biology (bioRxiv) and health sciences (medRxiv)
+- **Monitoring**: RSS feeds by subject area
+- **Alert service**: Email alerts for specific keywords
+- **Note**: Preprints are NOT peer-reviewed — flag accordingly in digests
+
+### Key Preprint Monitoring Rules
+
+1. Always label preprint sources clearly: `[PREPRINT — not peer-reviewed]`
+2. Check whether a preprint has been published in a peer-reviewed journal (look for "Now published in..." banner)
+3. Preprints can change or be withdrawn — re-check before citing
+4. Preprint findings may differ from the final published version
+
+---
+
+## 6. Citation Tracking
+
+### Web of Science
+
+1. Find your key cited papers in Web of Science
+2. Click "Create Citation Alert" (requires institutional access)
+3. Receive email when someone cites that paper
+4. Use "Cited Reference Search" for older papers not in the database
+
+### Scopus
+
+1. Find your key cited papers in Scopus
+2. Click "Set Citation Alert" on the document page
+3. Configure email frequency
+4. Also available: author alerts (track all publications by an author)
+
+### Google Scholar
+
+1. Find the paper on Google Scholar
+2. Click "Cited by N" to see citing papers
+3. Click the "Follow" button (envelope icon) on author profiles
+4. Set up alerts for specific papers by quoting the exact title
+
+### Semantic Scholar
+
+- **URL**: [semanticscholar.org](https://www.semanticscholar.org)
+- **Alerts**: Click "Alert" on any paper to track citations
+- **Advantage**: AI-powered relevance ranking of citing papers
+- **Research feed**: Personalized recommendations based on your library
+
+---
+
+## 7. Recommended Monitoring Cadence by Field
+
+### Determining Your Field's Publication Velocity
+
+| Indicator | High Velocity | Moderate | Low |
+|-----------|--------------|----------|-----|
+| Papers per month (in your niche) | > 50 | 10-50 | < 10 |
+| Median time from submission to publication | < 6 months | 6-12 months | > 12 months |
+| Preprint prevalence | > 50% of key papers | 10-50% | < 10% |
+| Conference vs. journal dominance | Conference-first | Mixed | Journal-only |
+
+### Cadence Recommendations
+
+| Field | Check Frequency | Digest Period | Sunset |
+|-------|----------------|---------------|--------|
+| **AI/ML, NLP** | Daily (arXiv) + Weekly (journals) | Weekly | 6 months |
+| **Biomedical, Clinical** | Weekly (PubMed + preprints) | Biweekly | 12 months |
+| **Education Technology** | Biweekly | Monthly | 12 months |
+| **Higher Education Policy** | Monthly | Quarterly | 18 months |
+| **Social Sciences (general)** | Monthly | Quarterly | 18 months |
+| **Law, Philosophy** | Quarterly | Semi-annually | 24 months |
+| **History, Classics** | Semi-annually | Annually | 36 months |
+
+### Sunset Policy
+
+- **Sunset date**: The date after which active monitoring stops (topic presumed stable)
+- Set based on field velocity and research currency
+- After sunset: switch to annual check-ins or opportunistic monitoring
+- Exception: extend monitoring if a major development occurs (e.g., retraction of key source, paradigm shift)
+
+---
+
+## 8. Monitoring Maintenance Checklist
+
+Run this checklist every monitoring cycle:
+
+- [ ] Are all alerts still active? (some platforms deactivate after inactivity)
+- [ ] Are any alerts returning zero results? (keywords may need updating)
+- [ ] Are any alerts returning too many results? (keywords may need narrowing)
+- [ ] Has the field's terminology evolved? (add new keywords, retire old ones)
+- [ ] Any new major databases or preprint servers for this field?
+- [ ] Has any tracked author changed institutions? (update author tracking)
+- [ ] Is the sunset date still appropriate?
+- [ ] Have you checked the Retraction Watch Database recently?
+
+---
+
+## Quick Reference: Setting Up in 30 Minutes
+
+1. **Google Scholar** (5 min): Create 3-5 keyword alerts matching your original search strategy
+2. **PubMed** (5 min): Save your search and set weekly email alerts (if your field is indexed)
+3. **RSS** (5 min): Subscribe to RSS feeds for your top 5 cited journals in Feedly or Inoreader
+4. **Retraction Watch** (5 min): Run baseline check on all cited authors; subscribe to RSS feed
+5. **Citation tracking** (5 min): Set up citation alerts for your 5 most-cited sources in Google Scholar or Scopus
+6. **Preprints** (5 min): Subscribe to relevant arXiv/SSRN/bioRxiv categories if applicable to your field
+
+---
+
+## SKILL.md Extracted Content: Literature Monitoring (Optional Post-Pipeline)
+
+After any research mode is complete, users can optionally activate the `monitoring_agent` to set up post-research literature monitoring. This is not part of the main pipeline — it is an auxiliary capability triggered on demand.
+
+See `agents/monitoring_agent.md` for the detailed agent definition.
+
+**Trigger**: "monitor this topic", "set up alerts", "track new publications on this"
+
+**Capabilities**:
+- Weekly/monthly monitoring digest generation
+- Retraction alerts for cited sources
+- Contradictory findings detection
+- Key author tracking
+- Keyword evolution tracking
+
+**Input**: Completed bibliography + search strategy from any research mode
+**Output**: Monitoring configuration + digest template (markdown)
+
+**Limitation**: The monitoring agent produces configurations and templates for the user to act on. It cannot run autonomous background monitoring.

package/vendor/ars/deep-research/references/logical_fallacies.md

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+# Logical Fallacies Catalog — 30+ Fallacies for Research Review
+
+## Purpose
+Reference catalog of logical fallacies commonly encountered in research. Used by the devils_advocate_agent.
+
+## Formal Fallacies (Invalid Logical Structure)
+
+### 1. Affirming the Consequent
+**Structure**: If P then Q; Q is true; therefore P is true.
+**Example**: "If a university has high research funding, it has good outcomes. This university has good outcomes. Therefore, it must have high research funding."
+**Problem**: Q can have multiple causes.
+
+### 2. Denying the Antecedent
+**Structure**: If P then Q; not P; therefore not Q.
+**Example**: "If enrollment increases, revenue increases. Enrollment didn't increase. Therefore, revenue didn't increase."
+**Problem**: Revenue can increase from other sources.
+
+### 3. Undistributed Middle
+**Structure**: All A are B; All C are B; therefore All A are C.
+**Example**: "All successful programs use technology. Our program uses technology. Therefore, our program is successful."
+**Problem**: B (technology use) is shared but doesn't link A and C.
+
+### 4. False Dilemma / False Dichotomy
+**Structure**: Either A or B; not A; therefore B.
+**Example**: "Either we adopt online learning completely or maintain traditional methods."
+**Problem**: Many hybrid options exist.
+
+## Informal Fallacies
+
+### Relevance Fallacies
+
+### 5. Ad Hominem
+**Description**: Attacking the person rather than the argument.
+**Research Example**: "This study's conclusions are unreliable because the author works for a for-profit university."
+**Correct Approach**: Evaluate the methodology and evidence, not the author's affiliation (though COI should be noted).
+
+### 6. Appeal to Authority
+**Description**: Accepting a claim solely because an authority figure endorses it.
+**Research Example**: "Published in Nature, so the findings must be valid."
+**Correct Approach**: Even prestigious journals publish flawed studies. Evaluate on merit.
+
+### 7. Appeal to Tradition
+**Description**: Arguing something is correct because it has always been done that way.
+**Research Example**: "This metric has been used for 30 years, so it must be the best measure."
+**Correct Approach**: Evaluate whether the metric is still valid in current context.
+
+### 8. Appeal to Novelty
+**Description**: Arguing something is better because it's new.
+**Research Example**: "This new framework must be superior to the established one."
+**Correct Approach**: Novelty doesn't equal improvement. Compare on evidence.
+
+### 9. Appeal to Popularity (Bandwagon)
+**Description**: Arguing something is true because many people believe it.
+**Research Example**: "Most researchers in the field use this method, so it must be the best."
+**Correct Approach**: Popularity doesn't validate methodology. Assess independently.
+
+### 10. Red Herring
+**Description**: Introducing an irrelevant topic to divert from the argument.
+**Research Example**: Responding to criticism of methodology by discussing the importance of the topic.
+
+### Evidence Fallacies
+
+### 11. Cherry-Picking (Selection Bias)
+**Description**: Selecting evidence that supports the conclusion while ignoring contradictory evidence.
+**Research Example**: Citing 5 studies that support the hypothesis while omitting 12 that don't.
+**Detection**: Compare cited sources against comprehensive search results.
+
+### 12. Confirmation Bias
+**Description**: Seeking, interpreting, and remembering information that confirms pre-existing beliefs.
+**Research Example**: Designing search terms that are more likely to return supportive results.
+**Detection**: Check if search strategy was neutral; look for actively sought disconfirming evidence.
+
+### 13. Survivorship Bias
+**Description**: Drawing conclusions only from "survivors" (successes), ignoring those that didn't survive.
+**Research Example**: "All top-ranked universities implemented X" — ignoring universities that implemented X and didn't improve.
+**Detection**: Ask "what about those that failed?"
+
+### 14. Anecdotal Evidence
+**Description**: Using individual stories as proof of a general claim.
+**Research Example**: "One university tripled enrollment after rebranding, so rebranding drives enrollment."
+**Detection**: Is this a systematic finding or an isolated case?
+
+### 15. Hasty Generalization
+**Description**: Drawing broad conclusions from insufficient evidence.
+**Research Example**: "Three case studies from Taiwan show X, therefore this applies to all Asian universities."
+**Detection**: Is the sample representative? Is the generalization proportionate to the evidence?
+
+### Causal Fallacies
+
+### 16. Post Hoc Ergo Propter Hoc
+**Description**: Assuming that because B followed A, A caused B.
+**Research Example**: "After implementing the new curriculum, graduation rates improved. Therefore the curriculum caused the improvement."
+**Detection**: Were there confounders? Was there a control group?
+
+### 17. Cum Hoc Ergo Propter Hoc (Correlation ≠ Causation)
+**Description**: Assuming that correlation implies causation.
+**Research Example**: "Universities with more international students have higher rankings, so international students cause higher rankings."
+**Detection**: Is there a plausible mechanism? Could both be caused by a third factor?
+
+### 18. Reverse Causation
+**Description**: Getting cause and effect backwards.
+**Research Example**: "Good facilities attract students" when actually "student fees fund better facilities."
+**Detection**: Consider temporal order and alternative causal directions.
+
+### 19. Ecological Fallacy
+**Description**: Inferring individual-level conclusions from group-level data.
+**Research Example**: "Countries with more education spending have higher GDP, so spending on education makes individuals richer."
+**Detection**: Are individual-level and group-level relationships the same?
+
+### 20. Simpson's Paradox
+**Description**: A trend present in subgroups reverses when groups are combined.
+**Research Example**: Department A and B both show improving retention, but the university overall shows declining retention (due to shifting enrollment proportions).
+**Detection**: Always check disaggregated data alongside aggregate.
+
+### Reasoning Fallacies
+
+### 21. Straw Man
+**Description**: Misrepresenting an opponent's argument to make it easier to attack.
+**Research Example**: Critic says "this method has limitations" → Author responds "my critic says the entire study is worthless."
+**Detection**: Does the refutation address the actual criticism?
+
+### 22. Moving the Goalposts
+**Description**: Changing the criteria for success after seeing results.
+**Research Example**: Defining "program success" as enrollment growth, then shifting to "student satisfaction" when enrollment drops.
+**Detection**: Were success criteria pre-defined?
+
+### 23. Slippery Slope
+**Description**: Arguing that one action will inevitably lead to an extreme outcome.
+**Research Example**: "If we allow flexible admission criteria, academic standards will collapse entirely."
+**Detection**: Is each step in the chain actually probable?
+
+### 24. Circular Reasoning (Begging the Question)
+**Description**: The conclusion is assumed in the premise.
+**Research Example**: "This university is excellent because it is highly ranked, and it is highly ranked because it is excellent."
+**Detection**: Does the argument depend on the truth of what it's trying to prove?
+
+### 25. No True Scotsman
+**Description**: Redefining a category to exclude counterexamples.
+**Research Example**: "All quality assurance systems improve outcomes." "But system X didn't." "Well, X wasn't a true quality assurance system."
+**Detection**: Is the definition being modified to fit the claim?
+
+### 26. Equivocation
+**Description**: Using a term in two different senses within the same argument.
+**Research Example**: "Quality" used sometimes to mean "standards compliance" and sometimes to mean "student satisfaction."
+**Detection**: Is the key term defined consistently throughout?
+
+### Statistical Fallacies
+
+### 27. Base Rate Neglect
+**Description**: Ignoring the base rate (overall probability) in favor of specific information.
+**Research Example**: "This program has a 90% satisfaction rate" — but the base rate for all programs is 88%.
+**Detection**: Always compare against relevant base rates.
+
+### 28. Regression to the Mean
+**Description**: Extreme performances naturally tend back toward average on subsequent measurements.
+**Research Example**: "Our intervention improved scores for the lowest-performing students" — they may have improved anyway.
+**Detection**: Was there a control group? Were initial measurements extreme?
+
+### 29. Texas Sharpshooter
+**Description**: Finding a pattern in random data by focusing on clusters and ignoring misses.
+**Research Example**: Running 20 statistical tests and reporting only the 1 that was significant.
+**Detection**: Were hypotheses pre-registered? Was multiple testing corrected for?
+
+### 30. Gambler's Fallacy
+**Description**: Believing past random events influence future random events.
+**Research Example**: "This institution has declined for 5 years, so it's due for improvement."
+**Detection**: Is there a causal mechanism for reversal, or is this just pattern-seeking?
+
+### 31. McNamara Fallacy (Quantitative Bias)
+**Description**: Making decisions based solely on quantitative metrics while ignoring qualitative factors.
+**Research Example**: Ranking universities only by publication counts, ignoring teaching quality and community impact.
+**Detection**: Are important but hard-to-measure factors being excluded?
+
+### 32. Goodhart's Law
+**Description**: "When a measure becomes a target, it ceases to be a good measure."
+**Research Example**: Universities gaming rankings metrics instead of genuinely improving quality.
+**Detection**: Has the metric become a target? Are there signs of metric manipulation?
+
+## Quick Reference: Detection Questions
+
+| Ask This | Detects |
+|----------|---------|
+| "Does B have other possible causes?" | Post hoc, false cause |
+| "What about the failures?" | Survivorship bias |
+| "Is this sample representative?" | Hasty generalization |
+| "Were criteria defined before results?" | Moving goalposts, Texas sharpshooter |
+| "Is the key term used consistently?" | Equivocation |
+| "What's the base rate?" | Base rate neglect |
+| "What evidence was left out?" | Cherry-picking, confirmation bias |
+| "Is this the actual argument being made?" | Straw man |
+| "Can we distinguish correlation from causation?" | Cum hoc, ecological fallacy |
+| "Are individual and group levels being mixed?" | Ecological fallacy, Simpson's paradox |