gyoshu 0.1.0 → 0.2.1

package/src/skill/scientific-method/SKILL.md

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----
-name: scientific-method
-description: Framework for hypothesis-driven scientific research
----
-
-# Scientific Method Framework
-
-## When to Use
-Load this skill when conducting hypothesis-driven research that requires rigorous methodology.
-
-## The Scientific Method
-
-### 1. Observation
-- Examine existing data or phenomena
-- Note patterns, anomalies, or questions
-- Document initial observations with `[OBSERVATION]` marker
-
-### 2. Question
-- Formulate a specific, testable question
-- Use `[OBJECTIVE]` marker to state clearly
-
-### 3. Hypothesis
-- Propose a testable explanation
-- Make specific, falsifiable predictions
-- Use `[HYPOTHESIS]` marker
-
-### 4. Experiment
-- Design controlled experiments
-- Identify variables (independent, dependent, controlled)
-- Use `[EXPERIMENT]` marker for procedures
-
-### 5. Analysis
-- Collect and analyze data
-- Use statistical methods appropriately
-- Use `[ANALYSIS]` marker for interpretations
-
-### 6. Conclusion
-- Accept or reject hypothesis based on evidence
-- Acknowledge limitations
-- Use `[CONCLUSION:confidence=X]` marker
-
-## Best Practices
-
-1. **Null Hypothesis**: Always consider the null hypothesis
-2. **Controls**: Include appropriate control groups/conditions
-3. **Sample Size**: Ensure adequate sample size for statistical power
-4. **Reproducibility**: Document all steps for replication
-5. **Peer Review**: Validate findings before final conclusions
-
----
-
-## Hypothesis-First Workflow
-
-**CRITICAL**: State your hypotheses BEFORE looking at the data. This prevents p-hacking and confirmation bias.
-
-### 1. State H0/H1 Before Data Analysis
-
-```python
-# ALWAYS document hypotheses before running analysis
-print("[HYPOTHESIS] H0: No difference between groups (μ1 = μ2)")
-print("[HYPOTHESIS] H1: Treatment group shows improvement (μ1 > μ2)")
-```
-
-**Requirements:**
-- H0 (Null Hypothesis): The default assumption of no effect/difference
-- H1 (Alternative Hypothesis): The specific effect you're testing
-- Both must be stated BEFORE examining the data
-
-### 2. Define Endpoints and Alpha Before Analysis
-
-```python
-# Pre-specify statistical parameters
-print("[DECISION] Primary endpoint: mean response time")
-print("[DECISION] Alpha level: 0.05 (two-tailed)")
-print("[DECISION] Minimum effect size of interest: Cohen's d = 0.5")
-```
-
-**Before running any tests, document:**
-- Primary endpoint (what you're measuring)
-- Alpha level (typically 0.05)
-- Directionality (one-tailed vs two-tailed)
-- Minimum effect size of practical significance
-
-### 3. Pre-registration
-
-Document your complete analysis plan before data analysis:
-
-```markdown
-## Pre-Registration
-- **Primary Hypothesis**: [H0/H1 statements]
-- **Primary Endpoint**: [What metric]
-- **Statistical Test**: [Which test and why]
-- **Alpha Level**: [Significance threshold]
-- **Sample Size Rationale**: [Power analysis results]
-- **Multiple Testing**: [Correction method if >1 test]
-- **Exclusion Criteria**: [When to remove data points]
-```
-
-**Why Pre-register?**
-- Distinguishes confirmatory from exploratory analysis
-- Prevents HARKing (Hypothesizing After Results are Known)
-- Increases credibility of findings
-
----
-
-## Statistical Rigor Requirements
-
-### Always Report Confidence Intervals
-
-**NEVER** report only point estimates. Always include confidence intervals:
-
-```python
-# Calculate and report CI
-from scipy.stats import sem
-mean_val = data.mean()
-ci_margin = 1.96 * sem(data)
-ci_low, ci_high = mean_val - ci_margin, mean_val + ci_margin
-
-print(f"[STAT:estimate] Mean = {mean_val:.3f}")
-print(f"[STAT:ci] 95% CI [{ci_low:.3f}, {ci_high:.3f}]")
-```
-
-**CI communicates:**
-- Precision of the estimate
-- Range of plausible values
-- Whether effect is meaningfully different from zero
-
-### Always Report Effect Size with Interpretation
-
-**NEVER** claim significance without effect size:
-
-```python
-import numpy as np
-
-def cohens_d(group1, group2):
-    n1, n2 = len(group1), len(group2)
-    var1, var2 = group1.var(), group2.var()
-    pooled_std = np.sqrt(((n1-1)*var1 + (n2-1)*var2) / (n1+n2-2))
-    return (group1.mean() - group2.mean()) / pooled_std
-
-d = cohens_d(treatment, control)
-effect_label = "small" if abs(d) < 0.5 else "medium" if abs(d) < 0.8 else "large"
-print(f"[STAT:effect_size] Cohen's d = {d:.3f} ({effect_label})")
-```
-
-### Use Appropriate Tests for Data Type
-
-| Data Type | Comparison | Recommended Test |
-|-----------|------------|------------------|
-| Continuous, normal | 2 groups | Welch's t-test |
-| Continuous, non-normal | 2 groups | Mann-Whitney U |
-| Continuous, normal | >2 groups | ANOVA |
-| Continuous, non-normal | >2 groups | Kruskal-Wallis |
-| Categorical | 2x2 table | Chi-square or Fisher's exact |
-| Proportions | 2 groups | Z-test for proportions |
-| Correlation | Continuous | Pearson (normal) or Spearman |
-
-```python
-# Document test selection
-print("[DECISION] Using Welch's t-test: two independent groups, unequal variance assumed")
-
-# Check assumptions
-from scipy.stats import shapiro, levene
-_, p_norm = shapiro(data)
-print(f"[CHECK:normality] Shapiro-Wilk p = {p_norm:.3f}")
-```
-
----
-
-## Multiple Comparison Correction
-
-When running multiple statistical tests, adjust for inflated false positive rate.
-
-### Bonferroni Correction (Conservative)
-
-**Use when:** Small number of planned comparisons (≤10)
-
-```python
-import numpy as np
-
-n_tests = 5
-alpha = 0.05
-bonferroni_alpha = alpha / n_tests
-
-print(f"[DECISION] Bonferroni correction: α = {alpha}/{n_tests} = {bonferroni_alpha:.4f}")
-
-# Report both raw and adjusted p-values
-p_values = [0.01, 0.03, 0.02, 0.15, 0.04]
-for i, p in enumerate(p_values):
-    adjusted_p = min(p * n_tests, 1.0)
-    sig = "***" if p < bonferroni_alpha else ""
-    print(f"[STAT:p_value] Test {i+1}: raw p = {p:.4f}, adjusted p = {adjusted_p:.4f} {sig}")
-```
-
-### Benjamini-Hochberg FDR (Less Conservative)
-
-**Use when:** Large number of tests (>10), exploratory analysis
-
-```python
-from scipy.stats import false_discovery_control
-
-p_values = np.array([0.001, 0.008, 0.039, 0.041, 0.042, 0.06, 0.074, 0.205, 0.212, 0.35])
-adjusted_p = false_discovery_control(p_values, method='bh')
-
-print("[DECISION] Benjamini-Hochberg FDR correction for 10 tests")
-for i, (raw, adj) in enumerate(zip(p_values, adjusted_p)):
-    sig = "***" if adj < 0.05 else ""
-    print(f"[STAT:p_value] Test {i+1}: raw p = {raw:.4f}, BH-adjusted p = {adj:.4f} {sig}")
-```
-
-### Decision Guide
-
-| Scenario | Correction | Rationale |
-|----------|------------|-----------|
-| 1-5 planned comparisons | Bonferroni | Simple, conservative |
-| 6-20 tests | Bonferroni or BH-FDR | Balance rigor/power |
-| >20 tests (genomics, etc.) | BH-FDR | Maintains power |
-| Exploratory screening | BH-FDR | Focus on discovery |
-| Confirmatory study | Bonferroni | Focus on rigor |
-
-**Always report both raw AND adjusted p-values** to allow readers to assess significance under different criteria.
-
----
-
-## Effect Size Interpretation
-
-Use these thresholds to interpret effect magnitudes:
-
-### Cohen's d (Group Differences)
-
-| Cohen's d | Interpretation | Practical Meaning |
-|-----------|----------------|-------------------|
-| 0.2 | Small | Barely noticeable difference |
-| 0.5 | Medium | Noticeable, potentially meaningful |
-| 0.8 | Large | Obvious, substantial difference |
-
-```python
-d = 0.65
-if abs(d) < 0.2:
-    interpretation = "negligible"
-elif abs(d) < 0.5:
-    interpretation = "small"
-elif abs(d) < 0.8:
-    interpretation = "medium"
-else:
-    interpretation = "large"
-
-print(f"[STAT:effect_size] Cohen's d = {d:.2f} ({interpretation})")
-```
-
-### Correlation Coefficient (r)
-
-| |r| | Interpretation | Variance Explained |
-|-----|----------------|-------------------|
-| 0.1 | Small | ~1% |
-| 0.3 | Medium | ~9% |
-| 0.5 | Large | ~25% |
-
-```python
-r = 0.42
-r_squared = r ** 2
-if abs(r) < 0.1:
-    interpretation = "negligible"
-elif abs(r) < 0.3:
-    interpretation = "small"
-elif abs(r) < 0.5:
-    interpretation = "medium"
-else:
-    interpretation = "large"
-
-print(f"[STAT:effect_size] r = {r:.2f} ({interpretation}, explains {r_squared*100:.1f}% variance)")
-```
-
-### Odds Ratio (OR)
-
-| Odds Ratio | Interpretation |
-|------------|----------------|
-| 1.5 | Small effect |
-| 2.5 | Medium effect |
-| 4.0 | Large effect |
-
-**Note:** Odds ratios are symmetric around 1.0. An OR of 0.25 is equivalent in magnitude to OR of 4.0.
-
-```python
-OR = 3.2
-if OR > 1:
-    if OR < 1.5:
-        interpretation = "negligible"
-    elif OR < 2.5:
-        interpretation = "small"
-    elif OR < 4.0:
-        interpretation = "medium"
-    else:
-        interpretation = "large"
-else:
-    # For protective effects (OR < 1)
-    reciprocal = 1 / OR
-    if reciprocal < 1.5:
-        interpretation = "negligible"
-    elif reciprocal < 2.5:
-        interpretation = "small"
-    elif reciprocal < 4.0:
-        interpretation = "medium"
-    else:
-        interpretation = "large"
-
-print(f"[STAT:effect_size] OR = {OR:.2f} ({interpretation})")
-```
-
-### Quick Reference Table
-
-| Measure | Small | Medium | Large |
-|---------|-------|--------|-------|
-| **Cohen's d** | 0.2 | 0.5 | 0.8 |
-| **Correlation r** | 0.1 | 0.3 | 0.5 |
-| **Odds Ratio** | 1.5 | 2.5 | 4.0 |
-| **R² (variance)** | 1% | 9% | 25% |
-| **η² (eta squared)** | 0.01 | 0.06 | 0.14 |
-
-### From Effect Size to Practical Significance
-
-Always translate statistical effect size to real-world meaning:
-
-```python
-# Good: Connect to practical significance
-print(f"[STAT:effect_size] Cohen's d = 0.5 (medium)")
-print(f"[SO_WHAT] A medium effect means the treatment reduces wait time by ~15 seconds on average")
-
-# Bad: Just reporting the number
-print(f"[STAT:effect_size] d = 0.5")  # Missing interpretation and practical meaning
-```