@wentorai/research-plugins 1.2.3 → 1.3.0

package/skills/analysis/statistics/general-statistics-guide/SKILL.md

@@ -1,226 +0,0 @@
----
-name: general-statistics-guide
-description: "Conceptual foundations of statistical inference for empirical research"
-metadata:
-  openclaw:
-    emoji: "📈"
-    category: "analysis"
-    subcategory: "statistics"
-    keywords: ["statistical inference", "hypothesis testing", "probability", "regression", "confidence intervals", "statistical thinking"]
-    source: "https://clawhub.com/ivangdavila/statistics"
----
-
-# Statistical Foundations for Empirical Research
-
-## Overview
-
-This guide builds statistical intuition from probability fundamentals through inferential methods to practical application in research. It is language-agnostic (not tied to R, Python, or Stata) and focuses on the concepts, assumptions, and interpretation of statistical methods commonly used in empirical papers. Use it as a reference when designing studies, choosing tests, or interpreting results.
-
-## Probability Foundations
-
-### Key Distributions
-
-| Distribution | When to Use | Parameters | Example |
-|-------------|-------------|-----------|---------|
-| **Normal** | Continuous, symmetric data; CLT applications | μ (mean), σ (std) | Height, test scores |
-| **Binomial** | Count of successes in n trials | n (trials), p (probability) | Survey yes/no responses |
-| **Poisson** | Count of rare events in fixed interval | λ (rate) | Paper citations per year |
-| **t-distribution** | Small sample means (n < 30) | df (degrees of freedom) | Pilot study comparisons |
-| **Chi-squared** | Goodness of fit, contingency tables | df | Category frequency tests |
-| **F-distribution** | Ratio of variances, ANOVA | df₁, df₂ | Comparing model fits |
-
-### Central Limit Theorem
-
-The sample mean $\bar{X}$ of n independent observations approaches a normal distribution as n increases, regardless of the population distribution:
-
-```
-If X₁, X₂, ..., Xₙ are i.i.d. with mean μ and variance σ²:
-  √n(X̄ - μ) / σ → N(0, 1) as n → ∞
-
-Practical rule: n ≥ 30 is usually sufficient
-Exception: heavily skewed distributions may need n ≥ 100
-```
-
-This is why most inferential statistics (confidence intervals, t-tests, regression) work even when the underlying data is not normally distributed.
-
-## Descriptive Statistics
-
-### Measures of Central Tendency
-
-| Measure | Formula | When to Use | Sensitive to Outliers? |
-|---------|---------|-------------|----------------------|
-| Mean | Σxᵢ / n | Symmetric distributions | Yes |
-| Median | Middle value when sorted | Skewed distributions, ordinal data | No |
-| Mode | Most frequent value | Categorical data, multimodal distributions | No |
-
-### Measures of Spread
-
-| Measure | Interpretation | When to Report |
-|---------|---------------|----------------|
-| Standard deviation (σ) | Average distance from mean | With the mean |
-| IQR (Q3 - Q1) | Spread of middle 50% | With the median |
-| Range (max - min) | Total spread | Rarely (sensitive to outliers) |
-| Coefficient of variation (σ/μ) | Relative spread | Comparing variability across scales |
-
-## Hypothesis Testing
-
-### The Testing Framework
-
-```
-1. State hypotheses:
-   H₀: null hypothesis (no effect, no difference)
-   H₁: alternative hypothesis (there is an effect)
-
-2. Choose significance level: α = 0.05 (conventional)
-
-3. Compute test statistic from data
-
-4. Compare to critical value or compute p-value
-
-5. Decision:
-   p < α → Reject H₀ (statistically significant)
-   p ≥ α → Fail to reject H₀ (not significant)
-```
-
-### Common Errors
-
-| | H₀ is True | H₀ is False |
-|---|---|---|
-| **Reject H₀** | Type I Error (α) | Correct (Power = 1 - β) |
-| **Fail to Reject H₀** | Correct | Type II Error (β) |
-
-**Practical interpretation**:
-- Type I (false positive): Claiming a drug works when it doesn't
-- Type II (false negative): Missing a real drug effect
-- Power: Probability of detecting a real effect (target ≥ 0.80)
-
-### Choosing the Right Test
-
-| Question | Data Type | Test | Assumptions |
-|----------|-----------|------|-------------|
-| Compare 2 means | Continuous, normal | Independent t-test | Equal variance (or Welch's) |
-| Compare 2 means (paired) | Continuous, normal | Paired t-test | Paired observations |
-| Compare 2 means (non-normal) | Continuous/ordinal | Mann-Whitney U | Independent samples |
-| Compare >2 means | Continuous, normal | One-way ANOVA | Equal variance, normality |
-| Compare >2 means (non-normal) | Ordinal | Kruskal-Wallis | Independent samples |
-| Association (categorical) | Categorical × Categorical | Chi-squared test | Expected count ≥ 5 |
-| Correlation | Continuous × Continuous | Pearson r | Linear relationship, bivariate normal |
-| Correlation (non-normal) | Ordinal or non-normal | Spearman ρ | Monotonic relationship |
-
-## Regression Analysis
-
-### Linear Regression
-
-```
-Y = β₀ + β₁X₁ + β₂X₂ + ... + βₖXₖ + ε
-
-Interpretation:
-  β₁ = change in Y for a 1-unit increase in X₁, holding other X's constant
-  R² = proportion of variance in Y explained by the model
-  Adjusted R² = R² penalized for number of predictors
-```
-
-**Key assumptions** (check before trusting results):
-1. **Linearity**: Y is a linear function of X's
-2. **Independence**: Observations are independent
-3. **Homoscedasticity**: Constant variance of residuals
-4. **Normality**: Residuals are approximately normal (for inference)
-5. **No multicollinearity**: X's are not highly correlated with each other
-
-**Diagnostic checks**:
-
-```
-Linearity:        Plot residuals vs. fitted values (no pattern)
-Homoscedasticity: Breusch-Pagan test or residual plot (no funnel shape)
-Normality:        Q-Q plot of residuals, Shapiro-Wilk test
-Multicollinearity: VIF (Variance Inflation Factor) — VIF > 10 is concerning
-Influential obs:  Cook's distance — D > 4/n warrants investigation
-```
-
-### Logistic Regression
-
-For binary outcomes (0/1):
-
-```
-log(p / (1-p)) = β₀ + β₁X₁ + β₂X₂ + ...
-
-Where p = P(Y = 1 | X)
-
-Interpretation:
-  exp(β₁) = odds ratio
-  exp(β₁) = 1.5 means "a 1-unit increase in X₁ multiplies the odds by 1.5"
-  Report: odds ratios with 95% CI
-```
-
-## Confidence Intervals
-
-```
-Point estimate ± (critical value × standard error)
-
-For a mean: X̄ ± z*(σ/√n)  or  X̄ ± t*(s/√n)
-
-Interpretation (frequentist):
-  "If we repeated this study many times, 95% of the resulting intervals
-   would contain the true population parameter."
-
-NOT: "There is a 95% probability that the true value is in this interval."
-```
-
-## Effect Sizes
-
-p-values tell you IF an effect exists; effect sizes tell you HOW BIG it is.
-
-| Measure | Context | Small | Medium | Large |
-|---------|---------|-------|--------|-------|
-| Cohen's d | Mean difference | 0.2 | 0.5 | 0.8 |
-| Pearson r | Correlation | 0.1 | 0.3 | 0.5 |
-| η² (eta-squared) | ANOVA | 0.01 | 0.06 | 0.14 |
-| Odds ratio | Logistic regression | 1.5 | 2.5 | 4.3 |
-| R² | Regression | 0.02 | 0.13 | 0.26 |
-
-**Always report effect sizes alongside p-values** — a "significant" result with d = 0.05 is trivial in practice.
-
-## Multiple Testing
-
-When testing multiple hypotheses simultaneously, the chance of at least one false positive increases:
-
-```
-With α = 0.05 and 20 independent tests:
-P(at least one false positive) = 1 - (1 - 0.05)^20 = 0.64
-
-Corrections:
-  Bonferroni:         α_adj = α / m  (conservative)
-  Benjamini-Hochberg: Controls false discovery rate (FDR) (less conservative)
-  Holm-Bonferroni:    Step-down procedure (more powerful than Bonferroni)
-```
-
-## Sample Size and Power
-
-Before collecting data, determine the required sample size:
-
-```
-Inputs needed:
-  1. Desired power (typically 0.80)
-  2. Significance level (α = 0.05)
-  3. Expected effect size (from pilot study or literature)
-  4. Type of test (t-test, ANOVA, regression, etc.)
-
-Rule of thumb for two-sample t-test:
-  n per group ≈ 16 / d²  (for 80% power, α = 0.05)
-  d = 0.5 → n ≈ 64 per group
-  d = 0.2 → n ≈ 400 per group
-```
-
-## Common Pitfalls
-
-1. **p-hacking**: Trying many analyses until p < 0.05. Fix: pre-register analyses.
-2. **Absence of evidence ≠ evidence of absence**: p > 0.05 does not prove H₀. Consider equivalence tests.
-3. **Correlation ≠ causation**: Regression coefficients are causal only with proper identification strategy.
-4. **Simpson's paradox**: A trend in subgroups can reverse when combined. Always check stratified analyses.
-5. **Overfitting**: Too many predictors relative to sample size. Rule of thumb: n ≥ 10-20 per predictor.
-
-## References
-
-- Agresti, A. (2018). *Statistical Methods for the Social Sciences* (5th ed.). Pearson.
-- Wasserstein, R. L., & Lazar, N. A. (2016). "The ASA Statement on p-Values." *The American Statistician*, 70(2), 129-133.
-- Cohen, J. (1988). *Statistical Power Analysis for the Behavioral Sciences* (2nd ed.). Routledge.

package/skills/analysis/statistics/infiagent-benchmark-guide/SKILL.md

@@ -1,106 +0,0 @@
----
-name: infiagent-benchmark-guide
-description: "Agent benchmark for data analysis evaluation (ICML 2024)"
-metadata:
-  openclaw:
-    emoji: "🏆"
-    category: "analysis"
-    subcategory: "statistics"
-    keywords: ["InfiAgent", "benchmark", "data analysis", "agent evaluation", "ICML", "DABench"]
-    source: "https://github.com/InfiAgent/InfiAgent"
----
-
-# InfiAgent Data Analysis Benchmark Guide
-
-## Overview
-
-InfiAgent (ICML 2024) is a benchmark for evaluating AI agents on data analysis tasks. It provides DABench — a standardized set of data analysis problems ranging from basic EDA to complex statistical modeling, each with ground-truth solutions and automated evaluation metrics. Measures agent capabilities in code generation, statistical reasoning, and visualization.
-
-## Benchmark Structure
-
-```
-DABench (Data Analysis Benchmark)
-├── Task Categories
-│   ├── Data Understanding (profiling, cleaning)
-│   ├── Exploratory Analysis (distributions, correlations)
-│   ├── Statistical Testing (hypothesis tests)
-│   ├── Visualization (appropriate chart selection)
-│   ├── Modeling (regression, classification)
-│   └── Interpretation (insights, conclusions)
-├── Difficulty Levels
-│   ├── Easy (single-step operations)
-│   ├── Medium (multi-step analysis)
-│   └── Hard (complex reasoning + code)
-└── Evaluation Metrics
-    ├── Code executability
-    ├── Answer correctness
-    ├── Visualization quality
-    └── Statistical validity
-```
-
-## Usage
-
-```python
-from infiagent import DABench
-
-bench = DABench()
-
-# List tasks
-for task in bench.tasks[:5]:
-    print(f"[{task.difficulty}] {task.id}: {task.description}")
-    print(f"  Dataset: {task.dataset}")
-    print(f"  Category: {task.category}")
-
-# Evaluate an agent
-from infiagent import evaluate
-
-results = evaluate(
-    agent_fn=my_data_agent,
-    tasks="all",
-    timeout=120,
-)
-
-print(f"Executability: {results.exec_rate:.1%}")
-print(f"Correctness: {results.correct_rate:.1%}")
-print(f"Statistical validity: {results.stats_valid:.1%}")
-```
-
-## Task Examples
-
-```python
-# Easy: "What is the mean and standard deviation of column X?"
-# Medium: "Is there a significant correlation between A and B?
-#          Control for confounders C and D."
-# Hard: "Build a predictive model for Y using all available
-#        features. Report cross-validated performance and
-#        identify the 3 most important features."
-```
-
-## Leaderboard Results
-
-```python
-# Selected results from DABench
-scores = {
-    "GPT-4 + Code": {"exec": 95, "correct": 67},
-    "Claude 3.5 Sonnet": {"exec": 93, "correct": 64},
-    "GPT-3.5 + Code": {"exec": 88, "correct": 45},
-    "CodeLlama-34B": {"exec": 72, "correct": 31},
-}
-
-print(f"{'Agent':<22} {'Exec%':>6} {'Correct%':>9}")
-for agent, s in scores.items():
-    print(f"{agent:<22} {s['exec']:>5}% {s['correct']:>8}%")
-```
-
-## Use Cases
-
-1. **Agent evaluation**: Standard benchmark for data analysis agents
-2. **Model comparison**: Compare LLMs on analytical tasks
-3. **Capability testing**: Assess statistical reasoning abilities
-4. **Research**: Study agent strengths and failure modes
-5. **Development**: Target specific weak areas for improvement
-
-## References
-
-- [InfiAgent GitHub](https://github.com/InfiAgent/InfiAgent)
-- [DABench Paper (ICML 2024)](https://arxiv.org/abs/2401.05507)

package/skills/analysis/statistics/pywayne-statistics-guide/SKILL.md

@@ -1,192 +0,0 @@
----
-name: pywayne-statistics-guide
-description: "37+ statistical testing methods for rigorous hypothesis testing"
-metadata:
-  openclaw:
-    emoji: "📐"
-    category: "analysis"
-    subcategory: "statistics"
-    keywords: ["hypothesis testing", "statistical tests", "p-value", "parametric tests", "nonparametric tests", "effect size", "multiple comparisons"]
-    source: "https://github.com/AcademicSkills/pywayne-statistics-guide"
----
-
-# PyWayne Statistics Guide
-
-A comprehensive reference for 37+ statistical testing methods covering parametric, nonparametric, and resampling-based hypothesis tests. Provides decision trees for test selection, implementation in Python (scipy, statsmodels, pingouin), effect size calculation, and proper reporting standards for academic publications.
-
-## Overview
-
-Hypothesis testing remains the backbone of quantitative research across the sciences, social sciences, and engineering. However, selecting the appropriate test for a given research question, data structure, and assumption profile is a persistent challenge, especially for researchers outside statistics. This skill provides a structured decision framework that maps research questions to the correct statistical test, verifies assumptions, computes test statistics and effect sizes, and formats results for publication.
-
-All 37+ tests are organized by the type of comparison (one-sample, two-sample, k-sample, association, agreement) and whether parametric assumptions are met. Each test entry includes when to use it, assumptions to verify, the Python implementation, and the correct APA-style reporting format.
-
-## Test Selection Decision Tree
-
-### Step 1: Identify the Research Question Type
-
-| Question Type | Examples |
-|--------------|----------|
-| **One-sample** | Is this sample mean different from a known value? |
-| **Two-sample (independent)** | Do treatment and control groups differ? |
-| **Two-sample (paired)** | Do pre-test and post-test scores differ? |
-| **K-sample (independent)** | Do 3+ groups differ on an outcome? |
-| **K-sample (repeated)** | Do measurements differ across 3+ time points? |
-| **Association** | Is variable X related to variable Y? |
-| **Agreement** | Do two raters/methods agree? |
-
-### Step 2: Check Data Type and Assumptions
-
-```
-Is the outcome variable continuous?
-├── Yes → Are the data normally distributed?
-│   ├── Yes → Are variances equal (for group comparisons)?
-│   │   ├── Yes → Use PARAMETRIC test
-│   │   └── No → Use Welch's correction or nonparametric
-│   └── No → Use NONPARAMETRIC test
-└── No → Is it ordinal or nominal?
-    ├── Ordinal → Use rank-based NONPARAMETRIC test
-    └── Nominal → Use CHI-SQUARE or exact test
-```
-
-## Parametric Tests
-
-### Two-Sample Tests
-
-```python
-from scipy import stats
-import pingouin as pg
-import numpy as np
-
-def two_sample_comparison(group_a, group_b, paired=False):
-    """
-    Perform the appropriate two-sample test with assumption checks.
-    """
-    results = {}
-
-    # Assumption: Normality
-    _, p_norm_a = stats.shapiro(group_a)
-    _, p_norm_b = stats.shapiro(group_b)
-    normal = p_norm_a > 0.05 and p_norm_b > 0.05
-
-    if paired:
-        if normal:
-            # Paired t-test
-            t, p = stats.ttest_rel(group_a, group_b)
-            d = pg.compute_effsize(group_a, group_b, paired=True, eftype='cohen')
-            results = {'test': 'paired t-test', 't': t, 'p': p, 'cohens_d': d}
-        else:
-            # Wilcoxon signed-rank
-            w, p = stats.wilcoxon(group_a, group_b)
-            r = w / (len(group_a) * (len(group_a) + 1) / 2)
-            results = {'test': 'Wilcoxon signed-rank', 'W': w, 'p': p, 'rank_biserial': r}
-    else:
-        if normal:
-            # Check equal variances
-            _, p_levene = stats.levene(group_a, group_b)
-            if p_levene > 0.05:
-                t, p = stats.ttest_ind(group_a, group_b)
-                results = {'test': 'independent t-test', 't': t, 'p': p}
-            else:
-                t, p = stats.ttest_ind(group_a, group_b, equal_var=False)
-                results = {'test': "Welch's t-test", 't': t, 'p': p}
-            d = pg.compute_effsize(group_a, group_b, eftype='cohen')
-            results['cohens_d'] = d
-        else:
-            # Mann-Whitney U
-            u, p = stats.mannwhitneyu(group_a, group_b, alternative='two-sided')
-            results = {'test': 'Mann-Whitney U', 'U': u, 'p': p}
-
-    return results
-```
-
-### K-Sample Tests (ANOVA Family)
-
-| Test | Use Case | Assumptions |
-|------|----------|-------------|
-| One-way ANOVA | 3+ independent groups, continuous outcome | Normality, homoscedasticity |
-| Welch's ANOVA | 3+ groups, unequal variances | Normality |
-| Repeated measures ANOVA | 3+ related measurements | Normality, sphericity |
-| Two-way ANOVA | Two factors, continuous outcome | Normality, homoscedasticity |
-| ANCOVA | Group comparison controlling for covariate | Normality, homogeneity of slopes |
-| MANOVA | Multiple dependent variables | Multivariate normality |
-
-```python
-def k_sample_test(groups: list, method: str = 'auto'):
-    """Run the appropriate k-sample comparison."""
-    # Check normality for all groups
-    all_normal = all(stats.shapiro(g)[1] > 0.05 for g in groups)
-
-    if all_normal:
-        # Check homogeneity of variance
-        _, p_levene = stats.levene(*groups)
-        if p_levene > 0.05:
-            f, p = stats.f_oneway(*groups)
-            return {'test': 'one-way ANOVA', 'F': f, 'p': p}
-        else:
-            # Welch's ANOVA via pingouin
-            return {'test': "Welch's ANOVA", 'note': 'Use pg.welch_anova()'}
-    else:
-        h, p = stats.kruskal(*groups)
-        return {'test': 'Kruskal-Wallis H', 'H': h, 'p': p}
-```
-
-## Nonparametric Tests Reference
-
-| Parametric Test | Nonparametric Alternative | When to Use |
-|----------------|--------------------------|-------------|
-| One-sample t-test | Wilcoxon signed-rank | Non-normal single sample |
-| Independent t-test | Mann-Whitney U | Non-normal, 2 independent groups |
-| Paired t-test | Wilcoxon signed-rank | Non-normal, paired data |
-| One-way ANOVA | Kruskal-Wallis H | Non-normal, 3+ groups |
-| Repeated measures ANOVA | Friedman test | Non-normal, 3+ related measures |
-| Pearson correlation | Spearman rho / Kendall tau | Non-linear or ordinal association |
-
-## Multiple Comparisons Correction
-
-When performing multiple hypothesis tests, control the family-wise error rate:
-
-```python
-from statsmodels.stats.multitest import multipletests
-
-def correct_multiple_tests(p_values: list, method: str = 'fdr_bh') -> dict:
-    """
-    Apply multiple comparisons correction.
-
-    Methods:
-        'bonferroni': Conservative, controls FWER
-        'holm': Less conservative than Bonferroni, controls FWER
-        'fdr_bh': Benjamini-Hochberg, controls FDR (recommended default)
-        'fdr_by': Benjamini-Yekutieli, conservative FDR control
-    """
-    reject, corrected_p, _, _ = multipletests(p_values, method=method)
-    return {
-        'method': method,
-        'original_p': p_values,
-        'corrected_p': corrected_p.tolist(),
-        'reject': reject.tolist(),
-        'n_significant': int(reject.sum())
-    }
-```
-
-## Effect Size Reference
-
-| Test | Effect Size | Small | Medium | Large |
-|------|------------|-------|--------|-------|
-| t-test | Cohen's d | 0.2 | 0.5 | 0.8 |
-| ANOVA | Eta-squared | 0.01 | 0.06 | 0.14 |
-| Correlation | r | 0.1 | 0.3 | 0.5 |
-| Chi-square | Cramér's V | 0.1 | 0.3 | 0.5 |
-| Mann-Whitney | Rank-biserial r | 0.1 | 0.3 | 0.5 |
-
-## APA Reporting Examples
-
-- **t-test**: "An independent samples t-test revealed a significant difference, t(58) = 2.45, p = .017, d = 0.63."
-- **ANOVA**: "A one-way ANOVA showed a significant main effect of condition, F(2, 87) = 4.12, p = .020, eta-squared = 0.09."
-- **Mann-Whitney**: "A Mann-Whitney U test indicated that scores were significantly higher in the treatment group, U = 245, p = .003, r = 0.42."
-- **Chi-square**: "A chi-square test of independence revealed a significant association, X2(2, N = 150) = 8.34, p = .015, V = 0.24."
-
-## References
-
-- Cohen, J. (1988). *Statistical Power Analysis for the Behavioral Sciences* (2nd ed.). Routledge.
-- Vallat, R. (2018). Pingouin: Statistics in Python. *JOSS*, 3(31), 1026.
-- Lakens, D. (2013). Calculating and Reporting Effect Sizes. *Frontiers in Psychology*, 4, 863.