meta-analysis-psych

Meta-Analysis for Psychology

TL;DR — Complete meta-analysis pipeline in pure Python/NumPy: Cohen's d and Hedges' g from raw statistics, DerSimonian-Laird random-effects pooling, I² heterogeneity, forest plot with summary diamond, funnel plot, Egger test, trim-and-fill, PET-PEESE regression correction, and p-curve analysis.

---

When to Use

Use this Skill when you need to:

• Pool effect sizes from multiple independent studies on the same research question
• Quantify and visualize heterogeneity across studies (I², τ²)
• Detect and correct for publication bias (Egger test, trim-and-fill, PET-PEESE)
• Assess whether p-values are consistent with a true effect (p-curve analysis)
• Generate publication-quality forest and funnel plots
• Run sensitivity analyses (leave-one-out, cumulative meta-analysis)

---

Background

Effect Size Measures

Cohen's d (raw mean difference standardized by pooled SD):

d = (M1 - M2) / SD_pooled

Hedges' g (small-sample bias correction for d):

J = 1 - 3 / (4 * (n1 + n2 - 2) - 1)
g = J × d
Var(g) = (n1 + n2) / (n1 × n2) + g² / (2 × (n1 + n2))

Random-Effects Model (DerSimonian-Laird)

Under the random-effects model, true effect sizes θi vary:

θi = θ + ui + εi       where ui ~ N(0, τ²), εi ~ N(0, vi)

Between-study variance τ² is estimated by the DerSimonian-Laird method:

Q    = Σ wi(gi - g_FE)²        (Cochran's Q statistic)
τ²   = max(0, (Q - (k-1)) / (Σwi - Σwi²/Σwi))
wi*  = 1 / (vi + τ²)           (RE weights)
g_RE = Σ(wi* × gi) / Σwi*
I²   = (Q - (k-1)) / Q × 100%  (% of total variance due to heterogeneity)

Publication Bias Methods

Method	Description
Funnel plot	Asymmetry suggests missing small-n null studies
Egger test	Regress std normal deviate on precision; intercept ≠ 0 = bias
Trim-and-fill	Impute mirror studies to restore funnel symmetry
PET-PEESE	Regress g on SE (PET) or SE² (PEESE); intercept = bias-corrected effect
p-curve	Distribution of p-values below .05; right-skew = real effect

---

Environment Setup

conda create -n meta_env python=3.11 -y
conda activate meta_env

pip install numpy>=1.23 scipy>=1.9 pandas>=1.5 matplotlib>=3.6

# Verify
python -c "import numpy, scipy, pandas, matplotlib; print('All OK')"

---

Core Workflow

Step 1 — Effect Size Computation

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
from scipy import stats
from typing import Optional, Dict, List, Tuple

# ── Cohen's d from various input formats ─────────────────────────────────────

def cohens_d_from_means(
    m1: float, m2: float,
    sd1: float, sd2: float,
    n1: int, n2: int,
) -> Dict:
    """
    Compute Cohen's d and Hedges' g from group means and SDs.

    Args:
        m1, m2:     Group means.
        sd1, sd2:   Group standard deviations.
        n1, n2:     Sample sizes.

    Returns:
        Dict with d, g, var_g, se_g, 95% CI.
    """
    # Pooled SD
    sd_pooled = np.sqrt(((n1 - 1) * sd1**2 + (n2 - 1) * sd2**2) / (n1 + n2 - 2))
    d = (m1 - m2) / sd_pooled

    # Hedges' g correction
    df_total = n1 + n2 - 2
    J = 1 - 3 / (4 * df_total - 1)
    g = J * d

    # Variance of g
    var_g = (n1 + n2) / (n1 * n2) + g**2 / (2 * (n1 + n2))
    se_g = np.sqrt(var_g)

    return {
        "d": round(d, 4),
        "g": round(g, 4),
        "J": round(J, 4),
        "var_g": round(var_g, 6),
        "se_g": round(se_g, 4),
        "ci_lo": round(g - 1.96 * se_g, 4),
        "ci_hi": round(g + 1.96 * se_g, 4),
        "n1": n1, "n2": n2,
    }


def cohens_d_from_t(
    t: float, n1: int, n2: int,
) -> Dict:
    """
    Compute Cohen's d from an independent-samples t-statistic.

    Args:
        t:      t-statistic (signed).
        n1, n2: Group sample sizes.

    Returns:
        Dict with d, g, var_g, se_g, 95% CI.
    """
    d = t * np.sqrt((n1 + n2) / (n1 * n2))
    df_total = n1 + n2 - 2
    J = 1 - 3 / (4 * df_total - 1)
    g = J * d
    var_g = (n1 + n2) / (n1 * n2) + g**2 / (2 * (n1 + n2))
    se_g = np.sqrt(var_g)
    return {
        "d": round(d, 4), "g": round(g, 4), "J": round(J, 4),
        "var_g": round(var_g, 6), "se_g": round(se_g, 4),
        "ci_lo": round(g - 1.96 * se_g, 4), "ci_hi": round(g + 1.96 * se_g, 4),
        "n1": n1, "n2": n2,
    }


def cohens_d_from_F(
    F: float, n1: int, n2: int,
) -> Dict:
    """
    Compute Cohen's d from a one-df F-ratio (two-group comparison).

    Args:
        F:      F-statistic (F = t²).
        n1, n2: Group sample sizes.

    Returns:
        Dict with d, g, var_g, se_g, 95% CI.
    """
    t = np.sqrt(F)  # F = t² for one-df tests
    return cohens_d_from_t(t, n1, n2)

Step 2 — Random-Effects Meta-Analysis

def run_meta_analysis(
    df: pd.DataFrame,
    g_col: str = "g",
    var_col: str = "var_g",
    study_col: str = "study",
) -> Dict:
    """
    DerSimonian-Laird random-effects meta-analysis.

    Args:
        df:       DataFrame with one row per study.
        g_col:    Column of Hedges' g effect sizes.
        var_col:  Column of effect size variances.
        study_col: Column of study labels.

    Returns:
        Dict with pooled estimate, heterogeneity statistics, and weights.
    """
    g = df[g_col].values
    v = df[var_col].values
    k = len(g)

    # Fixed-effects weights and estimate
    w_FE = 1 / v
    g_FE = np.sum(w_FE * g) / np.sum(w_FE)

    # Cochran's Q
    Q = np.sum(w_FE * (g - g_FE) ** 2)

    # DerSimonian-Laird tau²
    c = np.sum(w_FE) - np.sum(w_FE ** 2) / np.sum(w_FE)
    tau2 = max(0.0, (Q - (k - 1)) / c)

    # I²
    I2 = max(0.0, (Q - (k - 1)) / Q * 100) if Q > 0 else 0.0

    # Random-effects weights and estimate
    w_RE = 1 / (v + tau2)
    g_RE = np.sum(w_RE * g) / np.sum(w_RE)
    var_RE = 1 / np.sum(w_RE)
    se_RE = np.sqrt(var_RE)
    z_RE = g_RE / se_RE
    p_RE = 2 * stats.norm.sf(abs(z_RE))
    ci_lo = g_RE - 1.96 * se_RE
    ci_hi = g_RE + 1.96 * se_RE

    result = {
        "k": k,
        "g_RE": round(g_RE, 4),
        "se_RE": round(se_RE, 4),
        "ci_lo": round(ci_lo, 4),
        "ci_hi": round(ci_hi, 4),
        "z": round(z_RE, 3),
        "p": round(p_RE, 4),
        "Q": round(Q, 3),
        "Q_df": k - 1,
        "Q_p": round(float(stats.chi2.sf(Q, df=k - 1)), 4),
        "I2": round(I2, 1),
        "tau2": round(tau2, 6),
        "tau": round(np.sqrt(tau2), 4),
        "w_RE": w_RE,
        "g_FE": round(g_FE, 4),
    }

    print(
        f"Random-effects meta-analysis (k={k} studies):\n"
        f"  g = {g_RE:.3f} [{ci_lo:.3f}, {ci_hi:.3f}], p = {p_RE:.4f}\n"
        f"  Q({k-1}) = {Q:.2f}, p = {result['Q_p']:.4f}\n"
        f"  I² = {I2:.1f}%, τ = {result['tau']:.4f}\n"
        f"  Heterogeneity: "
        + ("low" if I2 < 25 else "moderate" if I2 < 75 else "high")
    )
    return result

Step 3 — Forest Plot

def forest_plot(
    df: pd.DataFrame,
    meta_result: Dict,
    g_col: str = "g",
    ci_lo_col: str = "ci_lo",
    ci_hi_col: str = "ci_hi",
    study_col: str = "study",
    sort_by: str = "g",
    output_path: Optional[str] = None,
) -> plt.Figure:
    """
    Generate a forest plot with study CIs and summary diamond.

    Args:
        df:           Study-level DataFrame (one row per study).
        meta_result:  Output from run_meta_analysis().
        g_col:        Column of effect sizes.
        ci_lo_col:    Column of lower 95% CIs.
        ci_hi_col:    Column of upper 95% CIs.
        study_col:    Column of study labels.
        sort_by:      Sort studies by 'g' (default) or 'year'.
        output_path:  Optional path to save figure.

    Returns:
        Matplotlib Figure.
    """
    if sort_by == "g":
        df = df.sort_values(g_col).reset_index(drop=True)

    k = len(df)
    g_RE = meta_result["g_RE"]
    ci_lo_RE = meta_result["ci_lo"]
    ci_hi_RE = meta_result["ci_hi"]

    fig, ax = plt.subplots(figsize=(10, max(6, k * 0.45 + 2)))
    y_positions = list(range(k, 0, -1))

    # Study rows
    for i, (_, row) in enumerate(df.iterrows()):
        y = y_positions[i]
        g = row[g_col]
        lo = row[ci_lo_col]
        hi = row[ci_hi_col]
        ci_width = hi - lo
        # Marker size proportional to inverse variance (weight)
        w = 1 / (hi - lo) ** 2 if (hi - lo) > 0 else 1
        ms = min(max(4, w * 0.5), 16)

        ax.plot([lo, hi], [y, y], color="black", linewidth=1)
        ax.plot(g, y, "s", color="steelblue", markersize=ms, zorder=5)
        ax.text(-0.05 + min(df[ci_lo_col]) - 0.3, y,
                row[study_col], ha="right", va="center", fontsize=8)
        ax.text(max(df[ci_hi_col]) + 0.3, y,
                f"{g:.2f} [{lo:.2f}, {hi:.2f}]",
                ha="left", va="center", fontsize=7, color="dimgray")

    # Summary diamond
    y_summary = 0
    diamond_x = [ci_lo_RE, g_RE, ci_hi_RE, g_RE]
    diamond_y = [y_summary, y_summary + 0.4, y_summary, y_summary - 0.4]
    ax.fill(diamond_x, diamond_y, color="crimson", alpha=0.85, zorder=6)

    ax.text(max(df[ci_hi_col]) + 0.3, y_summary,
            f"{g_RE:.2f} [{ci_lo_RE:.2f}, {ci_hi_RE:.2f}]",
            ha="left", va="center", fontsize=8, fontweight="bold", color="crimson")

    # Reference line at 0
    ax.axvline(0, color="gray", linestyle="--", linewidth=1)

    ax.set_yticks([])
    ax.set_xlabel("Hedges' g")
    ax.set_title(
        f"Forest Plot — {k} Studies\n"
        f"g = {g_RE:.3f}, I² = {meta_result['I2']:.1f}%, "
        f"τ = {meta_result['tau']:.3f}"
    )
    ax.set_xlim(min(df[ci_lo_col]) - 1.0, max(df[ci_hi_col]) + 1.5)
    fig.tight_layout()

    if output_path:
        fig.savefig(output_path, dpi=150)
    plt.show()
    return fig

---

Advanced Usage

Publication Bias: Egger Test, Trim-and-Fill, PET-PEESE

def egger_test(
    df: pd.DataFrame,
    g_col: str = "g",
    var_col: str = "var_g",
) -> Dict:
    """
    Egger's test for funnel p

---

*Content truncated.*