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name: pairwise-ma-methodology description: Deep methodology knowledge for pairwise meta-analysis including fixed vs random effects, heterogeneity assessment, publication bias, and sensitivity analysis. Use when conducting or reviewing pairwise MA.

Pairwise Meta-Analysis Methodology

Comprehensive methodological guidance for conducting rigorous pairwise meta-analysis following Cochrane and PRISMA guidelines.

When to Use This Skill

• Planning a pairwise meta-analysis
• Choosing between fixed and random effects models
• Interpreting heterogeneity statistics
• Assessing publication bias
• Designing sensitivity analyses
• Reviewing pairwise MA code or results

Fixed vs Random Effects

Decision Framework

Are studies functionally identical?
├── Yes → Fixed-effect model appropriate
│   - Same population, intervention, comparator, outcome
│   - Estimating single "true" effect
│
└── No (usually the case) → Random-effects model
    - Studies differ in ways that affect true effect
    - Estimating mean of distribution of effects
    - More generalizable inference

When to Use Fixed-Effect

• Studies are very similar (rare in practice)
• Want to estimate effect in "identical" studies
• Very few studies (< 5) - random effects unreliable
• Sensitivity analysis alongside random effects

When to Use Random-Effects

• Studies differ in populations, settings, methods
• Want inference applicable beyond included studies
• Default choice for most meta-analyses
• Use with appropriate adjustments (Knapp-Hartung)

Key Differences

Aspect	Fixed-Effect	Random-Effects
Assumption	Common true effect	Distribution of true effects
Weights	Based on precision only	Includes between-study variance
Small study	More weight	Less weight
Large study	Less relative weight	More weight
CI width	Narrower (if heterogeneity exists)	Wider (appropriately)
Inference	To identical studies	To broader population

Heterogeneity Assessment

Statistics Overview

Q Statistic (Cochran's Q)

• Tests null hypothesis of homogeneity
• Follows chi-square distribution under null
• Low power with few studies
• Overpowered with many studies

# Interpretation
Q_pvalue < 0.10  # Suggests heterogeneity (use 0.10, not 0.05)

I² (Inconsistency Index)

• Percentage of variability due to heterogeneity (vs sampling error)
• Independent of number of studies
• Has wide confidence interval with few studies

I² Value	Interpretation
0-25%	Low heterogeneity
25-50%	Moderate heterogeneity
50-75%	Substantial heterogeneity
>75%	Considerable heterogeneity

Caution: These thresholds are rules of thumb, not strict cutoffs.

τ² (Tau-squared)

• Absolute between-study variance
• On scale of effect measure
• Used for prediction intervals
• Compare to typical effect sizes for context

H²

• Relative excess heterogeneity
• H² = Q/(k-1) where k = number of studies
• H² = 1 means no heterogeneity

Prediction Intervals

Critical: Always report prediction intervals alongside confidence intervals.

• CI: Uncertainty in mean effect estimate
• PI: Range where 95% of true study effects would lie

# In meta package
metabin(..., prediction = TRUE)

If PI includes null but CI doesn't:

• Mean effect is statistically significant
• But future studies might show no effect or opposite effect
• Heterogeneity is clinically important

Investigation of Heterogeneity

Subgroup Analysis

# Categorical moderator
update(ma_result, subgroup = risk_of_bias)

# Requirements:
# - Pre-specified in protocol
# - Limited number of subgroups
# - Biological/clinical rationale
# - Report within and between subgroup heterogeneity

Meta-Regression

# Continuous moderator
rma(yi, vi, mods = ~ year + sample_size, data = es_data)

# Requirements:
# - Minimum 10 studies per moderator
# - Pre-specified moderators
# - Avoid overfitting
# - Use Knapp-Hartung adjustment
# - Permutation test for multiple moderators

Rule of Thumb for Investigation

• Need ≥10 studies for meaningful subgroup analysis
• Meta-regression requires even more studies
• Pre-specify investigations in protocol
• Report all investigated moderators (avoid selective reporting)

Publication Bias Assessment

Visual Assessment: Funnel Plot

funnel(ma_result)
# Look for:
# - Asymmetry (small studies with large effects)
# - Missing studies in certain regions
# - Outliers

Statistical Tests

Egger's Test (Continuous Outcomes)

metabias(ma_result, method.bias = "linreg")
# P < 0.10 suggests asymmetry
# Low power with < 10 studies

Peters' Test (Binary Outcomes)

metabias(ma_result, method.bias = "peters")
# Better for OR than Egger's

Begg's Rank Test

metabias(ma_result, method.bias = "rank")
# Non-parametric alternative
# Lower power than regression tests

Adjustment Methods

Trim-and-Fill

trimfill(ma_result)
# Imputes "missing" studies
# Provides adjusted estimate
# Sensitivity analysis, not definitive correction

Selection Models

# More sophisticated approaches
# Model the selection process
# Available in metafor and weightr packages

Interpretation Cautions

• Asymmetry ≠ publication bias (could be true heterogeneity)
• Tests have low power with few studies
• Don't over-interpret with < 10 studies
• Multiple causes of asymmetry exist

Sensitivity Analyses

Essential Sensitivity Analyses

1. Fixed vs Random Effects

   • Report both; if results differ, investigate why

2. Leave-One-Out

   metainf(ma_result)
   # Identifies influential studies
   

3. Risk of Bias

   • Exclude high risk of bias studies
   • Subgroup by risk of bias

4. Influence Diagnostics

   influence(ma_result)
   # DFBETAS, Cook's distance
   

5. Different Effect Measures

   • OR vs RR vs RD for binary
   • May give different conclusions

6. Estimation Method

   • DerSimonian-Laird vs REML vs ML

GOSH Analysis

# Graphical display of study heterogeneity
gosh(ma_result)
# Identifies subsets with different results

Reporting Checklist (PRISMA)

Methods

• Effect measure and rationale
• Model choice (fixed/random) and rationale
• Heterogeneity measures planned
• Publication bias assessment planned
• Sensitivity analyses planned
• Software and packages used

Results

• Number of studies and participants
• Pooled effect with CI
• Prediction interval
• Heterogeneity statistics (Q, I², τ²)
• Forest plot
• Funnel plot (if ≥10 studies)
• Publication bias test results
• Sensitivity analysis results

Common Pitfalls

1. Using Q p-value to Choose Model

• Wrong: "Q p > 0.05, so use fixed-effect"
• Right: Choose based on study similarity, report both

2. Ignoring Prediction Intervals

• CI shows precision of mean estimate
• PI shows variability in true effects
• Both are clinically important

3. Over-interpreting I²

• I² has wide CI with few studies
• Context matters (clinical significance)
• Don't use arbitrary thresholds mechanically

4. Selective Subgroup Analysis

• Pre-specify in protocol
• Report all, not just significant ones
• Adjust for multiple testing

5. Publication Bias Assessment with Few Studies

• Tests unreliable with < 10 studies
• State this limitation, don't perform test

Quick Reference Code

library(meta)

# Basic random-effects MA (binary)
ma <- metabin(
  event.e, n.e, event.c, n.c,
  studlab = study,
  data = dat,
  sm = "OR",
  method = "MH",
  method.tau = "REML",
  hakn = TRUE,           # Knapp-Hartung adjustment
  prediction = TRUE      # Prediction interval
)

# Forest plot
forest(ma, sortvar = TE, prediction = TRUE)

# Funnel plot and Egger's test
funnel(ma)
metabias(ma, method.bias = "linreg")

# Influence analysis
metainf(ma)

# Subgroup analysis
update(ma, subgroup = risk_of_bias)

Resources

• Cochrane Handbook: https://training.cochrane.org/handbook
• PRISMA Statement: http://www.prisma-statement.org/
• Higgins & Green: Cochrane Handbook for Systematic Reviews
• Borenstein et al.: Introduction to Meta-Analysis