scientific-writer 2.3.1__py3-none-any.whl

scientific_writer/.claude/skills/scientific-critical-thinking/references/statistical_pitfalls.md

@@ -0,0 +1,506 @@
+# Common Statistical Pitfalls
+
+## P-Value Misinterpretations
+
+### Pitfall 1: P-Value = Probability Hypothesis is True
+**Misconception:** p = .05 means 5% chance the null hypothesis is true.
+
+**Reality:** P-value is the probability of observing data this extreme (or more) *if* the null hypothesis is true. It says nothing about the probability the hypothesis is true.
+
+**Correct interpretation:** "If there were truly no effect, we would observe data this extreme only 5% of the time."
+
+### Pitfall 2: Non-Significant = No Effect
+**Misconception:** p > .05 proves there's no effect.
+
+**Reality:** Absence of evidence ≠ evidence of absence. Non-significant results may indicate:
+- Insufficient statistical power
+- True effect too small to detect
+- High variability
+- Small sample size
+
+**Better approach:**
+- Report confidence intervals
+- Conduct power analysis
+- Consider equivalence testing
+
+### Pitfall 3: Significant = Important
+**Misconception:** Statistical significance means practical importance.
+
+**Reality:** With large samples, trivial effects become "significant." A statistically significant 0.1 IQ point difference is meaningless in practice.
+
+**Better approach:**
+- Report effect sizes
+- Consider practical significance
+- Use confidence intervals
+
+### Pitfall 4: P = .049 vs. P = .051
+**Misconception:** These are meaningfully different because one crosses the .05 threshold.
+
+**Reality:** These represent nearly identical evidence. The .05 threshold is arbitrary.
+
+**Better approach:**
+- Treat p-values as continuous measures of evidence
+- Report exact p-values
+- Consider context and prior evidence
+
+### Pitfall 5: One-Tailed Tests Without Justification
+**Misconception:** One-tailed tests are free extra power.
+
+**Reality:** One-tailed tests assume effects can only go one direction, which is rarely true. They're often used to artificially boost significance.
+
+**When appropriate:** Only when effects in one direction are theoretically impossible or equivalent to null.
+
+## Multiple Comparisons Problems
+
+### Pitfall 6: Multiple Testing Without Correction
+**Problem:** Testing 20 hypotheses at p < .05 gives ~65% chance of at least one false positive.
+
+**Examples:**
+- Testing many outcomes
+- Testing many subgroups
+- Conducting multiple interim analyses
+- Testing at multiple time points
+
+**Solutions:**
+- Bonferroni correction (divide α by number of tests)
+- False Discovery Rate (FDR) control
+- Prespecify primary outcome
+- Treat exploratory analyses as hypothesis-generating
+
+### Pitfall 7: Subgroup Analysis Fishing
+**Problem:** Testing many subgroups until finding significance.
+
+**Why problematic:**
+- Inflates false positive rate
+- Often reported without disclosure
+- "Interaction was significant in women" may be random
+
+**Solutions:**
+- Prespecify subgroups
+- Use interaction tests, not separate tests
+- Require replication
+- Correct for multiple comparisons
+
+### Pitfall 8: Outcome Switching
+**Problem:** Analyzing many outcomes, reporting only significant ones.
+
+**Detection signs:**
+- Secondary outcomes emphasized
+- Incomplete outcome reporting
+- Discrepancy between registration and publication
+
+**Solutions:**
+- Preregister all outcomes
+- Report all planned outcomes
+- Distinguish primary from secondary
+
+## Sample Size and Power Issues
+
+### Pitfall 9: Underpowered Studies
+**Problem:** Small samples have low probability of detecting true effects.
+
+**Consequences:**
+- High false negative rate
+- Significant results more likely to be false positives
+- Overestimated effect sizes (when significant)
+
+**Solutions:**
+- Conduct a priori power analysis
+- Aim for 80-90% power
+- Consider effect size from prior research
+
+### Pitfall 10: Post-Hoc Power Analysis
+**Problem:** Calculating power after seeing results is circular and uninformative.
+
+**Why useless:**
+- Non-significant results always have low "post-hoc power"
+- It recapitulates the p-value without new information
+
+**Better approach:**
+- Calculate confidence intervals
+- Plan replication with adequate sample
+- Conduct prospective power analysis for future studies
+
+### Pitfall 11: Small Sample Fallacy
+**Problem:** Trusting results from very small samples.
+
+**Issues:**
+- High sampling variability
+- Outliers have large influence
+- Assumptions of tests violated
+- Confidence intervals very wide
+
+**Guidelines:**
+- Be skeptical of n < 30
+- Check assumptions carefully
+- Consider non-parametric tests
+- Replicate findings
+
+## Effect Size Misunderstandings
+
+### Pitfall 12: Ignoring Effect Size
+**Problem:** Focusing only on significance, not magnitude.
+
+**Why problematic:**
+- Significance ≠ importance
+- Can't compare across studies
+- Doesn't inform practical decisions
+
+**Solutions:**
+- Always report effect sizes
+- Use standardized measures (Cohen's d, r, η²)
+- Interpret using field conventions
+- Consider minimum clinically important difference
+
+### Pitfall 13: Misinterpreting Standardized Effect Sizes
+**Problem:** Treating Cohen's d = 0.5 as "medium" without context.
+
+**Reality:**
+- Field-specific norms vary
+- Some fields have larger typical effects
+- Real-world importance depends on context
+
+**Better approach:**
+- Compare to effects in same domain
+- Consider practical implications
+- Look at raw effect sizes too
+
+### Pitfall 14: Confusing Explained Variance with Importance
+**Problem:** "Only explains 5% of variance" = unimportant.
+
+**Reality:**
+- Height explains ~5% of variation in NBA player salary but is crucial
+- Complex phenomena have many small contributors
+- Predictive accuracy ≠ causal importance
+
+**Consideration:** Context matters more than percentage alone.
+
+## Correlation and Causation
+
+### Pitfall 15: Correlation Implies Causation
+**Problem:** Inferring causation from correlation.
+
+**Alternative explanations:**
+- Reverse causation (B causes A, not A causes B)
+- Confounding (C causes both A and B)
+- Coincidence
+- Selection bias
+
+**Criteria for causation:**
+- Temporal precedence
+- Covariation
+- No plausible alternatives
+- Ideally: experimental manipulation
+
+### Pitfall 16: Ecological Fallacy
+**Problem:** Inferring individual-level relationships from group-level data.
+
+**Example:** Countries with more chocolate consumption have more Nobel laureates doesn't mean eating chocolate makes you win Nobels.
+
+**Why problematic:** Group-level correlations may not hold at individual level.
+
+### Pitfall 17: Simpson's Paradox
+**Problem:** Trend appears in groups but reverses when combined (or vice versa).
+
+**Example:** Treatment appears worse overall but better in every subgroup.
+
+**Cause:** Confounding variable distributed differently across groups.
+
+**Solution:** Consider confounders and look at appropriate level of analysis.
+
+## Regression and Modeling Pitfalls
+
+### Pitfall 18: Overfitting
+**Problem:** Model fits sample data well but doesn't generalize.
+
+**Causes:**
+- Too many predictors relative to sample size
+- Fitting noise rather than signal
+- No cross-validation
+
+**Solutions:**
+- Use cross-validation
+- Penalized regression (LASSO, ridge)
+- Independent test set
+- Simpler models
+
+### Pitfall 19: Extrapolation Beyond Data Range
+**Problem:** Predicting outside the range of observed data.
+
+**Why dangerous:**
+- Relationships may not hold outside observed range
+- Increased uncertainty not reflected in predictions
+
+**Solution:** Only interpolate; avoid extrapolation.
+
+### Pitfall 20: Ignoring Model Assumptions
+**Problem:** Using statistical tests without checking assumptions.
+
+**Common violations:**
+- Non-normality (for parametric tests)
+- Heteroscedasticity (unequal variances)
+- Non-independence
+- Linearity
+- No multicollinearity
+
+**Solutions:**
+- Check assumptions with diagnostics
+- Use robust methods
+- Transform data
+- Use appropriate non-parametric alternatives
+
+### Pitfall 21: Treating Non-Significant Covariates as Eliminating Confounding
+**Problem:** "We controlled for X and it wasn't significant, so it's not a confounder."
+
+**Reality:** Non-significant covariates can still be important confounders. Significance ≠ confounding.
+
+**Solution:** Include theoretically important covariates regardless of significance.
+
+### Pitfall 22: Collinearity Masking Effects
+**Problem:** When predictors are highly correlated, true effects may appear non-significant.
+
+**Manifestations:**
+- Large standard errors
+- Unstable coefficients
+- Sign changes when adding/removing variables
+
+**Detection:**
+- Variance Inflation Factors (VIF)
+- Correlation matrices
+
+**Solutions:**
+- Remove redundant predictors
+- Combine correlated variables
+- Use regularization methods
+
+## Specific Test Misuses
+
+### Pitfall 23: T-Test for Multiple Groups
+**Problem:** Conducting multiple t-tests instead of ANOVA.
+
+**Why wrong:** Inflates Type I error rate dramatically.
+
+**Correct approach:**
+- Use ANOVA first
+- Follow with planned comparisons or post-hoc tests with correction
+
+### Pitfall 24: Pearson Correlation for Non-Linear Relationships
+**Problem:** Using Pearson's r for curved relationships.
+
+**Why misleading:** r measures linear relationships only.
+
+**Solutions:**
+- Check scatterplots first
+- Use Spearman's ρ for monotonic relationships
+- Consider polynomial or non-linear models
+
+### Pitfall 25: Chi-Square with Small Expected Frequencies
+**Problem:** Chi-square test with expected cell counts < 5.
+
+**Why wrong:** Violates test assumptions, p-values inaccurate.
+
+**Solutions:**
+- Fisher's exact test
+- Combine categories
+- Increase sample size
+
+### Pitfall 26: Paired vs. Independent Tests
+**Problem:** Using independent samples test for paired data (or vice versa).
+
+**Why wrong:**
+- Wastes power (paired data analyzed as independent)
+- Violates independence assumption (independent data analyzed as paired)
+
+**Solution:** Match test to design.
+
+## Confidence Interval Misinterpretations
+
+### Pitfall 27: 95% CI = 95% Probability True Value Inside
+**Misconception:** "95% chance the true value is in this interval."
+
+**Reality:** The true value either is or isn't in this specific interval. If we repeated the study many times, 95% of resulting intervals would contain the true value.
+
+**Better interpretation:** "We're 95% confident this interval contains the true value."
+
+### Pitfall 28: Overlapping CIs = No Difference
+**Problem:** Assuming overlapping confidence intervals mean no significant difference.
+
+**Reality:** Overlapping CIs are less stringent than difference tests. Two CIs can overlap while the difference between groups is significant.
+
+**Guideline:** Overlap of point estimate with other CI is more relevant than overlap of intervals.
+
+### Pitfall 29: Ignoring CI Width
+**Problem:** Focusing only on whether CI includes zero, not precision.
+
+**Why important:** Wide CIs indicate high uncertainty. "Significant" effects with huge CIs are less convincing.
+
+**Consider:** Both significance and precision.
+
+## Bayesian vs. Frequentist Confusions
+
+### Pitfall 30: Mixing Bayesian and Frequentist Interpretations
+**Problem:** Making Bayesian statements from frequentist analyses.
+
+**Examples:**
+- "Probability hypothesis is true" (Bayesian) from p-value (frequentist)
+- "Evidence for null" from non-significant result (frequentist can't support null)
+
+**Solution:**
+- Be clear about framework
+- Use Bayesian methods for Bayesian questions
+- Use Bayes factors to compare hypotheses
+
+### Pitfall 31: Ignoring Prior Probability
+**Problem:** Treating all hypotheses as equally likely initially.
+
+**Reality:** Extraordinary claims need extraordinary evidence. Prior plausibility matters.
+
+**Consider:**
+- Plausibility given existing knowledge
+- Mechanism plausibility
+- Base rates
+
+## Data Transformation Issues
+
+### Pitfall 32: Dichotomizing Continuous Variables
+**Problem:** Splitting continuous variables at arbitrary cutoffs.
+
+**Consequences:**
+- Loss of information and power
+- Arbitrary distinctions
+- Discarding individual differences
+
+**Exceptions:** Clinically meaningful cutoffs with strong justification.
+
+**Better:** Keep continuous or use multiple categories.
+
+### Pitfall 33: Trying Multiple Transformations
+**Problem:** Testing many transformations until finding significance.
+
+**Why problematic:** Inflates Type I error, is a form of p-hacking.
+
+**Better approach:**
+- Prespecify transformations
+- Use theory-driven transformations
+- Correct for multiple testing if exploring
+
+## Missing Data Problems
+
+### Pitfall 34: Listwise Deletion by Default
+**Problem:** Automatically deleting all cases with any missing data.
+
+**Consequences:**
+- Reduced power
+- Potential bias if data not missing completely at random (MCAR)
+
+**Better approaches:**
+- Multiple imputation
+- Maximum likelihood methods
+- Analyze missingness patterns
+
+### Pitfall 35: Ignoring Missing Data Mechanisms
+**Problem:** Not considering why data are missing.
+
+**Types:**
+- MCAR (Missing Completely at Random): Safe to delete
+- MAR (Missing at Random): Can impute
+- MNAR (Missing Not at Random): May bias results
+
+**Solution:** Analyze patterns, use appropriate methods, consider sensitivity analyses.
+
+## Publication and Reporting Issues
+
+### Pitfall 36: Selective Reporting
+**Problem:** Only reporting significant results or favorable analyses.
+
+**Consequences:**
+- Literature appears more consistent than reality
+- Meta-analyses biased
+- Wasted research effort
+
+**Solutions:**
+- Preregistration
+- Report all analyses
+- Use reporting guidelines (CONSORT, PRISMA, etc.)
+
+### Pitfall 37: Rounding to p < .05
+**Problem:** Reporting exact p-values selectively (e.g., p = .049 but p < .05 for .051).
+
+**Why problematic:** Obscures values near threshold, enables p-hacking detection evasion.
+
+**Better:** Always report exact p-values.
+
+### Pitfall 38: No Data Sharing
+**Problem:** Not making data available for verification or reanalysis.
+
+**Consequences:**
+- Can't verify results
+- Can't include in meta-analyses
+- Hinders scientific progress
+
+**Best practice:** Share data unless privacy concerns prohibit.
+
+## Cross-Validation and Generalization
+
+### Pitfall 39: No Cross-Validation
+**Problem:** Testing model on same data used to build it.
+
+**Consequence:** Overly optimistic performance estimates.
+
+**Solutions:**
+- Split data (train/test)
+- K-fold cross-validation
+- Independent validation sample
+
+### Pitfall 40: Data Leakage
+**Problem:** Information from test set leaking into training.
+
+**Examples:**
+- Normalizing before splitting
+- Feature selection on full dataset
+- Including temporal information
+
+**Consequence:** Inflated performance metrics.
+
+**Prevention:** All preprocessing decisions made using only training data.
+
+## Meta-Analysis Pitfalls
+
+### Pitfall 41: Apples and Oranges
+**Problem:** Combining studies with different designs, populations, or measures.
+
+**Balance:** Need homogeneity but also comprehensiveness.
+
+**Solutions:**
+- Clear inclusion criteria
+- Subgroup analyses
+- Meta-regression for moderators
+
+### Pitfall 42: Ignoring Publication Bias
+**Problem:** Published studies overrepresent significant results.
+
+**Consequences:** Overestimated effects in meta-analyses.
+
+**Detection:**
+- Funnel plots
+- Trim-and-fill
+- PET-PEESE
+- P-curve analysis
+
+**Solutions:**
+- Include unpublished studies
+- Register reviews
+- Use bias-correction methods
+
+## General Best Practices
+
+1. **Preregister studies** - Distinguish confirmatory from exploratory
+2. **Report transparently** - All analyses, not just significant ones
+3. **Check assumptions** - Don't blindly apply tests
+4. **Use appropriate tests** - Match test to data and design
+5. **Report effect sizes** - Not just p-values
+6. **Consider practical significance** - Not just statistical
+7. **Replicate findings** - One study is rarely definitive
+8. **Share data and code** - Enable verification
+9. **Use confidence intervals** - Show uncertainty
+10. **Think causally carefully** - Most research is correlational