Cited by 861Statistical Methods and Bayesian InferenceStatistical Methods and ApplicationsOptimal Experimental Design Methods

The DOI matches its Crossref record; 58 of the 58 references it cites were found in a registry or an index; 5 of the 44 sources its claims cite were checked for support.

Analysis of variance—why it is more important than ever

Open access
Gelman, Andrew·2005·The Annals of Statistics

Abstract

Analysis of variance (ANOVA) is an extremely important method in exploratory and confirmatory data analysis. Unfortunately, in complex problems (e.g., split-plot designs), it is not always easy to set up an appropriate ANOVA. We propose a hierarchical analysis that automatically gives the correct ANOVA comparisons even in complex scenarios. The inferences for all means and variances are performed under a model with a separate batch of effects for each row of the ANOVA table. We connect to classical ANOVA by working with finite-sample variance components: fixed and random effects models are characterized by inferences about existing levels of a factor and new levels, respectively. We also introduce a new graphical display showing inferences about the standard deviations of each batch of effects. We illustrate with two examples from our applied data analysis, first illustrating the usefulness of our hierarchical computations and displays, and second showing how the ideas of ANOVA are helpful in understanding a previously fit hierarchical model.

Overview

AI snapshot

Written from the paper’s full text.

TL;DR

Gelman argues that ANOVA remains central because it is essentially the batching of model parameters into variance-components groups, and that hierarchical modeling makes correct ANOVA comparisons automatic in complex designs. The paper proposes finite-population variance summaries and graphical displays, illustrating them with split-plot, nested industrial, Web connect-time, and election-poll examples.

Key findings

  • Treating every row of an ANOVA table as a batch of exchangeable effects with its own estimated variance avoids the classical need to manually choose error terms; the split-plot Latin square example has 9 variance components, and the nested machine-treatment example has 3 (treatment, treatment × machine, treatment × machine × measurement).
  • The paper introduces finite-population standard deviations \(s_m\) and a graphical ANOVA display with point estimates and 50% and 95% intervals; in the split-plot Latin square, this display shows simultaneous uncertainty for all variance components rather than testing each under a null model.
  • In the Web connect-time example, a \(4 \times 45 \times 2 \times 25 \times 2\) factorial of log connect times, the multilevel display shows destination as the largest source of variation, company as large on its own and in interactions, while classical ANOVA finds all main effects and almost all interactions statistically significant but does not directly compare their magnitudes.
  • In the 1988 election logistic example using seven CBS polls, ethnicity is the most important demographic factor and state explains substantial variation; ethnicity × state × region interactions are surprisingly large.

Methods

  • The paper is methodological and applied: it formulates ANOVA as a hierarchical regression in which each row \(m\) has coefficients \(\beta^{(m)}_j \sim N(0,\sigma^2_m)\), with classical method-of-moments estimation for balanced designs and Bayesian Gibbs sampling for more general models.
  • Data examples include a \(5 \times 5 \times 2\) split-plot Latin square; a nested industrial experiment with 4 treatments, 20 machines, and 6 measurements per machine (120 data points); Web connect times from 45 locations to 4 destinations for 2 companies over 25 hours and 2 weeks; and seven CBS News polls from the week before the 1988 U.S. presidential election with demographic, state, and region indicators.
  • Analysis focuses on estimating variance components and finite-population standard deviations, with simulation-based uncertainty intervals and graphical displays; the election example uses Bayesian posterior simulation via Bugs linked to R.

Limitations

  • The paper states that its exchangeable-effects model is not universally appropriate and discusses nonexchangeable, spatial, time-series, and nonadditive interaction structures as extensions beyond the basic framework.
  • The paper notes that with a uniform prior the posterior for \(\sigma_m\) is improper when a batch has one degree of freedom, so those coefficients are essentially estimated by maximum likelihood; near-zero variance components are expected and point estimates can understate uncertainty.
  • Discussants (Tjur, McCullagh, Hox and Hoijtink) argue that the model must be specified first, that automatic correctness is not guaranteed, that exchangeability may be inappropriate for ordered or structured factors, and that the approach is mainly descriptive with uninformative priors; Gelman’s rejoinder concedes that model specification comes first and that the automatic step can be inappropriate in particular cases.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1214/009053604000001048

Cites

58 of 58 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Verification

Claims the paper makes

5 of 44 cited sources checked · 3 supported · 0 flagged · accuracy not yet measured

Show all 71 claims

  • Probably not a substantial claim. 66
  • It may state two separate claims as one. 53
107 of 107
  • The authors state this as an assumption.

    Each batch of regression coefficients is modeled as exchangeable normal effects with mean zero and its own variance.

    “We shall use a hierarchical formulation in which each batch of regression coefficients is modeled as a sample from a normal distribution with mean 0 and its own variance σ 2 m :”
    “Model (7) corresponds to exchangeability of each set of factor levels, which is a form of partial exchangeability or invariance of the entire set of cell means [see Aldous (1981)].”
  • The authors state this as an assumption.

    All variance components are nonnegative.

    “the restriction that all the variance components be nonnegative.”
  • The paper relies on this without support.

    The Census adult population counts for each demographic-state category are accurate.

    “From the Census, we get the adult population N j for each category j .”
  • The paper relies on this without support.

    Numerous examples exist in which one or more factors have levels that are not exchangeable, and inference for a specific treatment or classification contrast is the primary purpose of the experiment.

    “However, numerous examples exist in which one or more factors have levels that are not of this type, where inference for a specific treatment contrast or a specific classification contrast is the primary purpose of the experiment.”
  • The authors state this as an assumption.

    The four treatments in the example exhaust all treatments of interest.

    “the multilevel analysis approach outlined above makes sense if we assume that the four treatments exhaust all treatments we are interested in.”
  • The authors state this as an assumption.

    There is a population of treatments, or variations in implementation can lead to different outcomes.

    “If we assume that there is a population of treatments, or that variations in implementation can lead to different outcomes, we can structure the data as a three-level model”
  • The paper relies on this without support.

    Health care is largely provided by doctors and hospitals that are organizationally independent of health plans and may contract with multiple plans.

    “The latter is largely provided by doctors and hospitals that are organizationally independent of the plans and might contract with multiple plans”
7 of 7

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • The treatment-trend predictor changes its second weight

    Minor

    The finite-population linear contrast assigns the second treatment a weight of −1, but the predictor given for its superpopulation counterpart assigns it +1. Those are different treatment patterns, rather than two interpretations of the same linear contrast.

  • Figure 3 labels finite-population deviations with the wrong symbol

    Minor

    The paper defines s_m as the finite-population standard deviation and σ_m as the superpopulation standard deviation. The Figure 3 caption calls σ_m finite-population, reversing that distinction.

  • State indicators are included and then said to be unnecessary

    Minor

    The model description says that the design matrix includes indicators for all 50 states, then says no state main effects are needed. State indicators are state main-effect terms, so the two descriptions conflict as written.

3 of 3

Citations

Cites

Flagged first, then by citations

Show all 53 references

Research works printed but not linked: 11

  1. Box, G. E. P. and Tiao, G. C. (1973). Bayesian Inference in Statistical Analysis. Addison–Wesley, Reading, MA.
  2. DeGroot, M. H. (1970). Optimal Statistical Decisions. McGraw-Hill, New York.
  3. Cochran, W. G. and Cox, G. M. (1957). Experimental Designs, 2nd ed. Wiley, New York.
  4. Cochran, W. G. and Cox, G. M. (1957). Experimental Designs, 2nd ed. Wiley, New York.
  5. Snedecor, G. W. and Cochran, W. G. (1989). Statistical Methods, 8th ed. Iowa State Univ. Press, Ames, IA.
  6. Boscardin, W. J. (1996). Bayesian analysis for some hierarchical linear models. Ph.D. dissertation, Dept. Statistics, Univ. California, Berkeley.
  7. James, W. and Stein, C. (1961). Estimation with quadratic loss. Proc. Fourth Berkeley Symp. Math. Statist. Probab. 1 361–379. Univ. California Press, Berkeley.
  8. LaMotte, L. R. (1983). Fixed-, random-, and mixed-effects models. In Encyclopedia of Statistical Sciences (S. Kotz, N. L. Johnson and C. B. Read, eds.) 3 137–141. Wiley, New York.
  9. Montgomery, D. C. (1986). Design and Analysis of Experiments, 2nd ed. Wiley, New York.
  10. Robinson, G. K. (1998). Variance components. In Encyclopedia of Biostatistics (P. Armitage and T. Colton, eds.) 6 4713–4719. Wiley, Chichester.
  11. Wu, C. F. J. and Hamada, M. (2000). Experiments: Planning, Analysis, and Parameter Design Optimization. Wiley, New York.

Cited by

Sorted by citations

Items 101–107 of 107

Metadata

Authors
Gelman, A.
Corresponding author
Gelman, Andrew
Venue
The Annals of Statistics
Published
2005-02-01
Volume
33
Issue
1
Pages
1-53
ISSN
  • 0090-5364 (ISSN-L)
  • 2168-8966
OpenAlex
W217328182
Cited by
861
References
53
Citations by year
2026: 4 · 2025: 39 · 2024: 60 · 2023: 53 · 2022: 50 · 2021: 80 · 2020: 67 · 2019: 69 · 2018: 55 · 2017: 55 · 2016: 49 · 2015: 70 · 2014: 42 · 2013: 37 · 2012: 46
FWCI
12.07
Type
journal article
Language
en
Open access
Locations
  • The Annals of Statistics (publishedVersion)
  • arXiv (Cornell University) (submittedVersion)
  • Project Euclid (Cornell University) (submittedVersion)
  • arXiv (Cornell University)
  • Quality Engineering
Funders
National Science Foundation (9987748, 9708424, 9796129, 0084368)
Topics
  • Physical Sciences › Mathematics › Statistics and Probability › Statistical Methods and Bayesian Inference
  • Physical Sciences › Mathematics › Statistics and Probability › Statistical Methods and Applications
  • Social Sciences › Decision Sciences › Management Science and Operations Research › Optimal Experimental Design Methods
Keywords
analysis of variance, hierarchical models, split-plot design, variance components, fixed and random effects, exploratory data analysis, confirmatory data analysis

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