EFA with ordinal and missing data

Two features of real data complicate an exploratory factor analysis: items are often ordinal (a handful of Likert categories rather than a continuous scale), and some responses are usually missing. EFAtools handles both within the ordinary efa_fit() workflow, without switching packages. This vignette shows how. It assumes familiarity with the basic workflow covered in the EFAtools vignette and focuses on what changes for ordinal and incomplete data.

So that the examples are self-contained and reproducible, we generate the data with efa_simulate() from a known three-factor population (18 indicators, six per factor, with moderately correlated factors), using fixed seeds throughout.

Ordinal Data

Rating-scale items are not continuous: they take a few ordered values, and a Pearson correlation between two such items underestimates the association between the underlying constructs. The polychoric correlation instead estimates the correlation of the continuous latent variables assumed to underlie the observed categories, and pairing it with a categorical estimator removes the bias that treating the items as continuous introduces.

We draw 400 responses on a four-category scale. Because the latent data are normal, cutting them at the standard-normal category thresholds already leaves the population polychoric correlation of the discretised data equal to the target correlation; match = "polychoric" records that this is what we are after, and would reject the request had we asked for non-normal marginals.

d_ord <- efa_simulate(N = 400, Lambda = Lambda, Phi = Phi,
                      categories = 4, match = "polychoric", seed = 2024)$data
d_ord[1:5, 1:6]
#>      V1 V2 V3 V4 V5 V6
#> [1,]  4  4  4  3  2  4
#> [2,]  3  1  1  1  3  1
#> [3,]  1  1  1  2  2  1
#> [4,]  4  4  3  4  4  3
#> [5,]  2  4  2  3  2  1

Screening Ordinal Data

efa_screen() reports, among its diagnostics, how many response categories each item has and whether the data are multivariate normal — the two things that decide whether an ordinal treatment is worthwhile.

efa_screen(d_ord, seed = 42)
#> 
#> ── Sampling adequacy and sphericity ────────────────────────────────────────────
#> 
#> ✔ The overall KMO value for your data is meritorious (Overall KMO = 0.828).
#> These data are probably suitable for factor analysis.
#> 
#> ✔ The Bartlett's test of sphericity was significant at an alpha level of .05.
#> These data are probably suitable for factor analysis.
#> 𝜒²(153) = 1306.76, p < .001
#> 
#> ── Multicollinearity ───────────────────────────────────────────────────────────
#> 
#> ✔ Determinant: 0.0357. No concern (a value near 0 signals multicollinearity).
#> ✔ Condition number: 7.919. No concern (large values signal near-collinear variables).
#> 
#> ── Per-variable diagnostics ────────────────────────────────────────────────────
#> 
#>     variance missing   SMC   MSA flags
#> V1     1.248       0 0.218 0.830      
#> V2     1.298       0 0.241 0.817      
#> V3     1.222       0 0.278 0.793      
#> V4     1.223       0 0.225 0.829      
#> V5     1.211       0 0.228 0.801      
#> V6     1.266       0 0.297 0.810      
#> V7     1.260       0 0.242 0.839      
#> V8     1.187       0 0.239 0.836      
#> V9     1.182       0 0.259 0.832      
#> V10    1.153       0 0.257 0.835      
#> V11    1.150       0 0.282 0.806      
#> V12    1.193       0 0.244 0.852      
#> V13    1.373       0 0.227 0.819      
#> V14    1.317       0 0.290 0.851      
#> V15    1.206       0 0.224 0.853      
#> V16    1.193       0 0.227 0.859      
#> V17    1.282       0 0.311 0.832      
#> V18    1.223       0 0.274 0.804      
#> 
#> ── Multivariate normality ──────────────────────────────────────────────────────
#> 
#> ✔ Mardia's skewness: 𝜒²(1140) = 1008.24, p = 0.998.
#> ✖ Mardia's kurtosis: z = -6.11, p < .001.
#> ✖ Henze-Zirkler: HZ = 1, p < .001.
#> These data depart from multivariate normality.
#> 
#> ── Outliers ────────────────────────────────────────────────────────────────────
#> 
#> ℹ 4 of 400 observations were flagged as multivariate outliers (robust distance > 5.61).
#> 
#> ── Recommendations ─────────────────────────────────────────────────────────────
#> 
#> ! 18 items have fewer than 5 response categories; treating them as ordinal
#>   (polychoric correlations with a categorical estimator such as DWLS) is less
#>   biased than normal-theory ML.
#> ! Bartlett's test is significant, but it assumes multivariate normality and
#>   grows more sensitive as N increases; because these data are non-normal, treat
#>   it as uninformative here and rely on the KMO.
#> ! 4 observations were flagged as potential multivariate outliers; inspect them
#>   (see `$outliers$flagged`) before down-weighting or excluding.

The sampling adequacy (KMO) and sphericity checks confirm the data are factorable. The telling parts are the multivariate-normality section and the recommendations: Mardia’s kurtosis and the Henze-Zirkler test reject normality, and the recommendations flag that every item has fewer than five response categories. Together these spell out the consequence — with few categories and non-normal data, a polychoric correlation with a categorical estimator such as DWLS is less biased than normal-theory maximum likelihood, and the normal-theory standard errors and fit indices are better replaced by robust (sandwich) versions.

Polychoric Correlations, DWLS, and Robust Standard Errors

efa_fit() computes the polychoric correlation when cor_method = "poly" and fits it with diagonally weighted least squares when estimator = "DWLS" — the estimator recommended for ordinal data, which weights each correlation residual by the inverse asymptotic variance of the corresponding polychoric correlation. Requesting se = "sandwich" adds robust standard errors and a scaled (Satorra-Bentler) chi-square that stay valid under the non-normality these data show.

efa_poly <- efa_fit(d_ord, n_factors = 3, cor_method = "poly", estimator = "dwls",
                    rotation = "oblimin", se = "sandwich")
efa_poly
#> 
#> EFA performed with estimator = 'DWLS' and rotation = 'oblimin'.
#> 
#> ── Rotated Loadings ────────────────────────────────────────────────────────────
#> 
#>        F1     F2     F3    h2    u2
#> V1    .053   .028   .521  .297  .703
#> V2    .070  -.034   .569  .339  .661
#> V3    .092  -.063   .621  .403  .597
#> V4   -.068   .110   .560  .337  .663
#> V5   -.063  -.048   .621  .359  .641
#> V6   -.041   .047   .683  .471  .529
#> V7    .024   .577   .017  .348  .652
#> V8   -.002   .584   .014  .345  .655
#> V9   -.012   .630  -.022  .385  .615
#> V10   .045   .622  -.070  .389  .611
#> V11  -.063   .656   .032  .416  .584
#> V12   .067   .532   .052  .332  .668
#> V13   .533   .023   .018  .299  .701
#> V14   .665   .005   .012  .449  .551
#> V15   .576  -.021   .044  .338  .662
#> V16   .563   .014   .026  .331  .669
#> V17   .675   .031  -.015  .466  .534
#> V18   .642  -.002  -.063  .395  .605
#> 
#> ── Factor Intercorrelations ────────────────────────────────────────────────────
#> 
#>       F1     F2     F3
#> F1  1.000
#> F2   .352  1.000
#> F3   .252   .254  1.000
#> 
#> ── Variances Accounted for ─────────────────────────────────────────────────────
#> 
#>                      F1     F2     F3
#> SS loadings        2.302  2.219  2.177
#> Prop Tot Var        .128   .123   .121
#> Cum Prop Tot Var    .128   .251   .372
#> Prop Comm Var       .344   .331   .325
#> Cum Prop Comm Var   .344   .675  1.000
#> 
#> ── Model Fit ───────────────────────────────────────────────────────────────────
#> 
#> scaled χ²(102) = 100.83, p = .514
#> CFI: 1.00
#> TLI: 1.00
#> RMSEA [90% CI]: .00 [.00; .03]
#> AIC: NA
#> BIC: NA
#> CAF: .51
#> SRMR: .03

The pattern matrix recovers the three factors cleanly (six indicators each), and the model fit reports a scaled chi-square with its CFI, TLI, and RMSEA. Because the chi-square is a scaled statistic, the AIC and BIC (which are defined on the unscaled likelihood discrepancy) are left NA.

For binary items, cor_method = "tetra" computes tetrachoric correlations and runs the same DWLS and sandwich machinery.

The robust standard errors accompany each estimated quantity; for the rotated loadings, for example:

round(efa_poly$SE$rot_loadings, 3)
#>        F1    F2    F3
#> V1  0.057 0.057 0.051
#> V2  0.057 0.054 0.051
#> V3  0.057 0.052 0.048
#> V4  0.055 0.055 0.052
#> V5  0.051 0.053 0.053
#> V6  0.052 0.052 0.049
#> V7  0.059 0.056 0.052
#> V8  0.051 0.053 0.048
#> V9  0.051 0.054 0.047
#> V10 0.052 0.054 0.050
#> V11 0.053 0.054 0.050
#> V12 0.058 0.054 0.054
#> V13 0.055 0.057 0.054
#> V14 0.051 0.055 0.052
#> V15 0.057 0.056 0.053
#> V16 0.056 0.057 0.049
#> V17 0.051 0.054 0.047
#> V18 0.056 0.055 0.049

The matching confidence intervals live in efa_poly$CI, and summary(efa_poly) prints them as a labelled table alongside the model diagnostics.

Why Not Just Treat the Items as Continuous?

To see what the ordinal treatment buys, fit the same data as if they were continuous — a Pearson correlation with maximum likelihood — and compare the rotated loadings with efa_compare().

efa_cont <- efa_fit(d_ord, n_factors = 3, cor_method = "pearson", estimator = "ML",
                    rotation = "oblimin")

cmp <- efa_compare(efa_poly$rot_loadings, efa_cont$rot_loadings,
                   x_labels = c("Polychoric / DWLS", "Pearson / ML"))
cmp
#> Mean [min, max] absolute difference:  0.0171 [ 0.0000,  0.0539]
#> Median absolute difference:  0.0064
#> Root mean squared distance (RMSE):  0.0252
#> Max decimals where all numbers agree in absolute value: 0
#> Minimum number of decimals provided: 17
#> Differing indicator-to-factor correspondences: 0 (highest loading), 0 (all |loadings| >= 0.3)
#> 
#>        F1      F2      F3
#> V1    .0066   .0024   .0317
#> V2    .0040  -.0061   .0332
#> V3    .0080  -.0055   .0455
#> V4   -.0053   .0121   .0435
#> V5   -.0013  -.0026   .0471
#> V6   -.0116   .0037   .0539
#> V7   -.0021   .0420   .0040
#> V8   -.0110   .0409   .0091
#> V9    .0044   .0371  -.0080
#> V10   .0003   .0491  -.0035
#> V11   .0035   .0411   .0010
#> V12   .0133   .0295  -.0023
#> V13   .0457   .0037  -.0041
#> V14   .0430  -.0007   .0075
#> V15   .0502   .0000   .0045
#> V16   .0393   .0016   .0014
#> V17   .0478   .0002  -.0041
#> V18   .0423  -.0006  -.0024
plot(cmp)

The two solutions agree on the structure, but the polychoric loadings are systematically a little larger: treating the items as continuous attenuates the loadings, because the Pearson correlation understates the latent associations. With only four categories here the gap is modest, but it widens as the number of categories drops (it is largest for binary items) and as the category thresholds grow more asymmetric (skewed items). This is why a polychoric or tetrachoric treatment is preferable for genuinely ordinal items with few categories.

The polychoric route does make its own demands, though: it assumes a normal latent variable underlies each item, and it needs an adequate sample size and reasonably populated response-category combinations. When categories are very sparse (rare responses, small samples), the polychoric asymptotic covariance behind the DWLS weights and the robust standard errors becomes unreliable — efa_fit() warns when empty category combinations are present — and collapsing rare categories can help.

Missing Data

When some responses are missing, dropping every incomplete case (listwise deletion) wastes data and can bias the results unless the values are missing completely at random. EFAtools offers two principled alternatives that assume only that the data are missing at random (MAR): a single-analysis route via full-information maximum likelihood, and a multiple-imputation route via efa_mi().

We simulate 250 continuous cases with about 15% of values missing at random, where each item’s missingness depends on another item’s value. efa_simulate() holes every column, so each item’s MAR predictor is itself partly missing: the mechanism is MAR given the complete data, but it is not ignorable for an analyst who sees only the observed data. Estimators that are consistent under ignorable MAR therefore keep a residual bias on data from this generator — a property of the generator rather than of the estimators, negligible at the modest missing rate used here but growing with missing_prop and missing_strength.

d_miss <- efa_simulate(N = 250, Lambda = Lambda, Phi = Phi,
                       missing = "MAR", missing_prop = 0.15, seed = 2024)$data
round(mean(is.na(d_miss)), 3)          # overall proportion missing
#> [1] 0.151

Two-Stage Full-Information Maximum Likelihood

With cor_method = "fiml", efa_fit() estimates the saturated mean and covariance from all the observed data by an EM algorithm (assuming the data are MAR) and analyses the resulting correlation — a single fit that uses every case rather than only the complete ones. The model fit is reported as corrected two-stage (Satorra-Bentler) statistics.

efa_fiml <- efa_fit(d_miss, n_factors = 3, cor_method = "fiml", estimator = "ml",
                    rotation = "oblimin")
efa_fiml
#> 
#> EFA performed with estimator = 'ML' and rotation = 'oblimin'.
#> Correlations: FIML (two-stage, missing data)
#> 
#> ── Rotated Loadings ────────────────────────────────────────────────────────────
#> 
#>        F1     F2     F3    h2    u2
#> V1   -.066  -.003   .552  .284  .716
#> V2    .080  -.079   .578  .361  .639
#> V3   -.010  -.005   .631  .393  .607
#> V4    .169   .050   .503  .353  .647
#> V5   -.029   .001   .531  .273  .727
#> V6   -.014   .031   .605  .367  .633
#> V7   -.113   .606   .062  .355  .645
#> V8    .000   .683  -.026  .462  .538
#> V9    .180   .500   .001  .329  .671
#> V10   .028   .527  -.004  .285  .715
#> V11   .037   .624  -.045  .395  .605
#> V12  -.046   .597  -.005  .344  .656
#> V13   .546   .151  -.028  .351  .649
#> V14   .422   .107   .226  .334  .666
#> V15   .702  -.101  -.068  .442  .558
#> V16   .595   .001  -.024  .345  .655
#> V17   .645  -.031   .063  .438  .562
#> V18   .558   .015   .072  .349  .651
#> 
#> ── Factor Intercorrelations ────────────────────────────────────────────────────
#> 
#>       F1     F2     F3
#> F1  1.000
#> F2   .251  1.000
#> F3   .336   .140  1.000
#> 
#> ── Variances Accounted for ─────────────────────────────────────────────────────
#> 
#>                      F1     F2     F3
#> SS loadings        2.212  2.182  2.064
#> Prop Tot Var        .123   .121   .115
#> Cum Prop Tot Var    .123   .244   .359
#> Prop Comm Var       .342   .338   .320
#> Cum Prop Comm Var   .342   .680  1.000
#> 
#> ── Model Fit ───────────────────────────────────────────────────────────────────
#> 
#> scaled χ²(102) = 101.71, p = .489
#> CFI: 1.00
#> TLI: 1.00
#> RMSEA [90% CI]: .00 [.00; .03]
#> AIC: NA
#> BIC: NA
#> CAF: .52
#> SRMR: .04

The solution again recovers the three factors, and the printout records that the correlation was obtained by two-stage FIML. Standard errors are available here too: for estimator = "ML" or "ULS", se = "information" or "sandwich" return the corrected two-stage standard errors, and se = "np-boot" works with any estimator.

Multiple Imputation with `efa_mi()`

The alternative is to impute the missing values several times, fit each completed dataset, and pool the results. EFAtools does not impute the data itself — use a dedicated tool such as the mice package — but efa_mi() takes the list of completed datasets and does the factor-analytic pooling.

Here we create five imputations with mice (a Bayesian linear-regression model, appropriate for these continuous items) and collect them into a list.

imp <- mice::mice(as.data.frame(d_miss), m = 5, method = "norm",
                  printFlag = FALSE, seed = 123)
dat_list <- lapply(seq_len(imp$m), function(i) mice::complete(imp, i))

efa_mi() fits the same efa_fit() model to each imputed dataset — the extraction, rotation, and standard-error options are passed through ... — aligns the solutions to a common factor space (rotation is only identified up to reflection and permutation, so the imputations must be matched before averaging), and pools them.

efa_pooled <- efa_mi(dat_list, n_factors = 3, estimator = "ml", rotation = "oblimin")
efa_pooled
#> 
#> Pooled EFA across 5 imputations performed with estimator = 'ML' and rotation = 'oblimin'.
#> Pooling settings: target_method = 'first_target', align_unrotated = 'signed_tucker_congruence', fit_pool_method = 'D2'.
#> 
#> ── Rotated Loadings ────────────────────────────────────────────────────────────
#> 
#>        F1     F2     F3    h2    u2
#> V1    .000  -.091   .582  .312  .688
#> V2   -.062   .087   .550  .333  .667
#> V3    .004  -.001   .602  .363  .637
#> V4    .052   .152   .508  .347  .653
#> V5    .010  -.004   .525  .276  .724
#> V6    .025  -.033   .620  .376  .624
#> V7    .587  -.091   .044  .332  .668
#> V8    .679  -.036   .012  .452  .548
#> V9    .503   .170  -.014  .322  .678
#> V10   .511   .002   .018  .265  .735
#> V11   .621   .038  -.042  .393  .607
#> V12   .601  -.037  -.040  .346  .654
#> V13   .148   .529  -.014  .336  .664
#> V14   .106   .390   .247  .317  .683
#> V15  -.065   .687  -.065  .428  .572
#> V16  -.014   .585   .010  .342  .658
#> V17  -.044   .634   .073  .426  .574
#> V18   .018   .562   .066  .351  .649
#> 
#> ── Factor Intercorrelations ────────────────────────────────────────────────────
#> 
#>       F1     F2     F3
#> F1  1.000
#> F2   .256  1.000
#> F3   .143   .332  1.000
#> 
#> ── Variances Accounted for ─────────────────────────────────────────────────────
#> 
#>                      F1     F2     F3
#> SS loadings        2.133  2.119  2.066
#> Prop Tot Var        .119   .118   .115
#> Cum Prop Tot Var    .119   .236   .351
#> Prop Comm Var       .338   .335   .327
#> Cum Prop Comm Var   .338   .673  1.000
#> 
#> ── Model Fit ───────────────────────────────────────────────────────────────────
#> 
#> D2-pooled χ²(102) = 182.80, p = .005
#> CFI: .89
#> TLI: .83
#> RMSEA [90% CI]: .06 [.05; .07]
#> AIC: -21.20
#> BIC: -380.38
#> ECVI: 1.29
#> CAF: .51
#> SRMR: .04
#> Note: the pooled χ² is the D2 statistic; its p uses the D2 reference F(102,
#> 69.6), not the χ²(102) tail.

The pooled loadings recover the three factors. Point estimates are averaged across the imputations after alignment. The model chi-square, and the RMSEA and AIC/BIC derived from it, are pooled with the D2 rule — which is why the printout labels the pooled chi-square as a D2 statistic with its own reference distribution — whereas the incremental CFI and TLI are averaged across the per-imputation fits. Requesting standard errors in the call (for example se = "information" or se = "np-boot") additionally pools them with Rubin’s rules, so the between-imputation variability inflates the pooled standard errors. Because multiple imputation propagates the extra uncertainty from the missing data, its pooled fit statistics are not directly comparable with the single FIML fit above; read them together with the per-imputation fits stored in the returned object.

Multiple imputation is not limited to continuous data: since efa_mi() forwards its arguments to efa_fit(), imputed ordinal datasets can be pooled with cor_method = "poly" and estimator = "DWLS" in exactly the same way.

Which route to prefer is largely practical. FIML is a single, efficient fit and is the simpler default when the analysis model is the whole story. Multiple imputation is more flexible when the imputation model should draw on auxiliary variables not in the factor model, or when the same imputations feed several downstream analyses.