calm.gof: Closed-form goodness-of-fit test for penalized logistic...

In ebrahim.gof: Goodness-of-Fit and Calibration Tests for Logistic Regression

Closed-form goodness-of-fit test for penalized logistic regression (CALM)

Description

Refers the shrinkage-corrected grouped goodness-of-fit statistics to an analytic reference distribution, so that no bootstrap is needed. It is the companion of shrink.gof, which refers the same statistics to a prepivoting bootstrap: the statistics are identical, only the reference differs. CALM stands for Calibration Assessment under Lambda-shrunk Models.

Usage

calm.gof(
  X,
  y,
  lambda,
  G = 10,
  basis = c("decile", "adaptive", "edge"),
  lambda_scale = c("theory", "glmnet"),
  tau = 0.2,
  inflate = c("kappa", "none")
)

Arguments

X	numeric matrix or data frame of predictors, without an intercept column. Standardize the columns as you would before any ridge fit.
y	numeric or integer vector of 0/1 responses.
lambda	the ridge penalty. On the theory scale by default, that is on the scale of the log-likelihood; pass lambda_scale = "glmnet" to give glmnet's value instead, which is lambda / n.
G	number of equal-frequency groups. Default 10.
basis	which statistics to compute: any of "decile", "adaptive" and "edge". Default: all three.
lambda_scale	"theory" (default) or "glmnet".
tau	threshold of the degree rule, in (0, 1). Default 0.2. Values below 0.2 keep the cubic direction too often in the proportional regime.
inflate	whether to inflate the reference for the selection effect, "kappa" (default) or "none". On the adaptive basis the inflation changes the size by at most 0.008 in the designs examined.

Details

Under a ridge penalty the grouped standardized residuals are displaced by shrinkage. Subtracting an estimate of that displacement restores the maximum likelihood covariance to first order, but the resulting reference is conservative, because it standardizes by the Bernoulli variance at the fitted probabilities, which shrinkage inflates towards one quarter. CALM replaces it by a de-noised estimate of the null Bernoulli variance, obtained from the fit alone through the observable adjustments of Bellec (2025), and inflates the result for the effect of grouping on an index that depends on the response.

Two bases are returned. The EDGE basis projects the corrected residual onto orthogonal polynomials in the group-mean fitted probability, and SC.EDGE.adaptive chooses the degree from the data: it keeps the cubic direction when the aspect ratio is small, or when the observable index correlation \hat\rho satisfies \hat\rho^{6} \ge \tau, and uses degree two otherwise. That basis is the one to prefer. The decile basis SC.HL is the shrinkage-corrected Hosmer-Lemeshow statistic and is reported for continuity with that tradition; because it spends every group direction it cannot avoid the direction the selection effect occupies, and its reference relies on a constant calibrated by simulation, which does not transfer to every design. See the reference for the designs in which it fails.

Value

An object of class "calm.gof": a list with components SC.HL, SC.EDGE and SC.EDGE.adaptive (each a list with statistic and p.value, and for the adaptive basis also the chosen degree and the observable rho_hat), together with the penalty on both scales and the observables used to build the reference.

Scope

The reference is validated for aspect ratios p/n up to 0.4 and for penalties that shrink towards zero; the lasso is not covered, because the displacement requires a differentiable penalty. The test asks whether the logistic form is correct along the fitted index. It does not ask whether the shrunk probabilities are calibrated, which under a penalty they are not, by an amount the analyst chose when selecting lambda.

The reference is validated for outcomes that are not strongly unbalanced. Once p/n is an appreciable fraction the level is lost as the prevalence falls: at p/n = 0.25 the smooth basis rejects 0.140, 0.574 and 0.884 of correctly specified models at prevalences 0.30, 0.15 and 0.08, and the decile basis 0.060, 0.204 and 0.492. At fixed dimension the decile basis is unaffected and the smooth one degrades far more slowly, to 0.130 at prevalence 0.08. What fails there is the response-dependent grouping inherited from the Hosmer-Lemeshow construction rather than the reference itself. With few events and p/n an appreciable fraction, neither statistic is validated and shrink.gof is the less badly behaved of the two.

References

Bellec, P. C. (2025). Observable adjustments in single-index models for regularized M-estimators with bounded p/n. The Annals of Statistics, 53(2), 531–560.

Davies, R. B. (1980). Algorithm AS 155: the distribution of a linear combination of chi-squared random variables. Journal of the Royal Statistical Society, Series C, 29(3), 323–333.

Ebrahim, E. K. (2026). A closed-form goodness-of-fit reference for penalised logistic regression in the proportional regime. Preprint. Reproduction materials: \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5281/zenodo.22467285")}

See Also

shrink.gof for the bootstrap reference for the same statistics, and edge.gof for the EDGE test on an unpenalized fit.

Examples

set.seed(1)
n <- 300; p <- 20
X <- matrix(rnorm(n * p), n)
y <- rbinom(n, 1, 1 / (1 + exp(-(X[, 1] - 0.5 * X[, 2]))))
calm.gof(X, y, lambda = 100)

ebrahim.gof documentation built on Oct. 11, 2026, 5:07 p.m.