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Published in final edited form as: Commun Stat Theory Methods. 2012 Oct 10;41(23):4240–4250. doi: 10.1080/03610926.2011.568157

Lack-of-fit Tests for Generalized Linear Models via Splines

CHIN-SHANG LI 1
PMCID: PMC3507466  NIHMSID: NIHMS412354  PMID: 23202300

Abstract

Cubic B-splines are used to estimate the nonparametric component of a semiparametric generalized linear model. A penalized log-likelihood ratio test statistic is constructed for the null hypothesis of the linearity of the non-parametric function. When the number of knots is fixed, its limiting null distribution is the distribution of a linear combination of independent chi-squared random variables, each with one df. The smoothing parameter is determined by giving a specified value for its asymptotically expected value under the null hypothesis. A simulation study is conducted to evaluate its power performance; a real-life dataset is used to illustrate its practical use.

Keywords: B-spline, Generalized linear model, Generalized partially linear model, Penalized log-likelihood ratio test, Semiparametric generalized linear model

1. Introduction

Generalized linear models (GLM) offer a unifying framework of regression analysis for data from the exponential family of distributions, which include Gaussian, Poisson, and binomial distributions among others (Nelder and Wedderburn, 1972; McCullagh and Nelder, 1989). More specifically, in a GLM, the response variable Y is assumed to have a density (or probability mass) function of the following form

f(y;θ,φ)=exp(yθ-b(θ)a(φ)+c(y,φ)), (1)

where φ is a scale or nuisance parameter; θ is the natural parameter of interest; a(φ), b(θ), and c(y, φ) are functions of known form, which determine a specific member in the one-parameter exponential family of distributions. It can be shown that the mean response μ = E(Y) = b′(θ) and the variance of the response var(Y ) = a(φ)b″(θ) = a(φ)v(μ), where v(μ) = b″(θ) is a variance function depending only on μ. Let u be the covariate of interest and x = (x0, x1, …, xp−1) the other covariates in the model, where x0 = 1. Under this formulation, we model the mean response μ = E(Y) = b′(θ), related to the covariate vector z = (x, u), through a monotonic differentiable link function g as follows:

g(μ)=g[b(θ)]=xα+s(u). (2)

Here α = (α0, …, αp−1)T is a vector of unknown p model parameters associated with the covariate vector x. s is an unknown but smooth function of u, which is to be estimated from the data, while the effects of x remain linear. The model in (2) is a generalized partially linear model and referred to as a semiparametric GLM, because it contains both parametric and nonparametric components.

There have been several methods of estimation proposed for estimating the parameters in (2), including, e.g., splines (Green and Yandell, 1985; Green, 1987; Hastie and Tibshirani, 1990; Green and Silverman, 1994; Ruppert, Wand, and Carroll, 2003), local likelihood (Kauermann and Tutz, 2001), and weighted quasi-likelihood (Severini and Staniswalis, 1994). Non-parametric regression techniques have been recently used for testing lack of fit of parametric regression models; see, e.g., Aerts, Claeskens, and Hart (1999), Cantoni and Hastie (2002), Crainiceanu and Ruppert (2004), Crainiceanu et al. (2005), and Liu and Wang (2004). Additionally, Hart (1997) gave a detailed survey on lack-of-fit tests using nonparametric regression techniques.

In contrast to these methods, we use a flexible alternative. That is, splines with a moderate number of knots are used. Specifically, the unknown functional form of the effect of the covariate u, s(u), is modeled by a linear combination of fixed-knot cubic B-spline basis functions (Schoenberg, 1946; Curry and Schoenberg, 1966). The model fitting is achieved by maximizing the penalized log-likelihood. A second-order difference penalty on the adjacent B-spline coefficients is imposed in order to prevent overfitting while estimating model parameters. In addition to the added modeling flexibility, the proposed model can be used to test for the linear effect of u.

The paper is organized as follows. In Section 2, we introduce the structure of the semiparametric GLM and the method of estimation of the model parameters. A penalized log-likelihood ratio test is constructed for the linear effect of the covariate u. Section 3 presents simulation results to study the power performance of the proposed test. In Section 4, we illustrate the use of the proposed method with a real-life example. Some discussion is given in Section 5. Proofs and technical conditions are given in the Appendix.

2. Method

2.1 Estimation

The unknown smooth function s can be approximated by a variety of spline functions, but the s is approximated by using a fixed-knot cubic spline because it provides the best compromise between computational cost and smoothness. The plus-function terms are intuitive and, hence, the truncated power basis is attractive from a statistical point of view (Smith, 1979). However, the B-spline basis provides a numerically superior alternative basis to the truncated power basis. Therefore, we model s as a linear combination of cubic B-spline basis functions with q preselected knots. We choose the kth knot corresponding to the kq+1th sample quantile of the distinct values of uis. Let B1(u), …, Bq+4(u) be the cubic B-spline basis functions. See de Boor (2001) for details of computation of B-splines and their mathematical properties. We are interested in testing the hypothesis that the effect of u is linear, i.e., testing H0: s(u) = τu versus Ha: s(u) ≠ τu, where τ is an unknown parameter. The space of cubic B-splines includes the constant and linear functions and the constant is given in the parametric component of the model in (2). Therefore, to model s and easily specify the null hypothesis of the linear effect of the covariate u, the linear term is given separately in (3). Consequently, it is needed to drop any two of the q + 4 cubic B-spline basis functions to have the full-rank model

s(u)=τu+k=1KβkBk(u). (3)

Here K = q + 2. The βks are cubic B-spline coefficients.

Let β = (β1, …, βK)T and Bu = (B1(u), …, BK(u)). By writing s(u) = τu + Buβ, we express the mean response μ = b′(θ) in (2) as g(μ) = g[b′(θ)] = + τu + Buβ, which can be written as in vector notation

g(μ)=g[b(θ)]=zξ+Buβ=Azψ, (4)

where Az = (z, Bu) = (x, u, Bu) and ψ = (ξT, βT)T for ξ = (αT, τ)T. Let Yi be the response from the ith subject with the covariate vector zi = (xi, ui), and Yi follows the one-parameter exponential family of distributions as described by (1) with mean μi = b′(θi), i = 1, 2, …, n. In most applications, the so-called canonical link function is used, i.e., g(·) = (b′)−1(·). For example, the model in (2) is a semiparametric Poisson regression model if g(·) is a logarithmic function; a semiparametric logistic regression model if g(·) is a logit function. Therefore, we focus on the case of canonical link function. The model in (4) can be expressed as θi = g[b′(θi)] = Aziψ.

By plugging θi = Aziψ into f(yi; θi, φ), i = 1, …, n, we can obtain the log-likelihood function (ψ,φ)=i=1n[yiAziψ-b(Aziψ)]/a(φ)+i=1nc(yi,φ). The scale parameter φ does not affect the estimating equation that leads to the estimate of ψ and a(φ) may be estimated consistently. Thus, for simplicity and without loss of generality, we take a(φ) = 1. Additionally, i=1nc(yi,φ) does not depend on ψ. Therefore, the log-likelihood function for the model in (1) with s(u) = τu + Buβ is (ψ)=i=1n[yiAziψ-b(Aziψ)]. For example, if Yi ~ Poisson(μi), (ψ)=i=1n[yiAziψ-exp(Aziψ)]. (ψ)=i=1n[yiAziψ-log(1+exp(Aziψ))]ifYi~Bernoulli(μi). Similarly, one can derive the log-likelihood functions for other members of the one-parameter exponential distribution family.

To estimate ψ and overcome the problem of overfitting the data, we employ the penalized likelihood technique introduced by Good and Gaskins (1971) in the context of nonparametric probability density estimation. Thus, by adding the roughness penalty −(1/2)βT Inline graphicβ to the ℓ(ψ) we obtain the penalized log-likelihood ℓp(ψ; λ) = ℓ(ψ) −(1/2)λβT Inline graphicβ. Here Inline graphic = Inline graphic Inline graphic is a K × K matrix, where Inline graphic is a matrix representation of the difference operator Δ2. βTGβ=k=3K(Δ2βk)2, which is a discrete approximation to ∫s″(t)2dt, where Δ2βk = βk − 2βk−1 + βk−2; see Eilers and Marx (1996). The smoothing parameter λ > 0 controls the tradeoff between fidelity to the data and smoothness of the fitting. Let Inline graphic be a (p + 1 + K) × (p + 1 + K) matrix with zeros in the first p + 1 rows and columns and Inline graphic in the remainder of the matrix. The ℓp(ψ; λ) can then be rewritten as

p(ψ;λ)=(ψ)-12λψTQψ. (5)

For given λ > 0, let ψ̂λ = (ξ̂λ, β̂λ) be the value of ψ maximizing the ℓp(ψ; λ), which is the maximum penalized likelihood estimate (MPLE) of ψ and can be obtained by solving the following weighted least-squares equations (ATWA + λ Inline graphic)ψ = ATWỹ. Here A=[ZB] is an n×(p+1+K) matrix for Z=(z1T,,znT)T being an n×(p+1) matrix and B=(Bu1T,,BunT)T an n × K matrix. W = diag(w1, …, wn) is an n × n matrix for wi = b″(Aziψ). = (1, …, n)T is a working response vector for i = Aziψ + [yib′(Aziψ)]/b″(Aziψ).

2.2 A penalized log-likelihood ratio test

It turns out from the model in (3) that testing H0: s(u) = τu is equivalent to testing the hypothesis that β = 0. It is noted that under H0: β = 0, Inline graphicψ = 0 and, hence, ℓp(ψ; λ) = ℓ(ψ). Let ξ0=(α0T,τ0)T be the true value of ξ = (αT, τ)T under H0: β = 0. Let ψ^0=(ξ^0T,0)T be the restricted MPLE of ψ0=(α0T,τ0,0T)T=(ξ0T,0T)T under H0: β = 0. That is, ψ̂0 is the value of ψ that maximizes the ℓp(ψ; λ) subject to β = Inline graphicψ = 0, where Inline graphic = [0K×(p+1) IK×K]T is a (p+1+KK matrix for IK×K being an identity matrix of order K.

To test H0: β = 0, because the model parameters are estimated by maximizing the penalized log-likelihood, by analogy with the unpenalized parametric log-likelihood procedures we construct a penalized log-likelihood ratio test (PLRT) statistic as follows:

Qλ=2[p(ψ^λ;λ)-p(ψ^0;λ)], (6)

where p(ψ^0;λ)=(ψ^0)-(1/2)λψ^0TQψ^0=(ψ^0) because Inline graphicψ̂0 = 0. The main difference between the PLRT statistic Qλ and the deviance statistic (Hastie and Tibshirani, 1990) is that the rough penalty is not included in the deviance.

Let I(ψ) be the Fisher’s information matrix as follows:

I(ψ)=[Iξξ(ψ)Iξβ(ψ)Iβξ(ψ)Iββ(ψ)]=E[-2(ψ)ψψT]=i=1nb(Aziψ)AziTAzi.

Let Iββξ(ψ)=Iββ(ψ)-Iβξ(ψ)Iξξ-1(ψ)Iξβ(ψ). The asymptotic results of Qλ are stated in the following theorem and the proof of the theorem is given in the Appendix.

Theorem 1

Assume that conditions (C1) and (C2) in the Appendix are satisfied. Let λn be the sequence of smoothing parameters with limnλn/n finite, which may be 0. When the number of knots is fixed, under H0

QλDQ=jγjχj2, (7)

where the χj2s are independent chi-squared random variables each with one degree of freedom, and the γjs are the eigenvalues of limnIββξ(ψ0)[Iββξ(ψ0)+λnG]-1

It can be seen from this theorem that for any α ∈ (0, 1) the test rejecting H0 if the observed value of Qλ exceeds the 100(1 − α)th percentile of the distribution of Q has an asymptotic significance level α. There have been several methods developed for calculation of the distribution of Q by, e.g., Imhof (1961), Davies (1973, 1980), Sheil and O’Muircheartaigh (1977), and Castaño-Martínex and López-Blázquez (2005). The algorithm of Davies (1980) is implemented in this work.

Because QλDQ under H0, one can have the asymptotically expected value of Qλ under H0 as follows:

γj=trace{limnIββξ(ψ0)[Iββξ(ψ0)+λnG]-1}. (8)

The asymptotically expected value would be the degrees of freedom of the test for the case of unpenalized log-likelihood (i.e., λ = 0). Although the Qλ in (6) does not have an asymptotic chi-squared distribution when λ ≠ 0, for simplicity and, hence, by following other researchers (e.g., Buja, Hastie, and Tibshirani, 1989), we adopt the terminology, degrees of freedom, for the test. We do not specify a value for the λ directly. Instead, in practice we give a specified value for the degrees of freedom, replace ψ0 with ψ̂0 in (8), and find the value of λ, denoted by λ̂, which gives the specified degrees of freedom. Therefore, Qλ̂ = 2[ℓp(ψ̂λ̂; λ̂) − ℓp(ψ̂0; λ̂)] is used as a test statistic.

3. Simulation study

We conducted a Monte Carlo simulation study to assess the performance of the proposed PLRT in Section 2. We assumed the covariate vector takes the form zi = (xi, ui), i = 1, …, 100. Here xi = (xi0, xi1), where xi0 = 1 and xi1 were generated from the uniform [0.5, 1.5] distribution. ui were generated from the uniform [0, 1] distribution. One thousand replications were conducted for each experimental configuration and all tests used nominal level α = 0.05.

To assess the empirical power of the test, we generated data yi from the following model

log[μ(zi;ξ,b)]=α0+α1x1i+s(ui;τ,b),i=1,2,,100. (9)

Here ξ = (αT, τ)T for α = (α0, α1) = (1, 0.7)T. s(ui; τ, b) = τui + b cos(3πui), where τ = 1.5 and b cos(3πui) are used as alternatives for b = 0, 0.02, …, 0.28. It is noted that when b = 0, the model in (9) produces the null model

log[μ(zi)]=α0+α1x1i+τui=log[μ(zi;ξ,0)]. (10)

The goal was to test H0: s(u) = τu = s(u; τ, 0), which is equivalent to testing b = 0.

We also computed two log-likelihood ratio test (LRT) statistics for H0: b = 0 to compare their power performances with the PLRT. The first LRT statistic for H0 is Q1=2[(ξ^,b^)-(ξ)]Dχ2(1) that has a chi-squared distribution with one degree-of-freedom. Here (ξ̂, ) is the value of (ξ, b) maximizing the (ξ,b)=i=1n[yi(ziξ+bcos(3πui))-exp(ziξ+bcos(3πui))] for the data generating model in (9). ξ̃ is the value of ξ maximizing the (ξ)=i=1n[yi(ziξ)-exp(ziξ)] for the null model in (10). The test gives an asymptotically optimal test that provides a useful comparison benchmark but is of limited practical value because its use requires very specific knowledge of the form of the alternative. We rejected H0 at α = 0.05 when the observed value of Q1 exceeded χ0.952(1) that denotes the 0.95-quantile of the chi-squared distribution with one degree-of-freedom.

To examine the power loss when the alternative parametric model is mis-specified, we fit data generated from the model in (9) by the misspecified alternative parametric model

log[μ(zi;ξ,c)]=α0+α1x1i+τui+cui2. (11)

The second LRT statistic for H0 is Q2=2[(ξ,c)-(ξ)]Dχ2(1). Here (ξ̆, ) is the value of (ξ, c) maximizing the (ξ,c)=i=1n[yi(ziξ+cui2)-exp(ziξ+cui2)] for the misspecified model in (11). H0 was rejected at α = 0.05 when the observed value of Q2 exceeded χ0.952(1).

To study the type I error and power performance of the PLRT Qλ under the different numbers of knots and different degrees of freedom, we considered 4, 4.5, and 5 degrees of freedom, each with q = 10, 15, 20, and 25 knots, to determine the value of λ while fitting the B-spline model. Under each of the combinations of different degrees of freedom and the different numbers of knots, the empirical significance level of the PLRT appeared to agree with the 0.05 nominal level. The empirical powers are shown in Figure 1. The power performances of the PLRTs, among the aforementioned combinations, are essentially the same. The first LRT, Q1, had the best power performance; however, the PLRT was competitive with the test and still retained the advantage of having the ability to detect more general alternatives. The second LR test, Q2, suffered a severe power loss and had the worst power performance among these tests; thus, it indicated the parametric test Q2 was not optimal under the case where a misspecified parametric regression model was used to fit data.

Figure 1.

Figure 1

Empirical power curve comparison of the PLRT (d; q), LRT1 (i.e., Q1), and LRT2 (i.e., Q2) for the null model s(u) = τu versus the alternative model s(u) = τu + b cos(3πu). Abbreviations: PLRT (d; q), penalized log-likelihood ratio test associated d degrees of freedom and q knots; LRT1, log-likelihood ratio test with data generating model s(u) = τu + b cos(3πu) as alternative model; LRT2, log-likelihood ratio test with misspecified model s(u) = τu + cu2 as alternative model.

4. Example

We illustrate the practical use of the methodology with the data set from a study of 173 nesting horseshoe crabs (Brockmann, 1996; Agresti, 2002). In the study, each female horseshoe crab had a male crab attached to her in her nest. The study investigated factors that affect whether the female crab had any other males, called satellites, residing nearby her. Explanatory variables included the female crab’s color, which is light medium, medium, dark medium, or dark, spine condition, which is both good, one worn or broken, or both worn or broken, carapace width (W) in centimeters, and weight (Wt) in kgs. The response outcome for each female crab is her number of satellites (Sa).

We fit the Poisson log-linear regression to the data to produce the fitted log-linear regression model log μ̂ = −0.801 + 0.531 × I{light medium} + 0.266 × I{medium} + 0.018 × I{dark medium} − 0.087 × I{both good} − 0.238 × I{one worn or broken} + 0.017 × W + 0.497 × Wt, where μ^=E(Sa)^. We employ the PLRT to evaluate whether there is a linear relation between the logarithm of the expected number of satellites, log μ = log E(Sa), and female crab’s weight. Because the p-values of the PLRT associated with 4, 4.5, and 5 degrees of freedom, each calculated by using 10, 15, 20, and 25 knots, are less than 0.0035, the female crab’s weight has a statistically significantly nonlinear effect on the logarithm of the expected number of satellites. Figures 2 and 3 show a cubic spline-fitted curve for the effect of female crab’s weight obtained with each of the above combinations of different degrees of freedom and the different numbers of knots.

Figure 2.

Figure 2

Cubic spline-fitted curves for the effect of female crab’s weight by using 4, 4.5, and 5 degrees of freedom with 10, 15, 20, and 25 knots.

Figure 3.

Figure 3

Cubic spline-fitted curves for the effect of female crab’s weight by using 4, 4.5, and 5 degrees of freedom with 10, 15, 20, and 25 knots.

5. Discussion

A flexible method has been proposed for modeling the nonparametric component of the semiparametric generalized linear model in (2) via a linear combination of fixed-knot cubic B-splines with the second-order difference penalty on the adjacent cubic B-spline coefficients to prevent overfitting to the data. Although automatic smoothing parameter selection methods such as cross-validation and generalized cross-validation, can be considered in the estimation procedure, we give a specified value for the degrees of freedom, and find the value of λ that gives the specified degrees of freedom. For comments on using fixed smoothing parameters, see, e.g., Buja et al. (1989, p. 545–546).

The focus is only on testing H0: s(u) = τu, but the idea also can be used to test the null hypothesis of no effect of u, H0: s(u) = 0, i.e., (τ, βT)T = 0. It is exactly the same as constructing the PLRT statistic for H0: s(u) = τu to construct one for H0: s(u) = 0. One can extend the methodology to examine the effects of several covariates of interest on the response variable.

Acknowledgments

The author is very grateful to the Editor and a referee whose helpful comments improved the presentation. This publication was made possible by Grant Number UL1 RR024146 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH), and NIH Roadmap for Medical Research.

Appendix

In this appendix, we set out the essential steps for proving Theorem 1. The following conditions are required.

  • (C1)

    limn1nI(ψ) is finite and positive definite.

  • (C2) supψB(δ)1ni=1n[b(Aziψ)-b(Aziψ)]AziTAzi0 as δ ↓ 0, where B(δ) = {ψ*Rp+1+K: ||ψ*ψ|| < δ}, δ ↓ 0 is an infinitesimal neighborhood of ψ.

Let ψ^λn=(ξ^λnT,β^λnT)T be the value of ψ that maximizes ℓp(ψ; λ) = ℓ(ψ) − (1/2)λψT Inline graphicψ for a sample of size n when λ = λn. Since p(ψ; λn)/ψ|ψ=ψ̂λn = 0, by using (C1), we consider a Taylor expansion of p(ψ; λn)/ψ|ψ=ψ̂λn around ψ0 to have 0=p(ψ;λn)/ψψ=ψ0+2p(ψ;λn)/(ψψT)ψ=ψ0(ψ^λn-ψ0+op(n), where op(an) indicates a vector whose components are uniformly op(an). Because Inline graphicψ = 0 under H0: β = 0, p(ψ; λn)/ψ|ψ=ψ0 = ℓ(ψ)/ψ|ψ=ψ0 = U (ψ0). Thus, it implies that under H0

n(ψ^λn-ψ0)=n[I(ψ0)+λnQ]-1n-1/2U(ψ0)+op(1). (12)

By using the assumption that limn→∞λn/n is finite, Liapounov’s Central Limit Theorem, and Cramér-Wold Theorem, one can show n-1/2U(ψ0)DNp+1+K(0,limnn-1I(ψ0)) under H0. Therefore, using Slutsky’s Theorem and (C2) can show n(ψ^λn-ψ0)DNp+1+K(0,limnnVλn(ψ0)) under H0, where Vλn(ψ0) = [I(ψ0) + λn Inline graphic]−1I(ψ0)[I(ψ0) + λn Inline graphic]−1. Then,

nβ^λn=LTn(ψ^λn-ψ0)DNK(0,limnnVββ;λn(ψ0)), (13)

where Vββ;λn(ψ0) = [Iββ|ξ (ψ0) + λn Inline graphic]−1Iββ|ξ(ψ0)[Iββ|ξ(ψ0) + λn Inline graphic]−1.

Under H0: Inline graphicψ = β = 0, ψ̂0 is the restricted MPLE of ψ0, so ψ̂0 must satisfy the restricted penalized log-likelihood equations

ψ{p(ψ;λn)+(LTψ-0)d}|ψ=ψ^0=ψp(ψ;λn)|ψ=ψ^0+Ld=0,LTψ^0=0, (14)

where d is a K ×1 vector of Lagrange multipliers. We use (C1) and Inline graphicψ0 = 0 to consider the Taylor expansion n1/2p(ψ;λn)/ψψ=ψ^0=n1/2U(ψ0)-n-1[I(ψ0)+λnQ]n(ψ^0-ψ0)+op(1). In addition, nLTψ^0=nLT(ψ^0-ψ0). One can then express n(ψ^0-ψ0) as

n(ψ^0-ψ0)=nL^[L^T(I(ψ0)+λnQ)L^]-1L^Tn-1/2U(ψ0)+op(1),

where Inline graphic = [I(p+1)×(p+1) 0K×(p+1)]T is a (p+1+K)×(p+1) matrix. Because by using a second-order Taylor expansion of ℓp(ψ̂λn; λn) and ℓp(ψ̂0; λn), one can have 2[ℓp(ψ̂λn; λn) − ℓp(ψ0; λn)] = U T(ψ0)[I(ψ0)+ λn Inline graphic]−1U(ψ0)+ op(1) and 2[ℓp(ψ̂0; λn)−ℓp(ψ0; λn)] = UT(ψ0) Inline graphic{ Inline graphic[I(ψ0)+λn Inline graphic] Inline graphic}−1 Inline graphicU(ψ0)+ op(1) under H0, using (12) can express Qλn=2[p(ψ^λn;λn)-p(ψ^0;λn)]=β^λnT[Iββξ(ψ0)+λnG]β^λn+op(1). By means of a non-singular linear transformation (Scheffé, 1959, p. 418) and Slutsky’s Theorem, one can show QλnDQ under H0. Let λ̂ be an estimator satisfying λ^/λnp1. From (13), we can show via Slutsky’s Theorem that nβ^λ^DNK(0,limnnVββ;λn(ψ0)) under H0. Then, β̂λ̂ and β̂λn have the same limiting null distribution. Let Q1λn=β^λnT[Iββξ(ψ0)+λnG]β^λn and Q1λ^=β^λ^T[Iββξ(ψ0)+λ^G]β^λ^. It follows via the Slutsky’s Theorem that Qλn = Q1λn + op(1), Q1λn and Q1λ̂ have the same limiting null distribution. Thus, one can show that Qλ̂ = 2[ℓp(ψ̂λ̂; λ̂) − ℓp(ψ̂0; λ̂)] = Q1λ̂ + op(1), Q1λ̂, Q1λn, and Qλn have the same limiting null distribution.

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