Informatica Medica Slovenica 2014; 19(1-2)
1
Research Paper ■
Bootstrap in Errors-in-Variables Regressions Applied to Methods Comparison Studies
Bernard G. Francq
Abstract. In method comparison studies, the measurements taken by two methods are compared to assess whether they are equivalent. If there is no analytical bias between the methods, they should provide the same results on average notwithstanding the measurement errors. This equivalence can be assessed with regression techniques by taking into account the measurement errors. Among them, the paper focuses on Deming Regression (DR) and Bivariate Least-Squares regression (BLS). The confidence intervals (CI's) of the regression parameters are useful to assess the presence or absence of bias. These CI's computed by errors-in-variables regressions are approximate (except the one for slope estimated by DR), which leads to coverage probabilities lower than the nominal value. Six bootstrap approaches and the jackknife are assessed in the paper as means to improve the coverage probabilities of the CI's.
Uporaba zankanja v regresiji za spremenljivke z merskimi napakami v študijah primerjave metod
Institucija avtorja / Author's institution: Université Catholique de Louvain, Institut de Statistique, Biostatistique et sciences Actuarielles, Louvain, Belgium.
Kontaktna oseba / Contact person: Bernard G. Francq, ISBA, Voie du Roman Pays 20 bte L1.04.01, B-1348 Louvain-la-Neuve. e-pošta / e-mail: bernard.g.francq@uclouvain.be.
Prejeto / Received: 15.10.2014. Sprejeto / Accepted:
30.10.2014.
Izvleček. V študijah primerjave metod primerjamo meritve z dvema metodama, da bi ocenili, ali sta ekvivalentni. Če nobena od metod ni pristranska, moramo z njima v povprečju dobiti enake rezultate ne glede na napake merjenja. Tovrstno ekvivalentnost lahko preverjamo z regresijskimi pristopi, ki upoštevajo merske napake. Prispevek se osredotoča na Demingovo regresijo (DR) in bivariatno regresijo po metodi najmanjših kvadratov. Z intervali zaupanja (IZ) za regresijske parametre lahko ocenimo, ali je prisotna pristranost. IZ so pri regresiji za spremenljivke z merskimi napakami le približni (razen za ocenjeni naklon pri DR), zato je dejanska stopnja zaupanja nižja od deklarirane. Prispevek primerja šest oblik zankanja in metodo pipca kot pristope za izboljšanje ustreznosti stopnje zaupanja IZ.
■ Infor Med Slov: 2014; 19(1-2): 1-11
2 Francq BG: Bootstrap in Errors-in-Variables Regressions Applied to Methods Comparison Studies
Introduction
The needs of the industries and laboratories to quickly assess the quality of products or samples leads to the development and improvement of new measurement methods that should be faster, easier to handle, less expensive or more accurate than the reference method. These alternative methods should ideally lead to results comparable to those obtained by a standard method [1]. Ideally, there should be no bias between the two methods, i.e., the measurement methods should be interchange able.
Different approaches are proposed in the literature to deal with method comparison studies. The most widely known and used is the approach proposed by Bland and Altman, which focuses directly on the differences between two measurement methods [2-4]. The approach based on regression analysis (a linear functional relationship [5]) is also widely applied; it focuses on the parameter estimates and their confidence intervals (CI's) [6]. This paper deals with the regression approach. In order to statistically test the equivalence between two measurement methods, a certain characteristic of a sample can be measured by the two methods in the experimental domain of interest. The pairs of measurements taken by the reference method and the alternative one can be modelled by a regression line and the parameter estimates used to test the equivalence. Obtaining an intercept significantly different from zero in such regression indicates a systematic analytical bias between the methods, and a slope significantly different from one indicates a proportional bias [6]. To perform the regression correctly it is essential to take into account the errors in both variables (i.e., dimensions, axes) and the heteroskedasticity if necessary [6]. Various types of regressions exist to tackle this problem [7]; this paper focuses on the Deming Regression (DR) and Bivariate Least Square (BLS), as well as the basic Ordinary Least Square (OLS) regression.
It is known that the coverage probabilities of the approximate confidence intervals computed by DR
or BLS can be lower than the nominal level especially when the ratio of the measurement errors' variances is lower than one. In the paper, different bootstrap procedures are briefly explained and assessed with simulations in order to improve these coverage probabilities and thus obtain more precise confidence intervals. The systolic blood pressure data set published by Bland and Altman [2] is used to illustrate these techniques.
How to test the equivalence?
In the systolic blood pressure data [2], simultaneous measurements were made using a sphygmomanometer and a semi-automatic blood pressure monitor. The Bland and Altman approach focuses on "practical" equivalence to assess whether the observed differences between the two measurement methods are meaningful or not in practice. The present paper focuses on "strict" or "statistical" equivalence. The bias between the two devices is considered because the two devices should provide equal (equivalent) measures notwithstanding the errors of measurement.
The standard design in method comparison studies is to measure each specimen/subject once using both devices/methods. However, with such design it is not possible to estimate the variances of measurement errors, as explained below.
The general model
To compare two measurement methods, a parameter of interest is measured on N sampling units (i = 1,2, ...,N) by both methods [10-12]:
= + ; Yij = Vi + Vij,	Q)
where Xij(j = 1,2, ...,nXi) and Yij(j = 1,2, ...,nYi) are the repeated measures for unit i by methods X and Y, respectively, and nXl and nYi are the number of repeated measures of unit i by each method. if; and ^ are the true but unobservable values of the parameter of interest for both methods, which are assumed to be linked
Informatica Medica Slovenica 2014; 19(1-2)
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by a linear relationship [10-12]:
Vi = a + Pti.
(2)
The means of the repeated measures for the unit i are given by Xi and Yi:
1 n-i,
(3)
and yi=-7Z?Il1yy;
nxt ] = 1 J
Tij and Vij are the measurement errors, which are supposed to be independent and normally distributed (with constant variances under homoskedasticity):
2
(4)
Hence, the means of the repeated measures are also normally distributed around >f; or ^:

0
Z/nyJ .
(5)
If the variances of£ and of£ are unknown, they can be estimated with repeated measures; otherwise, these variances are unknown and inestimable. The estimates of of£ and of£ are given by Sj. and sf£:
and

: =^ynYi(Y--Y)2 i nY.-^j = iyIlJ hJ .
(6)
In further explanations, the following notation will also be used:
X = $I?=1Xl and ?=±I?=iYi;
s.x =	-X)2; Syy = !f=1(7i -7)2 and
sxy = y=1(Xi-X)(Yi-Y).
The homoskedastic model
Under homoskedasticity, the measurement errors variances are constant through the domain of interest (of. = of and of. = of Vi). Moreover, a constant number of replicates will be assumed (nXi =nx and nYi =nY Vi) to prevent the model from becoming heteroskedastic even if the accuracies of the measurement methods are constant. Under homoskedasticity, the variances
sf. and sf. are estimates of of and of and the "overall" estimates for of and of are given by sf and sf:
I^K-lH and j2 ^(^H (7)
or with constant repeated measures:
yN „2	yN „2
s2=Zizifli and sf	.
(8)
How to test the equivalence?
If the two measurement methods are equivalent, they should give the same results for a given sample notwithstanding the measurement errors. In the model notation, method equivalence means that ifi Vi [6,13]. In practice, due to the measurement errors, these parameters are unobservable and the equivalence test will be based on the following regression model: Yi=a + pXi+£i with £i~N(o0, o£2.) and
„2=^ + 02*1,
n7j r nXi
(9)

where the intercept a and the slope ft are estimated respectively by a and /?. This regression model is applied on the averages of repeated measures because individual measures cannot be paired.
The estimated parameters a and /? provide the information to assess the equivalence. An intercept significantly different from 0 means that there is a constant bias between the two measurement methods, and a slope significantly different from 1 means that there is a proportional bias between the two measurement methods [6]. Therefore, the following two-sided hypothesis will be used to test method equivalence: H0:a = 0 ; H-t'.a ^ 0 and H0:P = 1;H1:P^1.	(10)
The null hypothesis H0.a = 0 is rejected if 0 is not included in the confidence interval (CI) for a and the null hypothesis H0.p = 1 is rejected if 1 is not included in the CI for ft. The joint CI is not considered in this paper.
4 Francq BG: Bootstrap in Errors-in-Variables Regressions Applied to Methods Comparison Studies
OLS regression versus errors-in-variables regressions
This section briefly reviews the formulas for the estimation of a regression line by means of the commonly used Ordinary Least Squares (OLS) regression when X is observed without errors. Next, the formulas for two errors-in-variables regressions are provided — the Deming Regression and the Bivariate Least Squares regression. Note that in practice O"^ or/and can be estimated with replicated data and replaced by S2 or/and S^ if needed.
Ordinary Least Squares (OLS) regression
The easiest way to estimate the parameters a and P of model (9) under homoskedasticity is to apply the basic technique of OLS [12-13]. The OLS regression minimises the sum of squared vertical distances (residuals) between each point and the line as shown in Figure 1. The corresponding parameter estimators are given by the following formulas:
ßoLS = and "OLS = Y -ßoLS*-
(11)
DR-BLS
V.Y
OLS

corresponding estimates are therefore obviously biased [14].
Supposing that ctt2 = 0, the 100(1—y)% CI for ft is symmetric around Pols and is computed as [15]
CI(ßoLs):ßoLS ±ti -y.N-2s,

with s
ßohs 1
— POLS
and
SOLS _	«OLS ßoLS^i)
(12)
(13)
where t1_Y/2]n-2 is the 100(1—y/2)% percentile of a t-distribution with N — 2 degrees of freedom.
In the same way, the 100(1—y)% CI for a is symmetric around CC0LS and can be computed as
ClOoLs):âoLS ±t1_r.N_?st 2'
-2J"OLS
with
s20ls
OLS
\N sxxJ
(14)
These Cl's are exact under the assumptions of OLS, especially that of no errors in the X-values (c^ = 0) and normality of .
Deming Regression (DR)
To take into account the errors in both variables, the following ratio between the two error variances can be computed:
Axy -
Oy/nY
(15)
It is the ratio of the errors' variance in the Y over the errors' variance in X.
The DR is the Maximum Likelihood (ML) solution of model (1) when Axv is known [10]. In practice, Axv can be estimated with replicated data.
Figure 1 Illustration of OLS and DR-BLS regressions criteria of minimisation.
Unfortunately, the OLS minimisation criterion does not take into account the errors in the independent variable [14]. OLS supposes that there is no error produced by the measurement method assigned to the X-axis, i.e., the t^- are supposed to be equal to zero or negligible. The
The DR minimises the sum of the (weighted) squares of the oblique distances between each point to the line [11,16] as shown in Figure 1. The angle of the direction is related to Axv and given by —Axy//3 [11]. The ML estimators are:
/?DR =-:-and
2s
xy
^DR — y
(16)
Informatica Medica Slovenica 2014; 19(1-2)
5
The ratio is assumed to be constant by DR. This assumption is fulfilled under homoskedasticity and balanced design (nXl and nYl constant).
Gillard and Iles [17-18] propose to compute the variance-covariance matrix of the estimators using the method of moments. When XXY is assumed to be known, the variances of the estimators can be computed with the following formulas (modified to take into account the replicated data):
/§dr
_ *xxsyy sxy
"S3
«DR
= Z2
s2 ^ Pdrg^/nx+av/nY ¡§DR	N	'
(17)
The approximate and symmetric CI for ft or a can be easily computed by associating a t-distribution to the standard error of the parameter because the estimators provided by ML are asymptotically normally distributed [19]:
ci(Pdr):/?DR ±t1-LN-2sB 2'
CIOdlr):
and
(18)
For the slope fi, an exact solution exists — the exact and asymmetric CI for fi can be computed as follows [11]:
Exact-CI(^DR): ^Axv tan(0s ±0) where CI(0s):0s±0 _	^	(19)
with fiDR = tan Ô, d = arctan/?DR, Ôs = arctan(/?DR/7I^7) and	(20)
0 =
2arcsinl ti-y--,N-2.
IN-2
account error and heteroskedasticity in both variables and is usually explained in matrix notation [6,21-23]. Here, the formulas are given under homoskedaticity with replicated data. The estimates of the parameters (the b vector) are computed by iteration using the following formulas:
Rb = g
i / N
WBLS
mi*
VW v VW vi
Li=iXi Li=i*i
If=i Yt
/«BLS\
VW
WBLS
^[XM + ^s b = R1g.
(Yi-a^s-foLsXi)'
nx
WBLS
(22)
(23)
(24)
Note that WBLs, the weighting factor, is equal for each data point under homoskedasticity and equals the variance of the residuals. The vector b provides the estimates Pbls and aBLS; under homoskedasticity it can be proven that Pels = PDR and &BLS = ^DR.
Riu and Rius [22] propose the following variance-covariance matrix for the BLS parameters:
V(b)BLS =slLSR-\	(25)
or equivalently

_2 _ ^BLS^BLslf=l^i2
and
«BLS

(26)
The approximate and symmetric Cl's for ft or a are then given by the following formulas [6]: cK£bls):/?bls ±t,_r.N_7s-s__ _ and


(27)
M
^XY^sxxsyy sxy)
(syy-ÀxY^xx) +4-&xYSxy
(21)
Bivariate Least Square regression (BLS)
The BLS is a generic name but this paper refers to BLS as defined first by Lisy et al. [20] and later by other authors [6,21-23]. The BLS can take into
Bootstrap in errors-in-variables regressions
In this section, two well-known bootstrap procedures (bootstrapping the pairs and bootstrap on the residuals) are briefly explained, as well as the jackknife procedure [24]. These approaches are compared using simulations and real data.
6 Francq BG: Bootstrap in Errors-in-Variables Regressions Applied to Methods Comparison Studies
Jackknife
The jackknife is a simplified version of the bootstrap, applied by the MedCalc software in method comparison studies and sometimes suggested in the literature [25-27]. The main advantages are its simplicity and its fast algorithm. Figure 2 illustrates the jackknife procedure for the estimation of a regression line. First, the regression line is estimated with the initial sample (the "true" sample) to obtain the estimated values of the slope and the intercept, /? and a. Then, each point in the scatterplot is removed alternately and for each step a new regression line is estimated. N "pseudo"-regressions are therefore obtained, each with N — 1 points. When the point {Xi,Y{) is removed, the estimated slope and intercept are given respectively by /?_; and . The jackknife estimators after N steps are respectively given by /?jack = N$-{N- 1)/iV2f=i/?-i and
«jack = W«-(JV-1)/VZr=ia-i.	(28)
The CI's are computed by the jackknife procedure as follow:
--S^jack and
CI(a):ajack ±q1_zs3jack,	(29)
where q±-Y/2 is the l—y/2 quantile of the standardized normal distribution, and
4.« = TT2"« (a-i - jEfai*-') and
=i^zj"., (p_< - izt^/î-,)1. (30)
Y = â + ßX/'
X
Initial sample (N=5)
Figure 2 Illustration of the jackknife procedure for the estimation of a regression line.
Informatica Medica Slovenica 2014; 19(1-2)
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Figure 3 Illustration of the bootstrapping the residuals procedure (left) and bootstrapping the pairs (right) for the estimation of a regression line (the circled point is a point resampled twice).
Bootstrapping the residuals
Figure 3 (left) illustrates the bootstrap procedure on the vertical residuals. First, the regression line is estimated with the initial sample to obtain the estimated values of the slope and the intercept, /? and a. Then, the vertical residuals are computed: e^ = Yi — a — ftXi = Yi — Yi and these residuals are resampled: e* is the ith resampled bootstrap residual. These resampled residuals are added to the initial predicted values to get a pseudo-sample of size N where the ith point is (Xi,Yi* = f; + e*). This is repeated B times (b = 1 ,..,B) and for each step the slope and the intercept are estimated (as well as their variances), respectively for the pseudo-sample b by (its variance being s^) and a^ (its variance being ). For each b step, the following standardised deviates are computed:
and Ulb=~^.	(31)
At this point, two different approaches can be followed to compute a confidence interval: the bootstrap-t or the percentile bootstrap. The percentile bootstrap is certainly the easiest
solution as the confidence interval is computed directly by the y /2 and 1—y/2 percentile of the empirical distribution (i.e., the B values) of or afj. The confidence interval by the bootstrap-t is computed as
CI(£):/? ±ut and
2
CI {a)\a±us 1_zsn	(32)
' 2
where U^ y is the 1 — y/2 quantile of the U■** b
p, 2 p,
values and u*. y is the 1—y/2 quantile of the , 2
U- b values.
Bootstrapping the pairs
Figure 3 (right) illustrates the technique of bootstrapping the pairs. First, the regression line is estimated with the initial sample to obtain the estimated values of the slope and the intercept, /? and a. Then, the points (Xi,Y{) are resampled where (Z*,^*) is the ith resampled point. This is repeated B times and for each step, as explained in the previous section, (^¡*	and (s^) are
computed. For each b step, the following values
8 Francq BG: Bootstrap in Errors-in-Variables Regressions Applied to Methods Comparison Studies
are obtained:
and Wib=^.	(33)
Pb	ab
As previously explained, the percentile bootstrap or the bootstrap-t can be applied on the W^b or
b values to obtain the confidence interval for ft or a.
Coverage probabilities of the bootstrap procedures
In order to compare the coverage probabilities of the confidence intervals provided by the DR and BLS regressions and the bootstrap procedures presented in the previous sections, 104 samples were simulated with N = 10 and 50 with unreplicated data (nx = nY = 1, A=AXY known) under equivalence (a = 0, /? = 1, rfc = ) for the values of ^ and AXY described in Francq and Govaerts [19]. For each simulated sample, the CI is computed by DR and BLS and with the bootstrap procedures described in the previous sections (with B = 500). Note that the percentile bootstrap provides the same results for DR and BLS because jiDR =fiBLS and aDR = aBLS, whereas the bootstrap-t provides different Cl's for DR and BLS because the variances of the parameters are taken into account (and are computed differently for DR and BLS). Finally, the
coverage probabilities of the slopes (with a 95% nominal level) are computed for a given AXY.
Figure 4 displays the coverage probabilities with respect to AXY (which is graphed on a logarithmic scale) for N = 10 (left) and N = 50 (right). The exact formula for the CI for the slope by DR obviously provides the best coverage probabilities; the approximate ones provided by DR or BLS are slightly lower, especially for N = 10 and also when Axv <1 for the BLS with N = 10 or N = 50. As expected, the jackknife approach provides coverage probabilities closer to the nominal level for N = 50 as the number of pseudo-samples is higher (the estimator obtained is therefore more precise). The coverage probabilities provided by bootstrapping the residuals collapse drastically when Axy decreases and when N increases, because the randomness of the errors in X is not taken into account by bootstrapping the vertical residuals. Lastly, the coverage probabilities provided by bootstrapping the pairs are very close to those obtained by the bootstrap-t technique on DR or BLS, while the percentile technique is slightly worse. When N increases, the three bootstrap techniques on the pairs move closer to each other and closer to the nominal level. It is noteworthy that bootstrapping the pairs can provide better coverage probabilities than the BLS formula, especially when AXY <1 and N = 50.
Informatica Medica Slovenica 2014; 19(1-2)
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Exact-DR	--DR
Paired-Percentile	Paired-t BLS
Residuals-Percentile-----Residuals-t BLS
Jacknife
-BLS — Paired-t DR --Residuals-t DR
Figure 4 Coverage probabilities of the CI for the slope (P), for N = 10 (left) or N = 50 (right) related to X (=AXY with nx = nY) in a logarithmic scale, for the Deming Regression (DR) with its exact formula or approximate one, the Bivariate Least Square regression (BLS) with its approximate formula, two bootstrap procedures (on the pairs or residuals) split into three approaches (percentile, bootstrap-t on DR and bootstrap-t on BLS) and the jackknife.
Application
In the systolic blood pressure data [2], simultaneous measurements were made by two observers (denoted J and R) using a sphygmomanometer and a semi-automatic blood pressure monitor (denoted S) for 85 patients. The systolic blood pressure was measured three times per patient by S and three times per patient by J (R is not considered here; for a brief overview of other designs and approaches see a recent example of a method comparison study from the field of rehabilitation [28]).
If the mean measurements given by S are assigned to the Y-axis and J to the X-axis, then it follows that the estimated value of A (=AXy as nx = nY) is 2.223, and therefore jiDR =Pbls = 0.956 and aDR =aBLS = 21.230 [19,29]. Figure 5 illustrates the different Cl's for ft computed using the exact and approximate DR formula, the approximate BLS formula, the jacknife procedure, and six bootstrap approaches (percentile method, bootstrap-t on DR or BLS, bootstrapping the pairs
and bootstrapping the residuals). The exact DR formula provides a slightly asymmetric CI while the approximate DR and BLS Cl's are symmetric. These three CI's are similar although the BLS one is slightly narrower. The CI obtained by jacknife is narrower than those obtained without resampling but the estimated slope is very similar to the previous ones. The bootstrap-t on either DR or BLS also yields very similar CI's while the percentile method provides a slightly wider CI and higher estimate. As expected, bootstrapping the residuals provides a shifted CI (upwards for the percentile method and downwards for the bootstrap-t). As explained in the previous section, the coverage probabilities of the bootstrap on the residuals collapse drastically and the Cl's are therefore wrong because the randomness of the errors in the X variable is not taken into account.
The hypothesis H0:fi = 1 is not rejected for the Cl's computed directly by DR or BLS, the jacknife or by bootstrapping the pairs. On the other hand, this hypothesis is erroneously rejected for the
10 Francq BG: Bootstrap in Errors-in-Variables Regressions Applied to Methods Comparison Studies
bootstrap on the residuals (except for the percentile method) as these CI's are shifted.
Figure 5 The CI for the slope (P) for the Systolic Blood Pressure data computed by Deming Regression (DR) with exact and approximate formula, the Bivariate Least Squares regression (BLS) with approximate formula, two bootstrap procedures (on the pairs and on the residuals) split into three approaches (percentile, bootstrap-t on DR and bootstrap-t on BLS), and the jackknife.
Conclusion
Six different bootstrap procedures were compared in order to improve the coverage probabilities of the approximate confidence intervals for the parameters of the DR and BLS regressions. The bootstrap-t on DR or BLS provides very similar results. These two regressions are actually confounded under homoskedasticity and the variances of the parameters, though computed differently, are similar in practice. The jacknife is a simple method but its coverage probabilities are lower than the nominal level for small sample sizes, and its CI may therefore be too narrow in practice. Bootstrapping the residuals is not recommended as the coverage probabilities collapse and the CI's are shifted in practice. Bootstrapping the pairs is recommended to improve the coverage probabilities especially when the ratio of the measurement errors' variances is less than one. It can provide better coverage
probabilities than the approximate CI computed directly by DR or BLS. Moreover, this bootstrap approach takes into account the measurement errors in both variables.
Acknowledgement
Support from the IAP Research Network P7/06 of the Belgian State (Belgian Science Policy) is gratefully acknowledged.
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