The ANOVA Approach to the Analysis of Linear Mixed-Effects Models c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 1 / 58 We begin with a relatively simple special case. Suppose yijk = µ + τi + uij + eijk , (i = 1, . . . , t; j = 1, . . . , n; k = 1, . . . , m) β = (µ, τ1 , . . . , τt )0 , u = (u11 , u12 , . . . , utn )0 , e = (e111 , e112 , . . . , etnm )0 , β ∈ Rt+1 , an unknown parameter vector, u e ∼N 0 0 2 σu I 0 , , where 0 σe2 I σu2 , σe2 ∈ R+ are unknown variance components. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 2 / 58 This is the standard model for a CRD with t treatments, n experimental units per treatment, and m observations per experimental unit. We can write the model as y = Xβ + Zu + e, where X = [1tnm×1 , It×t ⊗ 1nm×1 ] c Copyright 2016 Dan Nettleton (Iowa State University) and Z = [Itn×tn ⊗ 1m×1 ]. Statistics 510 3 / 58 Special Case of t = n = m = 2 X= 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 µ , β = τ1 , Z = τ2 c Copyright 2016 Dan Nettleton (Iowa State University) 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 1 , u = u11 u12 u21 u22 Statistics 510 4 / 58 Connection to ANOVA Let X1 = 1tnm×1 , X2 = [1tnm×1 , It×t ⊗ 1nm×1 ], X3 = [Itn×tn ⊗ 1m×1 ]. Note that C(X1 ) ⊂ C(X2 ) ⊂ C(X3 ), X = X2 , and Z = X3 . As usual, let Pj = PXj = Xj (X0j Xj )− X0j for j = 1, 2, 3. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 5 / 58 An ANOVA Table Sum of Squares Degrees of Freedom y0 (P2 − P1 )y rank(X2 ) − rank(X1 ) = t − 1 y0 (P3 − P2 )y rank(X3 ) − rank(X2 ) = tn − t y0 (I − P3 )y rank(I) − rank(X3 ) = tnm − tn y0 (I − P1 )y rank(I) − rank(X1 ) = tnm − 1 c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 6 / 58 Shortcut for Obtaining DF from Source Source DF treatments t−1 exp.units(treatments) (n − 1)t obs.units(exp.units, treatments) (m − 1)nt c.total tnm − 1 c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 7 / 58 Shortcut for Obtaining SS from DF Source DF Sum of Squares trt t−1 Pt Pn Pm − y··· )2 xu(trt) t(n − 1) Pt Pn Pm − yi·· )2 Pt Pn Pm − yij· )2 Pt Pn Pm − y··· )2 ou(xu, trt) tn(m − 1) c.total tnm − 1 c Copyright 2016 Dan Nettleton (Iowa State University) i=1 i=1 i=1 i=1 j=1 j=1 j=1 j=1 k=1 (yi·· k=1 (yij· k=1 (yijk k=1 (yijk Statistics 510 8 / 58 Source DF Sum of Squares trt t−1 nm xu(trt) tn − t m Pt i=1 (yi·· Pt i=1 Mean Square − y··· )2 Pn j=1 (yij· − yi·· )2 ou(xu, trt) tnm − tn Pt Pn Pm − yij· )2 tnm − 1 Pt Pn Pm − y··· )2 c.total i=1 i=1 c Copyright 2016 Dan Nettleton (Iowa State University) j=1 j=1 k=1 (yijk k=1 (yijk SS/DF Statistics 510 9 / 58 Expected Mean Squares Based on our linear mixed-effects model (y = Xβ + Zu + e and associated assumptions), we can find the expected value of each mean square in the ANOVA table. Examining these expected values helps us see ways to 1) test hypotheses of interest by computing ratios of mean squares, and 2) estimate variance components by computing linear combinations of mean squares. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 10 / 58 Expected Mean Squares For balanced designs, there are shortcuts (not presented here) for writing down expected mean squares. Rather than memorizing shortcuts, I think it is better to know how to derive expected mean squares. Before going through one example derivation, we will prove a useful result that you may already be familiar with. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 11 / 58 Expectation of Sample Variance Numerator ind Suppose w1 , . . . , wk ∼ (µw , σw2 ). Then kσw2 = k X σw2 = i=1 k X 2 E(wi − µw ) = i=1 k X E(wi − w̄· + w̄· − µw )2 i=1 ( k ) X 2 = E (wi − w̄· + w̄· − µw ) i=1 = E ( k X (wi − w̄· )2 + (w̄· − µw )2 + 2(w̄· − µw )(wi − w̄· ) ) i=1 ( k ) k k X X X 2 2 = E (wi − w̄· ) + (w̄· − µw ) + 2(w̄· − µw ) (wi − w̄· ) i=1 c Copyright 2016 Dan Nettleton (Iowa State University) i=1 i=1 Statistics 510 12 / 58 Expectation of Sample Variance Numerator (ctd.) kσw2 = E ( k X (wi − w̄· )2 + i=1 = E ( k X k X ) (w̄· − µw )2 i=1 ) 2 2 (wi − w̄· ) + k(w̄· − µw ) i=1 = E ( k X ) (wi − w̄· )2 + kE(w̄· − µw )2 i=1 = E = E ( k X i=1 ( k X ) (wi − w̄· )2 + kVar(w̄· ) ) (wi − w̄· ) i=1 c Copyright 2016 Dan Nettleton (Iowa State University) 2 + kσw2 /k ( k ) X 2 =E (wi − w̄· ) + σw2 i=1 Statistics 510 13 / 58 Expectation of Sample Variance Numerator (ctd.) We have shown kσw2 = E ( k X ) (wi − w̄· )2 + σw2 . i=1 Therefore, ( k ) X E (wi − w̄· )2 = (k − 1)σw2 . i=1 This is just a special case of the Gauss-Markov model result E(σ̂ 2 ) = σ 2 . (y = [w1 , . . . , wk ]0 , X = 1, β = [µw ], σ 2 = σw2 ) c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 14 / 58 Expected Value of MStrt E(MStrt ) = nm t−1 Pt E(yi.. − y··· )2 = nm t−1 Pt E(µ + τi + ui· + ei·· − µ − τ · − u·· − e··· )2 = nm t−1 Pt E(τi − τ · + ui· − u·· + ei·· − e··· )2 = nm t−1 Pt − τ · )2 + E(ui· − u·· )2 + E(ei·· − e··· )2 ] = nm [ t−1 Pt P − τ · )2 + E{ ti=1 (ui· − u·· )2 } i=1 i=1 i=1 i=1 [(τi i=1 (τi c Copyright 2016 Dan Nettleton (Iowa State University) +E{ Pt i=1 (ei·· − e··· )2 }] Statistics 510 15 / 58 So, to simplify E(MStrt ) further, note that σu2 i.i.d. u1· , . . . , ut· ∼ N 0, . n Thus, ) ( t X σ2 E (ui· − u·· )2 = (t − 1) u . n i=1 Similarly, e1·· , . . . , et·· so that E ( t X σ2 ∼ N 0, e nm i.i.d. ) (ei·· − e··· )2 i=1 c Copyright 2016 Dan Nettleton (Iowa State University) = (t − 1) σe2 . nm Statistics 510 16 / 58 It follows that ) " t ( t X nm X E(MStrt ) = (τi − τ · )2 + E (ui· − u·· )2 t − 1 i=1 i=1 ( t )# X +E (ei·· − e··· )2 i=1 " t nm X σ2 = (τi − τ · )2 + (t − 1) u t − 1 i=1 n σ2 +(t − 1) e nm = t nm X (τi − τ .)2 + mσu2 + σe2 . t − 1 i=1 c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 17 / 58 Similar calculations allow us to add an Expected Mean Squares (EMS) column to our ANOVA table. Source EMS trt σe2 + mσu2 + xu(trt) σe2 + mσu2 ou(xu, trt) σe2 c Copyright 2016 Dan Nettleton (Iowa State University) nm t−1 Pt i=1 (τi − τ .)2 Statistics 510 18 / 58 Expected Mean Squares (EMS) could be computed using E(y0 Ay) = tr(AΣ) + E(y)0 AE(y), where Σ = Var(y) = ZGZ0 + R = σu2 Itn× tn ⊗ 110 m× m + σe2 Itnm× tnm and E(y) = c Copyright 2016 Dan Nettleton (Iowa State University) µ + τ1 µ + τ2 . . . µ + τt ⊗ 1nm× 1 . Statistics 510 19 / 58 Furthermore, with some nontrivial work, it can be shown that ! t X nm y0 (P2 − P1 )y ∼ χ2t−1 (τi − τ .)2 , σe2 + mσu2 2(σe2 + mσu2 ) i=1 y0 (P3 − P2 )y ∼ χ2tn−t , 2 2 σe + mσu y0 (I − P3 )y ∼ χ2tnm−tn , σe2 and that these three χ2 random variables are independent. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 20 / 58 It follows that MStrt y0 (P2 − P1 )y/(t − 1) = 0 MSxu(trt) y (P3 − P2 )y/(tn − t) h0 i y (P2 −P1 )y /(t − 1) σe2 +mσu2 h i = y0 (P3 −P2 )y /(tn − t) σ 2 +mσ 2 F1 = e u ∼ Ft−1, tn−t ! t X nm (τi − τ · )2 . 2(σe2 + mσu2 ) i=1 Thus, we can use F1 to test H0 : τ1 = · · · = τt . c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 21 / 58 Also, MSxu(trt) y0 (P3 − P2 )y/(tn − t) = 0 MSou(xu,trt) y (I − P3 )y/(tnm − tn) h i y0 (P3 −P2 )y /(tn − t) 2 2 σ 2 +mσu2 σe + mσu h0 e i = 2 y (P3 −P2 )y σe /(tnm − tn) σe2 2 σe + mσu2 ∼ Ftn−t, tnm−tn . σe2 F2 = Thus, we can use F2 to test H0 : σu2 = 0. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 22 / 58 Estimating σu2 Note that E MSxu(trt) − MSou(xu,trt) m = (σe2 + mσu2 ) − σe2 = σu2 . m Thus, MSxu(trt) − MSou(xu,trt) m 2 is an unbiased estimator of σu . c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 23 / 58 Although MSxu(trt) − MSou(xu,trt) m 2 is an unbiased estimator of σu , this estimator can take negative values. This is undesirable because σu2 , the variance of the u random effects, cannot be negative. Later in the course, we will discuss likelihood based methods for estimating variance components that honor the parameter space. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 24 / 58 Estimation of Estimable Cβ As we have seen previously, Σ ≡ Var(y) = σu2 Itn× tn ⊗ 110 m× m + σe2 Itnm× tnm . It turns out that β̂ Σ = (X0 Σ−1 X)− X0 Σ−1 y = (X0 X)− X0 y = β̂. Thus, the GLS estimator of any estimable Cβ is equal to the OLS estimator in this special case. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 25 / 58 An Analysis Based on the Average for Each Experimental Unit Recall that our model is yijk = µ + τi + uij + eijk , (i = 1, ..., t; j = 1, ..., n; k = 1, ..., m) The average of observations for experimental unit ij is yij· = µ + τi + uij + eij· c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 26 / 58 If we define ij = uij + eij· ∀ i, j and σ 2 = σu2 + σe2 , m we have yij· = µ + τi + ij , where the ij terms are iid N(0, σ 2 ). Thus, averaging the same number (m) of multiple observations per experimental unit results in a Gauss-Markov linear model with normal errors for the averages yij· : i = 1, ..., t; j = 1, ..., n . c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 27 / 58 Inferences about estimable functions of β obtained by analyzing these averages are identical to the results obtained using the ANOVA approach as long as the number of multiple observations per experimental unit is the same for all experimental units. When using the averages as data, our estimate of σ 2 is an 2 estimate of σu2 + σme . We can’t separately estimate σu2 and σe2 , but this doesn’t matter if our focus is on inference for estimable functions of β. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 28 / 58 Because E(y) = µ + τ1 µ + τ2 . . . µ + τt ⊗ 1nm× 1 , the only estimable quantities are linear combinations of the treatment means µ + τ1 , µ + τ2 , ..., µ + τt , whose Best Linear Unbiased Estimators are y1·· , y2·· , . . . , yt·· , respectively. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 29 / 58 Thus, any estimable Cβ can always be written as µ + τ1 µ + τ2 for some matrix A. A .. . µ + τt It follows that the BLUE of Cβ can be written as y1·· y2·· A ... . c Copyright 2016 Dan Nettleton (Iowa State University) yt·· Statistics 510 30 / 58 Now note that Var(yi ..) = Var(µ + τi + ui . + ei ..) = Var(ui . + ei ..) = Var(ui .) + Var(ei ..) σ2 σ2 = u+ e n nm 1 σ2 = σu2 + e n m 2 σ . = n c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 31 / 58 Thus Var y1.. y2.. . . . yt.. σ 2 = It×t n which implies that the variance of the BLUE of Cβ is y1·· . 2 σ σ2 Var A . = A It×t A0 = AA0 . n n . yt·· c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 32 / 58 Thus, we don’t need separate estimates of σu2 and σe2 to carry out inference for estimable Cβ. We do need to estimate σ 2 = σu2 + σe2 . m This can equivalently be estimated by MSxu(trt) m or by the MSE in an analysis of the experimental unit means yij· : i = 1, ..., t; j = 1, ..., n. . c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 33 / 58 For example, suppose we want to estimate τ1 − τ2 . The BLUE is y1·· − y2·· whose variance is Var(y1·· − y2·· ) = Var(y1·· ) + Var(y2·· ) 2 σ2 σu σe2 + = 2 =2 n n nm 2 2 (σe + mσu2 ) = nm 2 = E(MSxu(trt) ) nm Thus, c 1·· − y2·· ) = 2MSxu(trt) . Var(y nm c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 34 / 58 A 100(1 − α)% confidence interval for τ1 − τ2 is r 2MSxu(trt) . y1·· − y2·· ± tt(n−1),1−α/2 nm A test of H0 : τ1 = τ2 can be based on τ1 − τ2 y − y2·· t = q1·· ∼ tt(n−1) q 2MSxu(trt) nm c Copyright 2016 Dan Nettleton (Iowa State University) 2(σe2 +mσu2 ) nm . Statistics 510 35 / 58 What if the number of observations per experimental unit is not the same for all experimental units? Let us look at two miniature examples to understand how this type of unbalancedness affects estimation and inference. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 36 / 58 First Example y111 y121 y= y211 , y212 1 1 X= 0 0 c Copyright 2016 Dan Nettleton (Iowa State University) 0 0 , 1 1 1 0 Z= 0 0 0 1 0 0 0 0 1 1 Statistics 510 37 / 58 First Example y111 y121 y= y211 , y212 1 1 X= 0 0 X1 = 1, ȳ··· ȳ··· P1 y = ȳ··· , ȳ··· 0 0 , 1 1 X2 = X, ȳ1·1 ȳ1·1 P2 y = ȳ21· , ȳ21· c Copyright 2016 Dan Nettleton (Iowa State University) 1 0 Z= 0 0 0 1 0 0 0 0 1 1 X3 = Z y111 y121 P3 y = ȳ21· ȳ21· Statistics 510 38 / 58 Note that ȳ1·1 − ȳ··· = ȳ1·1 − (ȳ1·1 + ȳ21· )/2 = (ȳ1·1 − ȳ21· )/2 and ȳ21· − ȳ··· = ȳ21· − (ȳ1·1 + ȳ21· )/2 = −(ȳ1·1 − ȳ21· )/2. Thus, MStrt = y0 (P2 − P1 )y = 2(y1·1 − y··· )2 + 2(y21· − y··· )2 = (y1·1 − y21· )2 1 MSxu(trt) = y0 (P3 −P2 )y = (y111 −y1·1 )2 +(y121 −y1·1 )2 = (y111 −y121 )2 2 1 MSou(xu,trt) = y0 (I−P3 )y = (y211 −y21· )2 +(y212 −y21· )2 = (y211 −y212 )2 . 2 c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 39 / 58 E(MStrt ) = E(y1·1 − y21· )2 = E(τ1 − τ2 + u1· − u21 + e1·1 − e21· )2 = (τ1 − τ2 )2 + Var(u1· ) + Var(u21 ) + Var(e1·1 ) + Var(e21· ) = (τ1 − τ2 )2 + σu2 2 + σu2 + σe2 2 + σe2 2 = (τ1 − τ2 )2 + 1.5σu2 + σe2 c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 40 / 58 E(MSxu(trt) ) = 1 E(y111 2 = 1 E(u11 2 = 1 (2σu2 2 − y121 )2 − u12 + e111 − e121 )2 + 2σe2 ) = σu2 + σe2 E(MSou(xu,trt) ) = 1 E(y211 2 − y212 )2 = 1 E(e211 2 − e212 )2 = σe2 c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 41 / 58 SOURCE EMS trt (τ1 − τ2 )2 + 1.5σu2 + σe2 xu(trt) σu2 + σe2 ou(xu, trt) σe2 With some nontrivial work, it can be shown that MSxu(trt) (τ1 − τ2 )2 MStrt F= / ∼ F1,1 . 1.5σu2 + σe2 σu2 + σe2 3σu2 + 2σe2 c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 42 / 58 The test statistic that we used to test H0 : τ1 = · · · = τt in the balanced case is not F distributed in this unbalanced case. 1.5σu2 + σe2 (τ1 − τ2 )2 MStrt ∼ F1,1 MSxu(trt) σu2 + σe2 3σu2 + 2σe2 c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 43 / 58 A Statistic with an Approximate F Distribution We’d like our denominator to be an unbiased estimator of 1.5σu2 + σe2 in this case. Consider 1.5MSxu(trt) − 0.5MSou(xu,trt) The expectation is 1.5(σu2 + σe2 ) − 0.5σe2 = 1.5σu2 + σe2 . The ratio MStrt 1.5MSxu(trt) − 0.5MSou(xu,trt) can be used as an approximate F statistic with 1 numerator DF and a denominator DF obtained using the Cochran-Satterthwaite method. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 44 / 58 The Cochran-Satterthwaite method will be explained in the next set of notes. We should not expect this approximate F-test to be reliable in this case because of our pitifully small dataset. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 45 / 58 Best Linear Unbiased Estimates in this First Example What do the BLUEs of the treatment means look like in this case? Recall 1 0 0 1 0 1 0 µ1 , Z = 0 1 0 . β= , X= 0 1 0 0 1 µ2 0 0 1 0 1 c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 46 / 58 Σ = Var(y) = ZGZ0 + R = σu2 ZZ0 + σe2 I 1 0 0 0 1 0 0 0 0 1 0 0 + σe2 0 1 0 0 = σu2 0 0 1 1 0 0 1 0 0 0 1 1 0 0 0 1 2 2 σu 0 0 0 σe 0 0 0 0 σu2 0 0 0 σe2 0 0 = 0 0 σu2 σu2 + 0 0 σe2 0 0 0 σu2 σu2 0 0 0 σe2 2 σu + σe2 0 0 0 0 σu2 + σe2 0 0 = 2 2 2 0 0 σu + σe σu 2 2 2 0 0 σu σu + σe c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 47 / 58 It follows that β̂ Σ = (X0 Σ−1 X)− X0 Σ−1 y 1 1 0 0 y1·1 2 2 y= = y21· 0 0 12 21 Fortunately, this is a linear estimator that does not depend on unknown variance components. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 48 / 58 Second Example y111 y112 y= y121 , y211 1 1 X= 1 0 c Copyright 2016 Dan Nettleton (Iowa State University) 0 0 , 0 1 1 1 Z= 0 0 0 0 1 0 0 0 0 1 Statistics 510 49 / 58 In this case, it can be shown that β̂ Σ = (X0 Σ−1 X)− X0 Σ−1 y " = " = σe2 +σu2 3σe2 +4σu2 σe2 +σu2 3σe2 +4σu2 σe2 +2σu2 3σe2 +4σu2 0 0 0 2σe2 +2σu2 3σe2 +4σu2 c Copyright 2016 Dan Nettleton (Iowa State University) y11· + y211 σe2 +2σu2 3σe2 +4σu2 0 1 # y121 y111 y112 y121 y211 # . Statistics 510 50 / 58 It is straightforward to show that the weights on y11· and y121 are 1 Var(y11· ) 1 Var(y11· ) + 1 Var(y121 ) and 1 Var(y121 ) 1 Var(y11· ) + 1 Var(y121 ) , respectively. This is a special case of a more general phenomenon: the BLUE is a weighted average of independent linear unbiased estimators with weights for the linear unbiased estimators proportional to the inverse variances of the linear unbiased estimators. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 51 / 58 Of course, in this case and in many others, " 2 2 # σe2 +2σu2 2σe +2σu y + y 3σe2 +4σu2 121 β̂ Σ = 3σe2 +4σu2 11· y211 is not an estimator because it is a function of unknown parameters. Thus, we use β̂ Σb as our estimator (i.e., we replace σe2 and σu2 by estimates in the expression above). c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 52 / 58 β̂ Σb is an approximation to the BLUE. β̂ Σb is not even a linear estimator in this case. Its exact distribution is unknown. When sample sizes are large, it is reasonable to assume that the distribution of β̂ Σb is approximately the same as the distribution of β̂ Σ . c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 53 / 58 Var(β̂ Σ ) = Var[(X0 Σ−1 X)−1 X0 Σ−1 y] = (X0 Σ−1 X)−1 X0 Σ−1 Var(y)[(X0 Σ−1 X)−1 X0 Σ−1 ]0 = (X0 Σ−1 X)−1 X0 Σ−1 ΣΣ−1 X(X0 Σ−1 X)−1 = (X0 Σ−1 X)−1 X0 Σ−1 X(X0 Σ−1 X)−1 = (X0 Σ−1 X)−1 −1 −1 −1 b X)−1 X0 Σ b y] =???? ≈ (X0 Σ b X)−1 Var(β̂ Σb ) = Var[(X0 Σ c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 54 / 58 Summary of Main Points Many of the concepts we have seen by examining special cases hold in greater generality. For many of the linear mixed models commonly used in practice, balanced data are nice because... c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 55 / 58 1 It is relatively easy to determine degrees of freedom, sums of squares, and expected mean squares in an ANOVA table. 2 Ratios of appropriate mean squares can be used to obtain exact F-tests. 3 For estimable Cβ, Cβ̂ Σ b = Cβ̂. (OLS = GLS). 4 5 When Var(c0 β̂) = constant × E(MS), exact inferences about c0 β can be obtained by constructing t-tests or confidence intervals based on c0 β̂ − c0 β ∼ tDF(MS) . t= p constant × (MS) Simple analysis based on experimental unit averages gives the same results as those obtained by linear mixed model analysis of the full data set. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 56 / 58 When data are unbalanced, the analysis of linear mixed may be considerably more complicated. 1 Approximate F-tests can be obtained by forming linear combinations of Mean Squares to obtain denominators for test statistics. 2 The estimator Cβ̂ Σb may be a nonlinear estimator of Cβ whose exact distribution is unknown. 3 Approximate inference for Cβ is often obtained by using the distribution of Cβ̂ Σb , with unknowns in that distribution replaced by estimates. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 57 / 58 Whether data are balanced or unbalanced, unbiased estimators of variance components can be obtained using linear combinations of mean squares from the ANOVA table. c Copyright 2016 Dan Nettleton (Iowa State University) Statistics 510 58 / 58