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7 Command file: Specifying variance structures 111See Chapter 13See Sections 6.3and 6.11See Sections 2.1and 7.5See Section 7.7augmented data file the yield data for the missing plots have all been madeNA (one of the missing value indicators in ASReml) and variety has beenarbitrarily coded LANCER for all of the missing plots (any of the variety namescould have been used),• !f mv is now included in the model specification. This tells ASReml to estimatethe missing values. The !f before mv indicates that the missing values are fixedeffects in the sparse set of terms,• unlike the case with G structures, ASReml automatically includes and estimatesa scale parameter for R structures (σe 2 for V = σe 2 (I 11⊗ Σ(ρ r )) in thiscase). This is why the variance models specified for row (AR1) and column(ID) are correlation models. The user could specify a non-correlation model(diagonal elements ≠ 1) in the R structure definition, for example, ID couldbe replaced by IDV to represent V = σe(σ 2 c 2 I 11) ⊗ Σ(ρ r ). However, IDV wouldthen need to be followed by !S2==1 to fix σe 2 at 1 and prevent ASReml trying(unsuccessfully) to estimate both parameters as they are confounded: the scaleparameter associated with IDV and the implicit error variance parameter, seeSection 2.1 under Combining variance models. Specifically, the code11 column IDV 48 !S2==1would be required in this case, where 48 is the starting value for the variances.This complexity allows for heterogeneous error variance.3b Two-dimensional separable autoregressive spatial modelThis model extends 3a by specifying a firstorder autoregressive correlation model of order11 for columns (AR1). The R structurein this case is therefore the direct product oftwo autoregressive correlation matrices thatis, V = σeΣ 2 c (ρ c ) ⊗ Σ r (ρ r ), giving a twodimensionalfirst order separable autoregressivespatial structure for error. The startingcolumn correlation in this case is also 0.3.Again note that σe 2 is implicit.NIN Alliance Trial 1989variety !Aid.row 22column 11nin89aug.asd !skip 1yield ∼ mu variety !f mv1 2 011 column AR1 0.322 row AR1 0.3