ASReml-S reference manual - VSN International

More documents

Recommendations

Info

8.9 Balanced longitudinal data - Random coefficients and cubic smoothing splines 120200 400 600 800 1200 160045Marginal250200150100Circumference2501 23500200150100500200 400 600 800 1200 1600200 400 600 800 1200 1600AgeFig. 8.15. Fitted values adjusted for Season and approximate confidence intervals for model 6those obtained by the nonlinear mixed effects analysis. The individual curves for eachtree are not convincingly modelled by a logistic function. There is a distinct pattern inthe residuals shown in Pinheiro and Bates [2000, p340], which is consistent for all trees;this is modelled here by the Season term.
ASome technical details about model fitting in asremlA.1 Sparse versus denseThe terms in the linear mixed model are partitioned into two sets; a dense set and asparse set. The partition is defined by the fixed formula; all terms in the fixed formulaare included in the dense set while terms in the random and sparse formulae are includedin the sparse set. The inverse coefficient matrix is fully formed for the terms in the denseset which are fitted using dense equations. The inverse coefficient matrix is only partiallyformed for terms in the sparse set. Typically, the sparse set is large resulting in savingsin memory and computing. A consequence is that the variance matrix of the BLUEs andBLUPs is only available for terms in the dense portion.A.2 Ordering of terms in asremlSolutions for the fixed and random effects in linear mixed model analysis using asreml areobtained by solving the corresponding mixed model equations in the numerical routines[Gilmour et al., 1995]. The sparse equations are processed first after being reordered toretain sparsity during solution. If keep.order=F, the remaining equations are processedwith main effects before interactions and low order interactions before higher ones so thatnormal marginality of terms is achieved. The order of effects in the solution vector(s) inthe returned object reflects the order of processing.A.3 Aliasing and singularitiesA singularity occurs when there is either• a linear dependence in the model and therefore no information left to estimate thecorresponding effect, or• no data for that fixed effect,• no data for a simple (uncorrelated) random effect.The REML routines handle singularities by deleting the equations in question. Sincethe equations are solved from the bottom up, the first level (and hence the last levelprocessed) of a factor is the one that will be declared singular and dropped from themodel. The number of singularities is returned in the asreml object (nsing) and reportedduring the iterative process. Solutions that are zero and have NA for their standard errorare the singular effects.
Page 1 and 2:
Analysis of mixed modelsfor S langu
Page 3 and 4:
D.G. ButlerQueensland Department of
Page 6:
ContentsPreface . . . . . . . . . .
Page 10 and 11:
ContentsviiB Available variance mod
Page 12 and 13:
List of Figures1.1 Weekly body weig
Page 14 and 15:
1.3 Data sets used 21.2.2 Help and
Page 16 and 17:
1.3 Data sets used 41.3.2 Repeated
Page 18 and 19:
1.3 Data sets used 6101 Sire 1 0102
Page 20 and 21:
2.1 The linear mixed model 8Direct
Page 22 and 23:
2.2 Estimation 10There is a corresp
Page 24 and 25:
2.2 Estimation 12where H ij = ∂ 2
Page 26 and 27:
2.5 Inference for random effects 14
Page 28 and 29:
2.6 Inference for fixed effects 16T
Page 30 and 31:
2.6 Inference for fixed effects 18t
Page 32 and 33:
3Fitting the mixed model3.1 Introdu
Page 34 and 35:
3.3 Introducing the asreml function
Page 36 and 37:
3.6 Getting help3.7 The asreml func
Page 38 and 39:
3.8 Fixed terms 26na.method.Xkeep.o
Page 40 and 41:
3.8 Fixed terms 28Summary of reserv
Page 42 and 43:
3.10 Conditional factors: the at()
Page 44 and 45:
Table 3.2. Families and link functi
Page 46 and 47:
3.15 Multivariate analysis 34R!trai
Page 48 and 49:
Source df F_inc F_con MSource df dd
Page 50 and 51:
4.1.1 Specifying variance models in
Page 52 and 53:
4.2 A sequence of structures for th
Page 54 and 55:
Σ = [σ ij ] :{σii = σ 2 , ∀i
Page 56 and 57:
4.4 Variance model functions 44init
Page 58 and 59:
The Matérn class4.4 Variance model
Page 60 and 61:
4.4 Variance model functions 48Chol
Page 62 and 63:
Required argumentsobj4.5 Rules for
Page 64 and 65:
4.7 Constraining variance parameter
Page 66 and 67:
5Genetic analysis5.1 IntroductionIn
Page 68 and 69:
5.2 Pedigree, G-inverse objects and
Page 70 and 71:
5.4 Using Pedigree and G-inverse ob
Page 72 and 73:
6Prediction from the linear model6.
Page 74 and 75:
Optional argumentslevels6.2 The pre
Page 76 and 77:
6.2 The predict method 64The predic
Page 78 and 79:
6.4 Complicated weighting 666.4 Com
Page 80 and 81:
7The asreml class and related metho
Page 82 and 83: maxiter maximum number of iteration
Page 84 and 85: 7.3 Methods and related functions 7
Page 88 and 89: pedigree7.3 Methods and related fun
Page 92 and 93: 8Examples8.1 IntroductionThis secti
Page 94 and 95: 8.2 Split Plot Design 82In this exa
Page 96 and 97: 8.3 Unbalanced nested design 84[4,]
Page 98 and 99: 8.3 Unbalanced nested design 86adju
Page 100 and 101: 8.4 Sources of variability in unbal
Page 102 and 103: 8.5 Balanced repeated measures 902
Page 104 and 105: 8.5 Balanced repeated measures 92Ta
Page 106 and 107: 8.5 Balanced repeated measures 94wh
Page 108 and 109: 8.6 Spatial analysis of a field exp
Page 110 and 111: 8.6 Spatial analysis of a field exp
Page 112 and 113: Variety predicted.value standard.er
Page 114 and 115: 8.7 Unreplicated early generation v
Page 116 and 117: 8.7 Unreplicated early generation v
Page 118 and 119: 8.8 Paired Case-Control Study 106Th
Page 120 and 121: Terms added sequentially; adjusted
Page 122 and 123: 8.8 Paired Case-Control Study 110[
Page 124 and 125: 8.8 Paired Case-Control Study 112..
Page 126 and 127: 8.9 Balanced longitudinal data - Ra
Page 134 and 135: A.3 Aliasing and singularities 122W
Page 136 and 137: Table B.1: Details of the available
Page 138 and 139: B Available variance models 126Deta
Page 140 and 141: ReferencesG. E. P. Box. Analysis of
Page 142 and 143: References 130W. W. Stroup, P. S. B
Page 144 and 145: Index 132F statistics, 17fa(,k), 49
show all

ASReml-S reference manual - VSN International

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?