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7 Command file: Specifying variance structures 136Check the orderwill check the overall size, it does not check that the order of effects matches thestructure definition so the user must be careful to get this right. Check that theterms are conformable by considering the order of the fitted effects and ensuringthe first term of the direct product corresponds to the outer factor in the nestingof the effects. Two examples are• random regressions where we want a covariance between intercept and slope.!r !{ animal animal.time !}.animal 22 0 US 3 -.5 2animalis equivalent (though not identical because of the scaling differences) to.!r pol(time,1).animal.pol(time,1).animal 2pol(time,1) 0 US 1 -.1 .2animal• maternal/direct genetic covariancelambid !Psireid !Pdamid !P.wwt ywt ∼ Trait Trait.sex !r !{ Trait.lambid at(Trait,2).damid !}.Trait.lambid 23 0 US1.3 # Var(wwt D)1.0 2.2 # Cov(wwt D,ywt D) Var(ywt D)-.1 -.2 0.8 # Cov(wwt D,wwt M) Cov(ywt D,wwt M) Var(wwt M)lambid 0 AINV # AINV explicitly requests to use A inverse
7 Command file: Specifying variance structures 1377.9 Constraining variance parametersParameter equality within and between variance structuresdifficultNewNewEquality of parameters in a variance model can be specified using the !=s qualifierwhere s is a string of letters and/or zeros (see Table 7.4). Positions in the stringcorrespond to the parameters of the variance model:• all parameters with the same letter in the structure are treated as the sameparameter,• 1-9 are different from a-z which are different from A-Z so that 61 equalitiescan be specified. 0 and . mean unconstrained. A colon generates a sequenceviz. a:e is the same as abcde• Putting % as the first characterin s makes the interpretation of codes absolute(so that they apply across structures).• Putting * as the first characterin s indicates that numbers are repeat counts,A-Z are equality codes and only . is unconstrained. Thus !=*.3A2. is equivalentto !=0AAA00 or !=0aaa00.Examples are presented in Table 7.5.Table 7.5: Examples of constraining variance parameters in ASRemlASReml codeaction!=ABACBA0CBAsite.gen 2 # G header linesite 0 US .3 !=0A0AA0 !GPUPUUP.1 .4 .1 .1 .3genconstrain all parameters correspondingto A to be equal, similarly for B and C.The 7th parameter would be left unconstrained.This sequence applied to anunstructured 4 × 4 matrix would makeit banded, that isAB AC B A0 C B Athis example defines a structure for thegenotype by site interaction effects in aMET in which the genotypes are independentrandom effects within sites butare correlated across sites with equal covariance.
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ASRemlUser GuideRelease 2.0A R Gilm
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Published by:E-mail:Website:VSN Int
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PrefaceiiASReml is one of several u
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ContentsPrefaceiList of TablesxviiL
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Contentsvi3.3 The ASReml data file
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ContentsviiiCombining rows from sep
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Contentsx7.6 Variance structure qua
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Contentsxii12.2 The command line .
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Contentsxiv15 Examples 24115.1 Intr
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List of Tablesxvi7.3 Details of the
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List of Figuresxix15.8 Rice bloodwo
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1 Introduction 21.1 What ASReml can
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1 Introduction 41.4 How to use this
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2 Some theoryThe linear mixed model
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2 Some theory 8laid out in a rectan
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2 Some theory 10product of matrices
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2 Some theory 12where H = R + ZGZ
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2 Some theory 14where y i is the
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2 Some theory 162.4 Combining varia
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2 Some theory 18balanced one-way cl
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2 Some theory 20L, r × p, and l, r
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2 Some theory 22the terms A, B, C,
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2 Some theory 24Kenward and Roger A
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3 A guided tourIntroductionNebraska
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3 A guided tour 28column rectangula
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3 A guided tour 30(see Chapter 2) t
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3 A guided tour 32els. Similarly fo
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3 A guided tour 34mand to run nin89
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3 A guided tour 36* SYNTAX change:
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3 A guided tour 38repl 3 -0.8713 1.
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3 A guided tour 40title linenin all
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4 Data file preparation 424.1 Intro
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4 Data file preparation 44Fixed for
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5 Command file: Reading the data 46
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6 Command file: Specifying theterms
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6 Command file: Specifying the term
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12 Command file: Running the job 18
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13 Description of output filesIntro
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13 Description of output files 190A
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13 Description of output files 192i
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13 Description of output files 194f
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13 Description of output files 196.
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13 Description of output files 198o
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13 Description of output files 200E
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13 Description of output files 202t
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13 Description of output files 204|
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NIN alliance trial 1989 9a 1Residua
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13 Description of output files 208w
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13 Description of output files 210T
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14 Error messagesIntroductionCommon
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14 Error messages 214filename!last
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14 Error messages 216variety !AQUAL
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14 Error messages 2188. misspelt va
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14 Error messages 220Missing/faulty
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14 Error messages 222Last line read
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14 Error messages 224Model specific
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14 Error messages 226:11 column 11
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14 Error messages 22814.5 Informati
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14 Error messages 230List of warnin
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14 Error messages 232Alphabetical l
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15 Examples 24215.1 IntroductionIn
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15 Examples 244For simple variance
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15 Examples 2460.2_cwt Marvellous 1
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15 Examples 248The input file conta
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15 Examples 250Source Model terms G
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15 Examples 252ltage example 5−3
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15 Examples 254The focus is modelli
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15 Examples 256y1 y3 y5 y7 y10 ~ Tr
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15 Examples 258power model shown in
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15 Examples 260Residual US=UnStr 2
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15 Examples 262the current model).
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15 Examples 264Slate Hall example f
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15 Examples 266Predicted values of
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15 Examples 268wheat.asd !skip 1 !D
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Tullibigeal trial i2 1Variogram of
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15 Examples 272column evaluated at
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15 Examples 274this is for the pair
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15 Examples 276Table 15.8: Estimate
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15 Examples 278(and in fact necessa
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15 Examples 280Tr.run 22 0 US .79 .
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15 Examples 282Interpretation of re
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15 Examples 284The independence of
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15 Examples 286Note that the data f
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15 Examples 288Table 15.11 Orange d
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15 Examples 290217Predicted values
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15 Examples 292105Residual0-5-10200
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15 Examples 294Table 15.13: REML es
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15 Examples 29615*0. #Asreml will e
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15 Examples 298Covariance/Variance/
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15 Examples 300Eigen values 4.382 0
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15 Examples 302Animal modelIn this
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15 Examples 304additive genetic var
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BibliographyAbramowitz, M. and Steg
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Bibliography 308Gilmour, A. R., Cul
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Bibliography 310Schall, R. (1991).
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IndexABORTASR.NOW, 65FINALASR.NOW,
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Index 314free format, 42functions o
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Index 316!==, 53!>, 53!>=, 53!*, 53
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Index 318!STEP, 71!SUBSET, 71!SUB,
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Index 320parameter, 7variance compo
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