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6 Command file: Specifying theterms in the mixed modelIntroductionSpecifying model formulae in ASRemlGeneral rulesExamplesFixed terms in the modelPrimary fixed termsSparse fixed termsRandom terms in the modelInteractions and conditional factorsInteractionsConditional factorsAlphabetic list of model functionsWeightsMissing valuesMissing values in the responseMissing values in the explanatory variablesSome technical details about model fitting in ASRemlSparse versus denseOrdering of terms in ASRemlAliassing and singularitiesExamples of aliassing82Analysis of Variance table
6 Command file: Specifying the terms in the mixed model 836.1 IntroductionThe linear mixed model is specified in ASReml as a series of model terms andqualifiers. In this chapter the model formula syntax is described.6.2 Specifying model formulae in ASRemlThe linear mixed model is specified in AS-Reml as a series of model terms and qualifiers.Model terms include factor and variate labels(Section 5.4), functions of labels, special termsand interactions of these. The model is specifiedimmediately after the datafile and any jobcontrol qualifier and/or tabulate lines. Thesyntax for specifying the model isNIN Alliance Trial 1989variety.column 11nin89.asd !skip 1yield ∼ mu variety !r repl,!f mv1 211 column AR1 .322 row AR1 .3response [!wt weight]∼ fixed [!r random] [!f sparse fixed]• response is the label for the response variable(s) to be analysed; multivariateanalysis is discussed in Chapter 8,• weight is a label of a variable containing weights; weighted analysis is discussedin Section 6.7,• ∼ separates response from the list of fixed and random terms,• fixed represents the list of primary fixed explanatory terms, that is, variates,factors, interactions and special terms for which analysis of variance (ANOVA)type tests are required. See Table 6.1 for a brief definition of reserved modelterms, operators and commonly used functions. The full definition is in Section6.6,• random represents the list of explanatory terms to be fitted as random effects,see Table 6.1,• sparse fixed are additional fixed terms not included in the ANOVA table.General rulesThe following general rules apply in specifying the linear mixed model• all elements in the model must be space separated,• the character ∼ separates the response variables(s) from the explanatory variablesin the model,
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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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Page 62 and 63: 3 A guided tour 40title linenin all
Page 64 and 65: 4 Data file preparation 424.1 Intro
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7 Command file: Specifying variance
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8 Command file: Multivariate analys
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9 Command file: Genetic analysisInt
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9 Command file: Genetic analysis 15
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10 Tabulation of the data andpredic
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10 Tabulation of the data and predi
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11 Functions of variancecomponentsI
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11 Functions of variance components
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11 Functions of variance components
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12 Command file: Running the jobInt
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12 Command file: Running the job 17
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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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