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11 Functions of variance components 174A more detailed exampleFor convenience in preparing the .pin file, some users copy the variance componentlines from the .asr file and insert them at the top of the .pin file, beingcareful to retain one leading space so that the lines will be just copied and otherwiseignored as the .pin file is processed.The following sample .pin file is a little morecomplicated. It relates to the bivariate siremodel in bsiremod.as shown in the code boxto the right.The first six lines of the .pin file contain thevariance component table on which the .pinfile is based, copied from the the .asr file forconverience in coding the rest of the file.Bivariate sire modelsire !Iywt fatbsiremod.asdywt fat ∼ Trait !r Trait.sire1 2 10 # ASReml will count unitsTrait 0 US3*0Trait.sire 2Trait 0 US3*0sireResidual UnStruct 1 26.2197 26.2197 18.01 0 UResidual UnStruct 1 2.85090 2.85090 9.55 0 UResidual UnStruct 2 1.71556 1.71556 18.00 0 UTr.sire UnStruct 1 16.5262 16.5262 2.69 0 UTr.sire UnStruct 1 1.14422 1.14422 1.94 0 UTr.sire UnStruct 2 0.132847 0.132847 1.88 0 UF phenvar 1:3 + 4:6F addvar 4:6 * 4H heritA 10 7H heritB 12 9R phencorr 7 8 9R gencor 4:6Numbering the parameters reported in bsiremod.asr (andbsiremod.vvp)123456thenerror variance for ywterror covariance for ywt and faterror variance for fatsire variance component for ywtsire covariance for ywt and fatsire variance for fat
11 Functions of variance components 175F phenvar 1:3 + 4:6creates new components 7 = 1+4, 8 = 2+5 and 9 = 3+6,F addvar 4:6 * 4creates new components 10 = 4 × 4, 11 = 5 × 4 and 12 = 6 × 4,H heritA 10 7forms 10 / 7 to give the heritability for ywt,H heritB 12 9forms 12 / 9 to give the heritability for fat,R phencorr 7 8 9forms 8 / √ 7 × 9, that is, the phenotypic correlation between ywt and fat,R gencorr 4:6forms 5 / √ 4×6, that is, the genetic correlation between ywt and fat..pvc fileThe result is:7 phenvar 1 42.75 6.2978 phenvar 2 3.995 0.67619 phenvar 3 1.848 0.118310 addvar 4 66.10 24.5811 addvar 5 4.577 2.35412 addvar 6 0.5314 0.2831h2ywt = addvar 10/phenvar 7= 1.5465 0.3574h2fat = addvar 12/phenvar 9= 0.2875 0.1430phencorr = phenvar /SQR[phenvar *phenvar ]= 0.4495 0.0483gencor 2 1 = Tr.si 5/SQR[Tr.si 4*Tr.si 6]= 0.7722 0.1537
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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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7 Command file: Specifying variance
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Page 178 and 179: 10 Tabulation of the data andpredic
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Page 198 and 199: 12 Command file: Running the jobInt
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Page 210 and 211: 13 Description of output filesIntro
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Page 214 and 215: 13 Description of output files 192i
Page 216 and 217: 13 Description of output files 194f
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Page 228 and 229: NIN alliance trial 1989 9a 1Residua
Page 230 and 231: 13 Description of output files 208w
Page 232 and 233: 13 Description of output files 210T
Page 234 and 235: 14 Error messagesIntroductionCommon
Page 236 and 237: 14 Error messages 214filename!last
Page 238 and 239: 14 Error messages 216variety !AQUAL
Page 240 and 241: 14 Error messages 2188. misspelt va
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Page 244 and 245: 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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