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15 Examples 304additive genetic variance. The dam variance component is this analysis only estimatesthe maternal variance component. It is only significant for the weaningand yearling weights. The litter variation remains unchanged. The ASReml inputfile again consists of several parts, which progressively build up to fitting unstructuredvariance models to Tr.tag, Tr.dam, Tr.litter and error. A portion of theoutput file istag !Pdam !Page wwt !m0 ywt !m0gfw !m0 fdm !m0 fat !m0A-inverse retrieved from ainverse.binPEDIGREE [pcoop.fmt ] has 10696 identities, 29474 Non zero elementsQUALIFIERS: !CONTINUE !MAXIT 20 !STEP 0.01QUALIFIERS: !EXTRA 4QUALIFIER: !DOPATH 3 is activeReading pcoop.fmt FREE FORMAT skipping 0 linesMultivariate analysis of wwt ywt gfw fdmMultivariate analysis of fatUsing 7043 records of 7043 readModel term Size #miss #zero MinNon0 Mean MaxNon01 tag !P 10696 0 0 3.000 5380. 0.1070E+052 sire 0 0 1.000 48.06 92.003 dam !P 10696 0 0 1.000 5197. 0.1070E+05:Forming 95033 equations: 40 dense.Initial updates will be shrunk by factor 0.010Restarting iteration from previous solutionNotice: LogL values are reported relative to a base of -20000.00NOTICE: 76 singularities detected in design matrix.1 LogL=-1437.10 S2= 1.0000 35006 df : 2 components constrained2 LogL=-1436.87 S2= 1.0000 35006 df : 3 components constrained3 LogL=-1434.97 S2= 1.0000 35006 df : 2 components constrained4 LogL=-1430.73 S2= 1.0000 35006 df : 2 components constrained5 LogL=-1424.71 S2= 1.0000 35006 df : 1 components constrained6 LogL=-1417.98 S2= 1.0000 35006 df : 1 components constrained7 LogL=-1417.77 S2= 1.0000 35006 df : 1 components constrained8 LogL=-1417.62 S2= 1.0000 35006 df : 1 components constrained9 LogL=-1417.28 S2= 1.0000 35006 df10 LogL=-1417.23 S2= 1.0000 35006 df:16 LogL=-1417.23 S2= 1.0000 35006 dfSource Model terms Gamma Component Comp/SE % Cat(Trait,1).age.grp 49 49 0.132682E-02 0.132682E-02 2.02 0 Pat(Trait,2).age.grp 49 49 0.908220E-03 0.908220E-03 1.15 0 Pat(Trait,4).age.grp 49 49 0.175614E-02 0.175614E-02 1.13 0 Pat(Trait,5).age.grp 49 49 0.223617E-03 0.223617E-03 1.73 0 P
15 Examples 305at(Trait,1).sex.grp 49 49 0.902586 0.902586 2.88 0 Pat(Trait,2).sex.grp 49 49 15.3623 15.3623 3.50 0 Pat(Trait,3).sex.grp 49 49 0.280673 0.280673 3.71 0 Pat(Trait,5).sex.grp 49 49 1.42136 1.42136 1.80 0 PResidual UnStru 1 1 7.47555 7.47555 13.86 0 U:Covariance/Variance/Correlation Matrix UnStructured Residual7.476 0.4918 0.1339 0.1875 0.13334.768 12.57 0.4381 0.3425 0.39380.1189 0.5049 0.1056 0.4864 0.12980.9377 2.221 0.2891 3.345 0.11710.4208 1.612 0.4869E-01 0.2473 1.333Covariance/Variance/Correlation Matrix UnStructured Tr.tag3.898 0.8164 0.5763 0.3899E-01 0.61484.877 9.154 0.3689 -0.1849 0.72170.3029 0.2971 0.7085E-01-0.2415E-01 0.30410.6021E-01-0.4375 -0.5027E-02 0.6117 -0.46720.6154 1.107 0.4104E-01-0.1853 0.2570Covariance/Variance/Correlation Matrix UnStructured at(Tr,1).dam0.9988 0.70240.5881 -0.7018Covariance/Variance/Correlation Matrix UnStructured at(Tr,1).lit3.714 0.5511 0.1635 -0.6157E-012.019 3.614 0.5176 -0.43800.4506E-01 0.1407 0.2045E-01-0.3338-0.1021 -0.7166 -0.4108E-01 0.7407Analysis of Variance NumDF F_inc15 Tr.age 5 99.1616 Tr.brr 15 116.5217 Tr.sex 5 59.9419 Tr.age.sex 4 5.10There is no guarantee that unstructured variance component matrices will bepositive definite unless !GP qualifier is set. This example highlights this issue.We used the !GU qualifier on the maternal component to obtain the matrix[ ]0.9988 0.5881.0.5881 −0.7018ASReml reports the correlation as 0.7024 which it obtains by ignoring the sign in-0.7018. This is the maternal component for ywt. Since it is entirely reasonableto expect maternal influences on growth to have dissipated at 12 months of age,it would be reasonable to refit the model omitting at(Tr,2).dam and changingthe dimension of the G structure.
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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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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
Page 276 and 277: 15 Examples 254The focus is modelli
Page 278 and 279: 15 Examples 256y1 y3 y5 y7 y10 ~ Tr
Page 280 and 281: 15 Examples 258power model shown in
Page 282 and 283: 15 Examples 260Residual US=UnStr 2
Page 284 and 285: 15 Examples 262the current model).
Page 286 and 287: 15 Examples 264Slate Hall example f
Page 288 and 289: 15 Examples 266Predicted values of
Page 290 and 291: 15 Examples 268wheat.asd !skip 1 !D
Page 292 and 293: Tullibigeal trial i2 1Variogram of
Page 294 and 295: 15 Examples 272column evaluated at
Page 296 and 297: 15 Examples 274this is for the pair
Page 298 and 299: 15 Examples 276Table 15.8: Estimate
Page 300 and 301: 15 Examples 278(and in fact necessa
Page 302 and 303: 15 Examples 280Tr.run 22 0 US .79 .
Page 304 and 305: 15 Examples 282Interpretation of re
Page 306 and 307: 15 Examples 284The independence of
Page 308 and 309: 15 Examples 286Note that the data f
Page 310 and 311: 15 Examples 288Table 15.11 Orange d
Page 312 and 313: 15 Examples 290217Predicted values
Page 314 and 315: 15 Examples 292105Residual0-5-10200
Page 316 and 317: 15 Examples 294Table 15.13: REML es
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Page 320 and 321: 15 Examples 298Covariance/Variance/
Page 322 and 323: 15 Examples 300Eigen values 4.382 0
Page 324 and 325: 15 Examples 302Animal modelIn this
Page 328 and 329: BibliographyAbramowitz, M. and Steg
Page 330 and 331: Bibliography 308Gilmour, A. R., Cul
Page 332 and 333: Bibliography 310Schall, R. (1991).
Page 334 and 335: IndexABORTASR.NOW, 65FINALASR.NOW,
Page 336 and 337: Index 314free format, 42functions o
Page 338 and 339: Index 316!==, 53!>, 53!>=, 53!*, 53
Page 340 and 341: Index 318!STEP, 71!SUBSET, 71!SUB,
Page 342: Index 320parameter, 7variance compo
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