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IndexABORTASR.NOW, 65FINALASR.NOW, 65Access, 44accuracy - genetic BLUP, 194advanced processing arguments, 185AI algorithm, 13AIC, 18Akaike Information Criteria, 18aliassing, 102Analysis of Deviance, 98animal breeding data, 2arguments, 5ASReml symbols∼, 83*, 43., 43#, 43$, 43!{, 85!}, 85*, 85+, 85,, 85-, 85/, 85:, 85autoregressive, 111Average Information, 2balanced repeated measures, 253Bayesian Information Criteria, 18BIC, 18binary files, 44Binomial divisor, 99BLUE, 14BLUP, 14, 15case, 84combining variance models, 16command file, 30genetic analysis, 149multivariate, 142Command line optionA ASK, 181B BRIEF, 181C CONTINUE, 183D DEBUG, 181F FINAL, 183Gg graphics , 181Hg HARDCOPY, 182I INTERACT, 181J JOIN, 181N NoGraphs, 181O ONERUN, 183Q QUIET, 182R RENAME, 183S WorkSpace, 184W WorkSpace, 184command line options, 179commonly used functions, 85conditional distribution, 12conditional factors, 90Conditional Wald F Statistics, 20constraining variance parameters, 137constraintson variance parameters, 115contrasts, 64Convergence criterion, 65correlated random effects, 15correlation, 173between traits, 142312
Index 313model, 10covariance model, 11isotropic, 10covariates, 42, 58, 101cubic splines, 95data field syntax, 48data file, 28, 41, 42binary format, 44fixed format, 44free format, 42using Excel, 44data file line, 32datafile line, 59qualifiers, 60syntax, 59datasetsbarley.asd, 262coop.fmt, 293grass.asd, 253harvey.dat, 149nin89.asd, 28oats.asd, 243orange.asd, 285rat.dat, 142rats.asd, 247ricem.asd, 279voltage.asd, 250wether.dat, 145wheat.asd, 267debug options, 181Denominator Degrees of Freedom, 20dense, 101design factors, 101diagnostics, 18diallal analysis, 91direct product, 7, 9, 106direct sum, 9discussion list, 4Dispersion parameter, 98distributionconditional, 12marginal, 12Ecode, 39Eigen analysis, 209Eigen analysis example, 299EM update, 134environment variablejob control, 63equationsmixed model, 14error varianceheterogeneity, 9errors, 213Excel, 44execution time, 209expected information matrix, 13F statistics, 20Factor qualifierDATE, 48DMY, 49LL Label Length, 49MDY, 49PRUNE, 50SKIP fields, 50SORT, 50SORTALL, 50TIME, 49factors, 42fileGIV, 154pedigree, 150Fisher-scoring algorithm, 13fixed effects, 7Fixed format files, 60fixed terms, 83, 88multivariate, 143primary, 88sparse, 89Forming a job template, 34
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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
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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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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
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Page 304 and 305: 15 Examples 282Interpretation of re
Page 306 and 307: 15 Examples 284The independence of
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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
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Page 322 and 323: 15 Examples 300Eigen values 4.382 0
Page 324 and 325: 15 Examples 302Animal modelIn this
Page 326 and 327: 15 Examples 304additive genetic var
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 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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