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3 A guided tourIntroductionNebraska Intrastate Nursery (NIN) field experimentThe ASReml data fileThe ASReml command fileThe title lineReading the dataThe data file lineSpecifying the terms in the mixed modelTabulationPredictionVariance structuresRunning the jobDescription of output filesThe .asr fileThe .sln fileThe .yht fileTabulation, predicted values and functions of the variancecomponents26
3 A guided tour 273.1 IntroductionThis chapter presents a guided tour of ASReml, from data file preparation andbasic aspects of the ASReml command file, to running an ASReml job and interpretingthe output files. You are encouraged to read this chapter before movingto the later chapters;• a real data example is used in this chapter for demonstration, see below,• the same data are also used in later chapters,• links to the formal discussion of topics are clearly signposted by margin notes.Note that some aspects of ASReml, in particular, pedigree files (see Chapter 9)and multivariate analysis (see Chapter 8) are only covered in later chapters.ASReml is essentially a batch program with some optional interactive features.The typical sequence of operations when using ASReml is• Prepare the data (typically using a spreadsheet or data base program)• Export that data as an ASCII file (for example export it as a .csv (commaseparated values) file from Excel)• Prepare a job file with filename extension .as.• Run the job file with ASReml• Review the various output files• revise the job and re run it, or• extract pertinant results for your report.NewYou will need a file editor to create the command file and to view the variousoutput files. On unix systems, vi and emacs are commonly used. Under Windows,there are several suitable program editors available such as ASReml-W andConText described in section 1.3.3.2 Nebraska Intrastate Nursery (NIN) field experimentThe yield data from an advanced Nebraska Intrastate Nursery (NIN) breedingtrial conducted at Alliance in 1988/89 will be used for demonstration, see Stroupet al. (1994) for details. Four replicates of 19 released cultivars, 35 experimentalwheat lines and 2 additional triticale lines were laid out in a 22 row by 11
Page 1 and 2: ASRemlUser GuideRelease 2.0A R Gilm
Page 3 and 4: Published by:E-mail:Website:VSN Int
Page 5 and 6: PrefaceiiASReml is one of several u
Page 7 and 8: ContentsPrefaceiList of TablesxviiL
Page 9 and 10: Contentsvi3.3 The ASReml data file
Page 11 and 12: ContentsviiiCombining rows from sep
Page 13 and 14: Contentsx7.6 Variance structure qua
Page 15 and 16: Contentsxii12.2 The command line .
Page 17 and 18: Contentsxiv15 Examples 24115.1 Intr
Page 19: List of Tablesxvi7.3 Details of the
Page 22 and 23: List of Figuresxix15.8 Rice bloodwo
Page 24 and 25: 1 Introduction 21.1 What ASReml can
Page 26 and 27: 1 Introduction 41.4 How to use this
Page 28 and 29: 2 Some theoryThe linear mixed model
Page 30 and 31: 2 Some theory 8laid out in a rectan
Page 32 and 33: 2 Some theory 10product of matrices
Page 34 and 35: 2 Some theory 12where H = R + ZGZ
Page 36 and 37: 2 Some theory 14where y i is the
Page 38 and 39: 2 Some theory 162.4 Combining varia
Page 40 and 41: 2 Some theory 18balanced one-way cl
Page 42 and 43: 2 Some theory 20L, r × p, and l, r
Page 44 and 45: 2 Some theory 22the terms A, B, C,
Page 46 and 47: 2 Some theory 24Kenward and Roger A
Page 50 and 51: 3 A guided tour 28column rectangula
Page 52 and 53: 3 A guided tour 30(see Chapter 2) t
Page 54 and 55: 3 A guided tour 32els. Similarly fo
Page 56 and 57: 3 A guided tour 34mand to run nin89
Page 58 and 59: 3 A guided tour 36* SYNTAX change:
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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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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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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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