ASReml-S reference manual - VSN International

3Fitting the mixed model3.1 IntroductionThis chapter begins with a brief introduction covering data frame preparation, fittingthe linear model and the fitted asreml object followed by a detailed description of theasreml function call and some technical details of model fitting, including the treatmentof missing values, and setting initial values for variance parameters. The basic conceptsare illustrated using a real example and pointers to following chapters are given. Forconsistency, the same data are also used for illustration in later chapters where possible.Advanced topics such as models for variance components or genetic models are consideredin later chapters. Chapter 8 gives a lengthy set of additional worked examples.3.2 The data frameData for analysis using asreml are generally contained in a text file or a spreadsheet andare read into a data frame using the appropriate S-PLUS functions. Variates and factorsin the data frame are then resolved through the data argument of the asreml functioncall.The first 25 lines of the comma separated text file nin89.csv containing the NIN fieldtrial data described in Section 1.3.1 are reproduced below. Note that the data are infield order (rows within columns) and a header line (first row) is included. In this casethere are 11 comma separated data fields (Variety. . . Column) and the complete file has224 data rows, one for each variety in each replicate.Variety,Id,pid,raw,Rep,nloc,yield,lat,long,Row,ColumnLANCER,1,1101,585,1,4,29.25,4.3,19.2,16,1BRULE,2,1102,631,1,4,31.55,4.3,20.4,17,1REDLAND,3,1103,701,1,4,35.05,4.3,21.6,18,1CODY,4,1104,602,1,4,30.1,4.3,22.8,19,1ARAPAHOE,5,1105,661,1,4,33.05,4.3,24,20,1NE83404,6,1106,605,1,4,30.25,4.3,25.2,21,1NE83406,7,1107,704,1,4,35.2,4.3,26.4,22,1NE83407,8,1108,388,1,4,19.4,8.6,1.2,1,2CENTURA,9,1109,487,1,4,24.35,8.6,2.4,2,2SCOUT66,10,1110,511,1,4,25.55,8.6,3.6,3,2COLT,11,1111,502,1,4,25.1,8.6,4.8,4,2NE83498,12,1112,492,1,4,24.6,8.6,6,5,2