CSS 590 Experimental Design in Agriculture

Lab exercise 10th week Augmented Designs Lattice Designs Suggested reading: Lattice Designs Kuehl Chapt. 9&10 Cochran and Cox Chapter 10

Part I. Augmented Design A lentil breeder had 12 new selections that she wanted to test against her new release. She had only a limited amount of seed and in order to have a plot size large enough to minimize error and generate meaningful results, she decided to use an augmented design rather than the more traditional RBD. She also included a long time check (C1) and placed it as the first entry in each block. The second check (C2) was the commercial standard. The lentil seed yields (kg/ha) in plot order were as follows:
Block 1 1 1 1 1 2 2 2 2 2 3 3 3 3 3 4 4 4 4 4 Entry C1 Sel7 Sel3 C2 Sel11 C1 Sel2 C2 Sel4 Sel6 C1 Sel10 Sel12 Sel9 C2 C1 C2 Sel8 Sel1 Sel5 Yield 553 619 710 689 686 601 761 749 616 692 501 737 694 693 695 577 695 758 813 631

Enter the data in SAS and run an analysis using PROC GLM; PROC GLM; TITLE 'Augmented Design using PROC GLM'; CLASS block entry; MODEL yield=block entry; LSMEANS entry/stderr pdiff=CONTROLU('C2'); LSMEANS entry/stderr pdiff=CONTROLU('C2') adjust=T; RUN; Which varieties were significantly better than the best control (C2)? What type of multiple comparison tests are you utilizing? For unbalanced data sets that involve both random and fixed factors, the use of mixed models is recommended. Is this data unbalanced? Which factor is random? Which is fixed? Analyze the data in SAS using PROC MIXED. The syntax is similar to PROC GLM, except that random effects are not included in the MODEL statement in PROC MIXED. PROC MIXED; TITLE 'Augmented Design using PROC MIXED'; CLASS block entry; MODEL yield=entry; RANDOM block; LSMEANS entry/pdiff=CONTROLU('C2') adjust=dunnett; RUN; How do the results of PROC GLM and PROC MIXED compare? Are the adjusted means (lsmeans) the same for both? The standard errors of means? The comparison of means? II. Lattice Design We will use the data from the partially balanced lattice example presented in class concerning the barley variety trial with 25 entries (Lab10_lattice.xls). Input the data into SAS and run an analysis using PROC LATTICE. The lattice procedure in SAS has some very specific requirements for naming of the classification variables. The plot on which the response variable is measured must be numbered and must be called Treatmnt (Note this is an intentional misspelling it goes back to the days when SAS variables could only be 8 characters long!) Then you must also have a variable named Block that is also numeric and refers to the Block number from the lattice design. The third required classification variable is also numeric and must be called Group. This is the replication number. Response variables (Yield in this case) follow the classification variables. You may have more than one response variable. SAS will analyze each individually. Once you have met all of the criteria for data formatting, the actual analysis is very simple:

PROC LATTICE; TITLE 'Analysis of Simple Lattice with PROC LATTICE'; RUN;

A copy of the output is provided below with annotations. Compare results with the calculations on the spreadsheet presented in class (Lattice.xls). Answer the following questions: Was the lattice an effective design in this experiment? What is your supporting evidence? What is the percentage of relative precision (or efficiency) of the lattice versus the RBD? How can you compare adjusted treatment means? Now try running the analysis using PROC MIXED. There are no restrictions on variable names as there are in PROC LATTICE, but we will use the same names as before. Note that random effects are not included in the Model statement in Proc Mixed.
PROC MIXED; TITLE 'Analysis of Simple Lattice with PROC MIXED'; class Block Group Treatmnt; model Yield = Treatmnt; random Group Block(Group); lsmeans Treatmnt/pdiff adjust=tukey; RUN;

How do results compare with those obtained from PROC LATTICE? (compare estimates of Mean Squares, F tests, adjusted means and their standard errors)

Barley Yield Trial - Peterson page 181 The Lattice Procedure Analysis of Variance for Yield Source Sum of Mean DF Squares Square

Replications 1 18.6050 18.6050 Blocks within Replications (Adj.) 8 77.5920 9.6990 Component B 8 77.5920 9.6990 Treatments (Unadj.) 24 621.82 25.9092 Intra Block Error 16 87.4080 5.4630 Randomized Complete Block Error 24 165.00 6.8750 Total 49 805.42 16.4372 Additional Statistics for Yield Variance of Means in Same Block 5.9402 Variance of Means in Different Bloc 6.4174 Average of Variance 6.2583 LSD at .01 Level 7.3068 LSD at .05 Level 5.3033 Efficiency Relative to RCBD 109.85 Adjusted Treatment Means for Yield Treatment 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 Mean

Familiar term for SSB (Blocks in a RBD is equivalent to replications in a lattice. This is often referred to as the error for blocks within replication or Eb. If this term is greater than Intra Block error, then blocking in the lattice was effective and treatment means will be adjusted with the appropriate block adjustments. Familiar term for SST (Sum of Squares for Treatments) calculated on the Unadjusted treatment means, the same as for any RBD. The Randomized Complete Block Error ERB is used to calculate relative precision (or efficiency) of the lattice design when compared to the RBD. ERB is in the numerator and effective error Ee is in the denominator. Multiply by 100 to get percentage. If you are testing lines to see which ones are better than checks, use LSI and the formula: LSI = t a
' 2 Ee /r

14.6899 14.4773 17.9991 19.4584 14.0506 17.6288 14.9661 15.6380 12.2473 17.5895 14.7919 12.1292 12.8011 12.2604 13.9026 17.2771 9.1645 12.6863 15.4456 14.2378 11.9366 8.1239 7.2958

being sure to use a 1-tailed t. LSD is calculated with the same error term the only difference is the 2-tailed t. Degrees of freedom will be the same as for Intra Block Error (16 in this case).

24 25

5.9551 18.99