Class Notes


Week Date Topic Notes Handouts/printouts
1 Jan. 17 Experiments in the age of Big Data
Planning an experiment
Jan. 19 Some terminology
2 Jan. 22 Completely randomized design, Factors, Blocking CRD/RCBD Handout
Jan. 26 Randomizing an experiment
Numerical summaries, graphical displays
3 Jan. 29 Alignment of data for better visual comparisons
Randomization for inference, nonparametric tests
One-way ANOVA, parameter estimates, sums of squares SAS: PROC GLM 1-way ANOVA [annotated]
4 Feb. 5 Model assumptions Comment on outliers
Feb. 7 Modeling trends (dosage-response) SAS: 1-way ANOVA vs. dosage-response [orig]
SAS: Transformation in dosage-response setting [orig]
Feb. 9 Model effects, additive model estimates for balanced design SAS: PROC GLM, two-factor additive model [annotated] [orig]
Setting reference group in SAS
SAS PROCEDURES
5 Feb. 12 Two-way ANOVA, parameter estimates, sums of squares SAS: PROC GLM, two-way ANOVA [annotated] [orig]
End of topics for Exam 1 (Friday Feb. 23)
Feb. 14 Contrasts SAS: 1-way ANOVA contrasts [orig]
SAS: 2-way ANOVA contrasts [orig]
6 Feb. 19 Orthogonal Contrasts SAS: 1-way ANOVA orthogonal contrasts [orig]
SAS: 2-way ANOVA orthogonal contrasts [orig]
Feb. 21 Orthogonal polynomial contrasts SAS: Orthogonal polynomial contrasts [orig]
Multiple comparisons part 1 SAS: 1-way ANOVA multiple comparison adjustments [orig]
7 Feb. 26 Multiple comparisons part 2 SAS: lines graphic and multiple comparisons [orig]
Feb. 28 SAS statements: LSmeans vs. means SAS: lsmeans vs. means in unbalanced design [orig]
Controlling the false discovery rate (FDR) part 1 qvalue package: [example histogram]
March 2 Controlling the false discovery rate (FDR) part 2 FDR Example: [slides for class]
8 March 5 Power and sample size Power calculations in SAS and R: [orig]
March 7 Factorial without replication and Tukey 1 d.f. test for nonadditivity   SAS: 1 d.f. Nonadditivity test [orig]
March 9 Factorial Design Analysis (includes slice option in SAS) Analysis of a 2-way ANOVA
End of topics for Exam 2 (Wednesday March 28)
Spring Break
9 March 19 General Factorial Design Analysis SAS: 3-way ANOVA [orig]
March 21 Unbalanced factorials, types of SS (I, II, III, IV) part 1
Unbalanced factorials, types of SS (I, II, III, IV) part 2
March 23 Random effects part 1: EMS, estimating variance components Linear Model Procedures in SAS
10 March 26 Random effects part 2: EMS from SAS, F-tests SAS: PROC MIXED, Random effects, intraclass correlation [orig]
Rainbow and CC cats
SAS: PROC GLM expected mean squares [orig]
ODS output in SAS  
11 Mar 30 More complex designs, part 1
April 2 More complex designs, part 2
April 6 Nested designs, mixed models SAS: Nested random effects [orig]
R: Visualizing Variability in Fully Nested Design   [R]
12 April 9 Randomized Complete Block Design (RCBD) SAS: Randomized Complete Block (RCBD) [orig]
SAS: RCBD [orig]
April 11 Intro to Lenth diagrams, getting EMS Lenth handout on EMS  
April 13 Approximate F-tests, split-plot designs SAS: split-plot design with CRD as whole-plot [orig]
SAS/R: Fancier split-plot [orig]
13 April 18 Putting a context with a diagram Exercise 12-3 OLRT
April 20 Some small group work Problem 12-3 OLRT
Tukey revisited, for non-CRDs
End of topics for Exam 3 (Wednesday April 25)
14 April 23 Correlation structures, repeated measures SAS: Repeated Statement [orig]
April 27 Latin square designs SAS: Latin Squares [orig]
15 April 30 Analysis of covariance (ANCOVA)
BLUPs SAS: BLUPs [orig]
May 2 Random Coefficient Model SAS: Random coefficients [orig]
Random Coefficients Growth Curve Example SAS/R: Growth curve example [orig]
Time and Farm effects plot