AfPBA, Session I

Hale – Homework, for the motivated

Lecture 1.4.2 – Distributions, Hypothesis Testing, and Sample Size Determination

1. The mean weight of a Conserviola olive is 1.9 g, with a sample variance of 0.4 g2
(population variance unknown). What is the probability that a bag of 18 randomly-picked
Conserviola olives has an average per-olive weight of more than 2.0 g?

2. Researchers want to determine whether over-irrigation decreases antioxidant levels in

tomatoes. They conclude that an irrigation rate of 15% over the ET rate does not significantly
decrease antioxidant levels at α = 0.05. Assume the true mean of the over-irrigated treatment
is 1.4 standard deviations less than the untreated mean and that there were 5 replications per
treatment. Assuming a one-tailed test, does the experiment have adequate power (i.e. > 80%)
to support the researchers' claim?

Lecture 1.4.3 – Introduction to R

t-test; independent observations

To test the lateral effect of a new sprayed herbicide on pollinator diversity, a researcher
selected 32 fields and randomly assigned them to two treatments. One week after application,
he examined five random 1 m2 sections in each field and calculated the average number of
pollinator species present. The data:

Field 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
Control 4.6 2.8 6.4 4.7 4.8 6.8 1.1 7.1 9.5 11.0 9.1 3.8 6.6 3.9 5.8 4.8
Sprayed 6.4 4.3 2.9 4.3 2.4 4.4 2.8 1.6 0.6 4.9 4.0 5.0 5.7 1.5 3.3 0.2

Answer the following questions using R.

1.1 For each sample (i.e. treatment), test normality using the Shapiro-Wilk test and present
a Quantile-Quantile plot. Comment.

1.2 What is the probability that these two samples are different just by chance?

1.3 Calculate the power of the test with R. Confirm the R result with a hand calculation of
the power.
Lecture 1.5.1 – Basics of ANOVA (CRD)

The following table shows the amount of bruised tissue that developed in Fuji apples over a
period of four hours after being dropped from a height of 30 cm onto a hard surface:

Treatment Bruised Tissue (g)

HWB 1.743 1.833 1.802 1.996 1.662
1-MCP 1.840 1.761 1.869 1.725 1.978
HW-MCP 1.734 1.653 1.526 1.689 1.556
Control 2.014 1.915 2.086 1.953 1.779

The 20 apples represent five independent replications of four different pre-drop treatments:
1) Hot water bath (HWB): The apples were submerged in 40°C water for three minutes and
allowed to cool; 2) 1-MCP: The apples were exposed to the chemical 1-MCP, an ethylene
blocker, for twelve hours; 3) HW-MCP: Apples were exposed to 1-MCP and then submerged
in the hot water bath; and 4) Control.

1.1 Test the normality of the observations within each treatment using the Shapiro-Wilk
test.

1.2 Is there a significant difference among treatments? What's the probability that this
detected "difference" is really just the result of random sampling from a single
population?

1.3 Are the variances homogeneous among treatments? To answer this, use the Levene
Test (default parameters) in R's 'car' package.

1.4 Present a box plot of the data.

Lecture 1.5.1 – Orthogonal contrasts and means separation

The objective of the following crop management experiment is to test the effect of a foliar
fungicide on grain yield by three methods: A single application for the season (1), two
applications over the course of the season (2), and three applications over the course of the
season (3). For each one of these application strategies, the total amount of fungicide was
applied at two rates (Hi and Lo). A control (C) receiving no fungicide was also included,
resulting in a total of 7 treatments (C, Lo1-3, Hi1-3) which were randomly assigned to 35
rows of plants in an experimental planting. The yield data (in pounds):

C Lo1 Lo2 Lo3 Hi1 Hi2 Hi3

507 568 586 629 586 612 595
551 525 612 577 612 595 612
525 551 620 568 568 586 647
533 577 577 595 551 629 595
516 586 568 586 595 647 612

1.1 Describe the design of this experiment [see table on the next page].

1.2 Present a table of orthogonal coefficients to answer the following questions:

a. Is there a significant yield response to the fungicide?

b. Is the average yield response different at the two rates (Hi and Lo)?
c. Are split applications superior to a single application?
d. Considering the split applications only, is there a difference between double and
triple applications?
e. Does the application method, single or split, influence the effects of the different
fungicide rates (Hi and Lo)?
f. Does the number of split applications influence the effects of the different
fungicide rates (Hi and Lo)?

Hint: The last two are interactions!

1.3 Use R to solve the contrasts you formulated. Compare the contrast SS with the model
SS and comment.

1.4 Interpret your output and write your conclusions to the six questions above based on the
results.

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1.5 Now let's assume you wish to analye these data by comparing each treatment to the
control, rather than using contrasts to ask the questions above. Use R to perform these
six pairwise comparisons, and interpret your output.
When you are asked to "describe the design of this experiment," please do so by completing
the following template:

Design:
Response Variable:
Experimental Unit:

Number
Class
of Description
Variable
Levels
1
2
↓
n

YES /
Subsamples? NO
Lecture 1.6.2 – RCBD's

A trial is conducted to compare the grain yields of four different advanced breeding lines of
pearl millet (A-D) to the most widely grown variety (Cont). An experiment station field was
divided into four quadrants, and the five treatments (i.e. genotypes) were randomly assigned
to five plots within each quadrant:

Block Cont A B C D
I 97 129 137 126 109
II 88 121 154 118 115
III 104 142 145 125 97
IV 94 123 140 110 100

1. Describe the design of this experiment.

2. Test the following assumptions of ANOVA, clearly stating the null hypothesis for each,
and interpret the output:

a. Normality of residuals
b. Homogeneity of variance among treatments
c. Additivity of model effects

3. Present an ANOVA table and indicate if there is a significant yield difference among
genotypes.

4. Present a plot of residual vs. predicted values (the tea leaves!) and comment.

5. Was any information gained by blocking? Provide a value for the efficiency of this
model relative to a CRD.

6. Maintaining the experimentwise error rate (EER) at α = 0.05, use the most appropriate
method to declare which variety (or varieties) outperformed the control.

7. Add 30 pounds to all the yields in Block II. Does this produce any effect on the SST,
MST, or F? Why or why not (one sentence)?
Lecture 1.8.1 – Factorials

A researcher interested in the effect of protein supplements on milk production tests three
different sources of protein (fish meal, soy protein extract, and meat & bone meal) at two
different levels in the diet (Low and High). Each source-level combination of protein was
randomly assigned to 10 goats. The measured gain in milk production in liters is presented:

MBM 143 170 161 189 164 148 123 151 154 161
High Soy 138 129 121 136 144 154 117 88 174 149
Fish 169 157 137 183 174 114 161 186 163 128
MBM 152 166 110 96 129 77 129 114 136 128
Low Soy 117 117 104 140 91 169 149 152 126 154
Fish 80 113 142 149 122 142 120 142 101 136

1. Analyzing this experiment as a 2x3 factorial, determine if there is a significant

interaction between the level of protein and the source of protein.

2. Now you are going to partition the SS found in the above ANOVA. Use contrasts to
answer questions a-e:

a. Are there differences between animal and vegetable sources of protein?

b. Are there differences between animal sources?

c. Compare the two previous SS with the Source SS in the first analysis.

d. Are the differences between animal and vegetable sources different at the two
protein levels?

e. Are the differences between animal sources different at the two protein levels?

f. Compare the two previous SS with the Interaction SS in the first analysis.

g. Discuss how it is possible that one of the components of the interaction is

significant (2.2d) when the total interaction (2.1) is not.