Sample Data from RCB Experiment

Introduction
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Data Manipulation
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Analysis of Variance

Violeta I. Bartolome
Senior Associate Scientist
Crop Research Informatics Laboratory
International Rice Research Institute

Import file to R

mydata <- read.table(

“RCBdata.csv", # name of csv file
sep = ",", # separator
header = TRUE)
 factor () Factor
• factor() is used to encode a vector as • A vector object used to specify a
a factor discrete classification (grouping) of the
• Example components of other vectors of the
same length
• Two types of factor
o Unordered – levels are binary or nominal
o Ordered – levels are quantitative

forward back

levels() aov()

• provides access to the levels • Fit an analysis of variance model

attribute of a variable. • Usage
• Usage: aov(formula, data = NULL)
levels(x) # returns the value of the levels • formula
levels(x) <- value # sets the attribute response ~ mean.formula + Error(strata.formula)
• Example • Model for an RCB single factor design:
 Defining ANOVA Models
aov()
• a+b # additive effects of a and b
• RCB factorial design • a:b # interaction between a and b

• a*b # same as a + b + a:b

• Split-plot design • ^n # includes all interactions up to level n

Ex. (a+b+c)^2 is identical to

• Split-split-plot design a + b + c + a:b + a:c + b:c
• b%in%a # effects of b are nested in a

a/b # identical to a+a:b

• Strip-plot design
• a-b # removes the effect of b

Ex. y~x-1 forces a model without an intercept

summary () residuals()

• generic function used to produce • generic function which extracts

summaries of the results of various model residuals from objects
model fitting functions returned by modeling functions
• Example: • Example:
 predict() coef()

• generic function for predictions from • generic function which extracts

the results of various model fitting model coefficients from objects
functions returned by modeling functions
• Example • Example

df.residual() deviance()

• Returns the residual degrees-of- • Returns the deviance or residual sum

freedom extracted from a fitted of squares of a fitted model object
model object • Example
• Example
 Residual plot
names()

• Function to list the elements in an

object
• Example

Comparing treatment means

• Using agricolae package

library (agricolae)
LSD.test (y, # response variable
trt, # variable whose levels
# are to be compared
DFerror, # error df
MSerror, # Mean Square of error
alpha = 0.05, # level of sig
group=TRUE, # TRUE or FALSE
main = NULL) # Title
HSD.test() can be use if number of treatments is 6 or more.
Bar Graph with mean comparison Split-plot

Source of Variation df
Block r-1
Factor A (A) a-1
Error (a) (r-1)(a-1)
Factor B (B) b-1
AxB (a-1)(b-1)
Error (b) a(r-1)(b-1)
Total rab-1

ANOVA for Split-plot Design SEDs for Split-plot

Type of pair comparison
sed t-value
Number Between

1 Two main-plot means

2E a tinv(α, dfa )
(averaged over all subplot
rb
Error (a) treatments)
2 Two subplot means
2E b tinv ( α, df b )
(averaged over all main-plot
treatments) ra
3 Two subplot means at the 2E b
tinv ( α, df b )
same main-plot treatment
Error (b) r
4 Two main-plot means at the 2[(b−1)E b +E a ]
same or different subplot tinv ( α, df ab )
rb
treatment
 Degrees of freedom and Error MS
Satterthwaite degrees of freedom

dfab =
[Ea + (b − 1) Eb ]2
2
Ea [(b − 1) Eb ]
2
+
dfa dfb

ANOVA for Strip plot design

Strip-plot

Source of Variation df
Block r-1
Horizontal Factor (H) h-1
Error(a)
Error (a) (r-1)(h-1)
Vertical Factor (V) v-1
Error (b) (r-1)(v-1)
Error(b)
HxV (h-1)(v-1)
Error (c) (r-1)(h-1)(v-1)
Total rhv-1
Error(c)
 Satterthwaite degrees of
SEDs for Strip-plot
freedom
Type of pair comparison
sed t-value
df ac =
[Ea + (b − 1) Ec ]2
2
Ea [(b − 1) Ec ]
Number Between 2
+
1 Two horizontal means
df a df c
2E a
(averaged over all vertical tinv ( α, df a )
treatments) rb
2 Two vertical means
2E b tinv ( α, df b )
[Eb + (a − 1) Ec]
dfbc = 2
2

(averaged over all horizontal

Eb [(a − 1) Ec]
ra 2
treatments)
3 Two vertical means at the 2[(a −1)E c + E b ]
+
same horizontal treatment ra
tinv ( α, df bc ) dfb dfc
4 Two horizontal means at the
2[(b −1)E c + E a ]
same vertical treatment tinv ( α, df ac )
rb

Degrees of freedom and EMS