R-SCRIPTS FOR STATISTICAL ANALYSES USING R-STUDIO

Compiled by
Rajender Parsad , B.N. Mandal , A. Dhandapani2, Sukanta Dash1, Eldho Varghese1 and
1 1

D.C. Mishra1
1
ICAR-I.A.S.R.I., Library Avenue, Pusa, New Delhi
2
ICAR-N.A.A.R.M, Rajendra Nagar, Hyderabad

A. Statistical Methods
A.1. Descriptive statistics
Datafile: descriptive.txt
v1 v2 v3 v4
12.4 45.15 1.25 1115.2
13.5 26.15 0.99 1216.4
16.3 78.14 1.63 1426.1
14.9 56.35 1.34 1635.2
14.5 65.21 0.96 1345.6
13.9 63.15 1.26 1248.3
18.2 46.15 0.64 1632.5
16.7 48.23 1.54 1458.6
23.2 86.35 1.48 1752.6
10.9 46.15 1.78 1496.8
23.9 31.25 0.69 1835.6
24.8 48.26 1.16 1934.6
26.1 46.23 1.49 1536.4
24.7 32.56 1.25 1269.7

# R-Script for obtaining Summary Statistics

attach(descriptive)
names(descriptive)
summary(descriptive)
mean1=mean(v1)
mean1
sd1=sd(v1)
sd1
cv1=sd1/mean1*100
cv1
meadian2=median(v2)
meadian2
var(v4)
v4

#obtaining summary using Library DescTools

library(DescTools)
mean(v1)
median(v1)
Mode(v1)

1 

 
sd(v1)
var(v1)
CoefVar(v1)
Skew(v1)
Kurt(v1)
Desc(descriptive)

# Histogram
library(Hmisc)
hist(descriptive,col="red")

# Density Plot
dens =density(descriptive)
plot(dens)

#Box Plot
boxplot(descriptive)

A.2 Tests of Significance

Datafile: test.txt
group X Y Z P
1 7 1.85 147.7 16.86
1 7 1.86 136.86 16.77
1 6 1.83 149.97 16.35
1 7 1.89 172.33 18.26
1 7 1.8 144.46 17.9
1 6 1.88 138.3 16.95
1 7 1.89 150.58 18.15
1 7 1.79 140.99 18.86
1 6 1.85 140.57 18.39
1 7 1.84 138.33 18.58
2 6.3 2.58 224.26 18.18
2 6.7 2.74 197.5 18.07
2 7.3 2.58 230.34 19.07
2 8 2.62 217.05 19
2 8 2.68 233.84 18
2 8 2.56 216.52 18.49
2 7.7 2.34 211.93 17.45
2 7.7 2.67 210.37 18.97
2 7 2.45 199.87 19.31
2 7.3 2.44 214.3 19.36

2 

 
# R-Script for tests of significance
# Single Sample t-test (two-tailed)
attach(test)
names(test)
t.test(X, mu=7)
# t-test for comparing means of two independent populations with unequal variances
t.test(group~X)

# t-test for comparing means of two independent populations with equal variances
t.test(group~Y,var.equal=TRUE)

# Paired t-test
t.test(X,Y,paired=TRUE)
detach(test)

A.3. Correlation
Datafile: correlation.txt
pp ph ngl yld
142 0.525 8.2 2.47
143 0.64 9.5 4.76
107 0.66 9.3 3.31
78 0.66 7.5 1.97
100 0.46 5.9 1.34
86.5 0.345 6.4 1.14
103.5 0.86 6.4 1.5
155.99 0.33 7.5 2.03
80.88 0.285 8.4 2.54
109.77 0.59 10.6 4.9
61.77 0.265 8.3 2.91
79.11 0.66 11.6 2.76
155.99 0.42 8.1 0.59
61.81 0.34 9.4 0.84
74.5 0.63 8.4 3.87
97 0.705 7.2 4.47
93.14 0.68 6.4 3.31
37.43 0.665 8.4 1.57
36.44 0.275 7.4 0.53
51 0.28 7.4 1.15
104 0.28 9.8 1.08
49 0.49 4.8 1.83
54.66 0.385 5.5 0.76
55.55 0.265 5 0.43
88.44 0.98 5 4.08
99.55 0.645 9.6 2.83
63.99 0.635 5.6 2.57
101.77 0.29 8.2 7.42
138.66 0.72 9.9 2.62
90.22 0.63 8.4 2
3 

 
76.92 1.25 7.3 1.99
126.22 0.58 6.9 1.36
80.36 0.605 6.8 0.68
150.23 1.19 8.8 5.36
56.5 0.355 9.7 2.12
136 0.59 10.2 4.16
144.5 0.61 9.8 3.12
157.33 0.605 8.8 2.07
91.99 0.38 7.7 1.17
121.5 0.55 7.7 3.62
64.5 0.32 5.7 0.67
116 0.455 6.8 3.05
77.5 0.72 11.8 1.7
70.43 0.625 10 1.55
133.77 0.535 9.3 3.28
89.99 0.49 9.8 2.69

# R-Script for Correlation

attach(correlation)
names(correlation)
# Correlation among all possible pairs of variables
cor(correlation, method="pearson")

# Correlation between specific pairs of variables

corr=cor.test(pp,ph)
str(corr)

# Testing the significance of Correlation Coefficient

corr$statistic
corr$p.value
corr$conf.int
detach(correlation)

A.4. Regression Analysis

Datafile: reg.txt
Y X1 X2 X3
2.76 79.11 0.66 11.6
0.59 155.99 0.42 8.1
0.84 61.81 0.34 9.4
3.87 74.5 0.63 8.4
4.47 97 0.705 7.2
3.31 93.14 0.68 6.4
1.57 37.43 0.665 8.4
0.53 36.44 0.275 7.4
1.15 51 0.28 7.4
1.08 104 0.28 9.8
1.83 49 0.49 4.8
0.76 54.66 0.385 5.5
4 

 
 0.43 55.55 0.265 5
4.08 88.44 0.98 5
2.83 99.55 0.645 9.6
2.57 63.99 0.635 5.6
7.42 101.77 0.29 8.2
2.62 138.66 0.72 9.9
2 90.22 0.63 8.4
1.99 76.92 1.25 7.3
1.36 126.22 0.58 6.9
0.68 80.36 0.605 6.8
5.36 150.23 1.19 8.8
2.12 56.5 0.355 9.7
4.16 136 0.59 10.2
3.12 144.5 0.61 9.8
2.07 157.33 0.605 8.8
1.17 91.99 0.38 7.7
3.62 121.5 0.55 7.7
0.67 64.5 0.32 5.7
3.05 116 0.455 6.8
1.7 77.5 0.72 11.8
1.55 70.43 0.625 10

# R-Script for Regression Analysis

attach(reg)
names(reg)
lm1 =lm(Y~X1+X2+X3, reg)
summary(lm1)
plot(lm1)

#Test for Non-Constant Variance - quick way from fitted values as in lm1
summary(lm(abs(residuals(lm1)) ~ fitted(lm1)))

# Testing the Normality Residuals Using Shapiro-Wilk Test

hist(residuals(lm1))
boxplot(residuals(lm1))
shapiro.test(residuals(lm1))
#test of independence of residuals using Durbin Watson test
library("lmtest")
dwtest(lm1)

#influential observations using Hat matrix

influence1 =influence(lm1)
summary(influence1)
summary(influence1$hat)

5 

 
# Looking for multi-collinearity
library(car)
vif(lm1)
detach(reg)

B. Design of Experiments
B.1. Completely Randomized Designs
datafile: crd.txt
trt yield
1 850.5
1 453.6
1 878.85
1 623.7
1 510.3
1 765.45
1 680.4
1 595.35
1 538.65
1 850.5
1 850.5
1 793.8
1 1020.6
1 708.75
1 652.05
1 623.7
1 396.9
1 822.15
1 680.4
1 652.05
1 538.65
1 850.5
1 680.4
2 510.3
2 963.9
2 652.05
2 1020.6
2 878.85
2 567
2 680.4
2 538.65
2 567
2 510.3
2 425.25
2 567
2 623.7
2 538.65
2 737.1
2 453.6
6 

 
2 481.95
2 368.55
2 567
2 595.35
2 567
2 595.35
3 992.25
3 850.5
3 1474.2
3 510.3
3 850.5
3 793.8
3 453.6
3 935.55
3 1190.7
3 481.95
3 623.7
3 878.85
3 1077.3
3 850.5
3 680.4
3 737.1
3 737.1
3 708.75
3 708.75
3 652.05
3 567
3 453.6
3 652.05
3 567
# R-Script for CRD
attach(crd)
names(crd)
trt=factor(trt)
lm1=lm(yield~trt)
anova(lm1)
library(lsmeans)
lsm=lsmeans(lm1,"trt")
lsm
pairs(lsm)
#pairs statement is an optional statement
#to provide letters for groups, need to install multcompView
library(multcompView)
cld(lsm,Letters="abc")
detach(crd)

7 

 
B.2. Randomized Complete Block Designs
Datafile: rbd.txt
trt blk yield
1 1 1539.69
2 1 1261.85
3 1 1389.19
4 1 1192.39
5 1 1250.27
6 1 1296.58
7 1 1227.12
8 1 1273.43
9 1 1180.82
10 1 1296.58
11 1 1122.93
12 1 1250.27
13 1 1180.82
14 1 1146.09
15 1 1574.42
16 1 914.55
17 1 891.4
18 1 1227.12
19 1 1389.19
20 1 1331.31
21 1 1250.27
22 1 717.75
23 1 1169.24
24 1 1203.97
1 2 1412.35
2 2 1065.05
3 2 1516.54
4 2 1215.55
5 2 1203.97
6 2 1273.43
7 2 1018.74
8 2 1157.66
9 2 1203.97
10 2 1458.65
11 2 1065.05
12 2 926.13
13 2 1053.47
14 2 1180.82
15 2 1412.35
16 2 972.44
17 2 937.71
18 2 1203.97
19 2 1180.82
20 2 1157.66
21 2 1250.27
22 2 740.9
8 

 
23 2 1157.66
24 2 1296.58
1 3 1319.73
2 3 1111.36
3 3 1203.97
4 3 1157.66
5 3 1366.04
6 3 1308.16
7 3 937.71
8 3 1088.2
9 3 1041.9
10 3 1250.27
11 3 1018.74
12 3 1030.32
13 3 717.75
14 3 856.67
15 3 1597.57
16 3 659.87
17 3 798.79
18 3 1389.19
19 3 1273.43
20 3 1180.82
21 3 1296.58
22 3 578.83
23 3 1111.36
24 3 1250.27

# R-Script for RCB Design (it is same for any block design)
attach(rbd)
names(rbd)
trt=factor(trt)
blk=factor(blk)
lm1=lm(yield~trt+blk)
anova(lm1)
library(lsmeans)
lsm=lsmeans(lm1,"trt")
lsm
pairs(lsm)
#pairs statement is an optional statement
#to provide letters for groups, need to install multcompView
library(multcompView)
cld(lsm, Letters="abcdefghij")
detach(rbd)

9 

 
B.3. Resolvable Block Designs
datafile: resolvable.txt
rep blk trt syield
1 1 1 1555.6
1 1 5 1160.5
1 1 9 1308.6
1 1 13 1382.7
1 1 17 987.7
1 1 21 1135.8
1 2 2 1284
1 2 6 1086.4
1 2 10 1284
1 2 14 1111.1
1 2 18 938.3
1 2 22 1308.6
1 3 3 1234.6
1 3 7 419.8
1 3 11 1308.6
1 3 15 963
1 3 19 963
1 3 23 987.7
1 4 4 1234.6
1 4 8 987.7
1 4 12 1284
1 4 16 913.6
1 4 20 1160.5
1 4 24 790.1
2 1 1 1481.5
2 1 6 1086.4
2 1 11 1308.6
2 1 16 1284
2 1 19 1111.1
2 1 22 1185.2
2 2 2 987.7
2 2 7 308.6
2 2 12 1234.6
2 2 13 1308.6
2 2 20 765.4
2 2 23 938.3
2 3 3 1012.3
2 3 8 864.2
2 3 9 1234.6
2 3 14 938.3
2 3 17 913.6
2 3 24 864.2
2 4 4 1135.8
2 4 5 987.7
2 4 10 987.7
2 4 15 740.7

10 

 
2 4 18 963
2 4 21 1135.8
3 1 1 1284
3 1 7 333.3
3 1 12 1135.8
3 1 15 839.5
3 1 18 814.8
3 1 24 888.9
3 2 2 1135.8
3 2 8 913.6
3 2 9 1456.8
3 2 16 1037
3 2 19 938.3
3 2 21 1037
3 3 3 963
3 3 5 1209.9
3 3 10 1259.3
3 3 13 1234.6
3 3 20 963
3 3 22 1111.1
3 4 4 1086.4
3 4 6 765.4
3 4 11 1111.1
3 4 14 1037
3 4 17 938.3
3 4 23 938.3

# R-Script for Resolvable block design or alpha design (infact similar steps can be used
for nested block designs)
attach(resolvable)
names(resolvable)
trt=factor(trt)
rep=factor(rep)
blk=factor(blk)
lm1=lm(syield~trt+blk+rep/blk-blk)
#anova(lm1)
library(car)
Anova(lm1,type="III")
library(lsmeans)
lsm=lsmeans(lm1,"trt")
lsm
pairs(lsm)
#pairs statement is an optional statement
#to provide letters for groups, need to install multcompView
library(multcompView)
cld(lsm,Letters="abcdefghij")
detach(resolvable)

11 

 
B.4: Latin Square Design (steps are similar for any row-column design)
Datafile: latin.txt
row col trt yield
1 1 3 3.1
1 2 6 5.95
1 3 1 1.75
1 4 5 6.4
1 5 2 3.85
1 6 4 5.3
2 1 2 4.8
2 2 1 2.7
2 3 3 3.3
2 4 6 5.95
2 5 4 3.7
2 6 5 5.4
3 1 1 3
3 2 2 2.95
3 3 5 6.7
3 4 4 5.95
3 5 6 7.75
3 6 3 7.1
4 1 5 6.4
4 2 4 5.8
4 3 2 3.8
4 4 3 6.55
4 5 1 4.8
4 6 6 9.4
5 1 6 5.2
5 2 3 4.85
5 3 4 6.6
5 4 2 4.6
5 5 5 7
5 6 1 5
6 1 4 4.25
6 2 5 6.65
6 3 6 9.3
6 4 1 4.95
6 5 3 9.3
6 6 2 8.4

# R-Script for Latin Square Design (steps are similar for any row-column design) 
attach(latin)
names(latin)
row=factor(row)
col=factor(col)
trt=factor(trt)
lm1=lm(yield~trt+row+col)
anova(lm1)
12 

 
library(lsmeans)
lsm=lsmeans(lm1,"trt")
lsm
pairs(lsm)
#pairs statement is an optional statement
#to provide letters for groups, need to install multcompView
library(multcompView)
cld(lsm, Letters="abcdefghij")
detach(latin)

B.5 Treatment Contrast Analysis in a Block Design (similarly one can write contrasts
for any design
datafile: tree1.txt
rep trt height
1 1 144.44
1 2 113.5
1 3 60.88
1 4 163.44
1 5 110.11
1 6 260.05
1 7 114
1 8 91.94
1 9 156.11
1 10 80.2
2 1 145.11
2 2 118.61
2 3 90.94
2 4 158.55
2 5 116
2 6 102.27
2 7 115.16
2 8 58.16
2 9 177.97
2 10 108.05
3 1 104
3 2 118.61
3 3 80.33
3 4 158.88
3 5 119.66
3 6 256.22
3 7 114.88
3 8 76.83
3 9 148.22
3 10 45.18
4 1 105.44
4 2 123
13 

 
4 3 92
4 4 153.11
4 5 103.22
4 6 217.8
4 7 106.33
4 8 79.5
4 9 183.17
4 10 79.55

# R-Script for Treatment Contrast Analysis (steps are similar for any design) 
attach(tree1)
names(tree1)
tree=factor(trt)
rep=factor(rep)
lm1=lm(height~rep+tree)
anova(lm1)
#contrast analysis
library(lsmeans)
lsm = lsmeans(lm1, "tree")
lsm
pairs(lsm)
#pairs statement is an optional statement
#For grouping of treatments with letters, you need to install multcompView package and run
the following code
cld(lsm,Letters="ABCDEFGHI", sort="false")
contrast(lsm, list(con1 = c(1,1,1,1,-1,-1,-1,-1,-1,1),con2 = c(9,-1,-1,-1,-1,-1,-1,-1,-1,-1),con3
= c(1,1,1,1,0,0,0,0,-4,0),con4 = c(1,1,1,1,0,0,0,0,0,-4),con5 = c(0,0,0,0,1,1,1,1,-4,0),con6 =
c(0,0,0,0,1,1,1,1,0,-4)))
detach(tree1)

B.6. Analysis of Covariance in RCB Design

Datafile: ANCOVA.txt
trt rep x y
1 1 5 2
2 1 6 4
3 1 5 4
4 1 6 3
5 1 7 7
6 1 6 4
7 1 6 3
8 1 6 6
9 1 7 4
10 1 7 7
11 1 6 5
12 1 6 5
13 1 5 4
14 1 5 5
14 

 
15 1 5 4
1 2 6 3
2 2 5 3
3 2 5 4
4 2 5 3
5 2 7 6
6 2 5 3
7 2 5 3
8 2 7 7
9 2 5 3
10 2 7 7
11 2 5 4
12 2 5 3
13 2 5 4
14 2 5 4
15 2 5 5
1 3 6 4
2 3 5 3
3 3 5 3
4 3 5 3
5 3 6 6
6 3 5 3
7 3 6 3
8 3 6 6
9 3 5 4
10 3 5 6
11 3 5 5
12 3 5 3
13 3 6 5
14 3 5 3
15 3 6 6

# R-Script for ANCOVA in RCB Design (steps are similar for any design)
attach(ANCOVA) 
trt=factor(trt)
#ancova with class variable treatments and contiuous initial body weight variable
lm3=lm(y~trt+rep+x)
anova(lm3)
library(lsmeans)
lsm=lsmeans(lm3,"trt")
lsm
pairs(lsm)
#pairs statement is an optional statement
Library(multcompView)
cld(lsm,Letters="abcdefgh")
detach(ANCOVA)

15 

 
B.7 Randomized Complete Block Design with Factorial Treatment Structure (Factorial
RCB Design)
Datafile: fact.txt
REP FYM P PSB TRT Yield
1 1 1 1 1 0.7
1 1 1 2 2 1.13
1 1 2 1 3 1.23
1 1 2 2 4 1.25
1 1 3 1 5 1.25
1 1 3 2 6 1.25
1 2 1 1 7 0.83
1 2 1 2 8 1.23
1 2 2 1 9 1.18
1 2 2 2 10 0.88
1 2 3 1 11 1.63
1 2 3 2 12 1.48
2 1 1 1 1 0.98
2 1 1 2 2 1.13
2 1 2 1 3 1.18
2 1 2 2 4 1.13
2 1 3 1 5 1.26
2 1 3 2 6 1.25
2 2 1 1 7 0.93
2 2 1 2 8 0.88
2 2 2 1 9 1.5
2 2 2 2 10 1.3
2 2 3 1 11 1.38
2 2 3 2 12 1.43
3 1 1 1 1 0.9
3 1 1 2 2 1.1
3 1 2 1 3 1.1
3 1 2 2 4 0.88
3 1 3 1 5 1.35
3 1 3 2 6 1.35
3 2 1 1 7 1.1
3 2 1 2 8 1.03
3 2 2 1 9 1.3
3 2 2 2 10 0.88
3 2 3 1 11 1.38
3 2 3 2 12 1.43
4 1 1 1 1 0.73
4 1 1 2 2 1.25
4 1 2 1 3 1.43
4 1 2 2 4 1.25
4 1 3 1 5 1.1
4 1 3 2 6 1.75
16 

 
4 2 1 1 7 0.98
4 2 1 2 8 1.38
4 2 2 1 9 1.35
4 2 2 2 10 1.43
4 2 3 1 11 1.3
4 2 3 2 12 1.5

# R-Script for Factorial RCB Design (steps are similar for partially confounded
factorial experiments) 
attach(fact)
names(fact)
rep=factor(REP)
fym=factor(FYM)
p=factor(P)
psb=factor(PSB)
lm1=lm(Yield~rep+fym+p+psb+fym:p+fym:psb+p:psb+fym:p:psb)
lm1
anova(lm1)
library(lsmeans)
lsm1=lsmeans(lm1,"fym")
lsm1
#All pairs statement are optional
pairs(lsm1)
lsm2=lsmeans(lm1,"p")
lsm2
pairs(lsm2)
lsm3=lsmeans(lm1,"psb")
lsm3
pairs(lsm3)
lsm4=lsmeans(lm1,~fym:p)
lsm4
pairs(lsm4)
lsm5=lsmeans(lm1,~fym:psb)
lsm5
pairs(lsm5)
lsm6=lsmeans(lm1,~p:psb)
lsm6
pairs(lsm6)
lsm7=lsmeans(lm1,~fym:p:psb)
lsm7
pairs(lsm7)
#to provide letters for groups, need to install multcompView
library(multcompView)
cld(lsm1, Letters="ABCDEF")
cld(lsm2, Letters="ABCDEF")
cld(lsm3,Letters="ABCDEF")
cld(lsm4,Letters="ABCDEFGHI")
cld(lsm5,Letters="ABCDEFGHI")
17 

 
cld(lsm6,Letters="ABCDEFGHI")
cld(lsm7,Letters="ABCDEFGHIJKLM")
detach(fact)

B.8: Fractional factorial Experiments

Datafile: fractional.txt
trt A B C D E F X
(1) 0 0 0 0 0 0 15
ab 1 1 0 0 0 0 4
ac 1 0 1 0 0 0 7
ad 1 0 0 1 0 0 12
ae 1 0 0 0 1 0 13
af 1 0 0 0 0 1 15
bc 0 1 1 0 0 0 17
bd 0 1 0 1 0 0 5
be 0 1 0 0 1 0 6
bf 0 1 0 0 0 1 14
cd 0 0 1 1 0 0 9
ce 0 0 1 0 1 0 12
cf 0 0 1 0 0 1 11
de 0 0 0 1 1 0 5
df 0 0 0 1 0 1 13
ef 0 0 0 0 1 1 6
abcd 1 1 1 1 0 0 3
abce 1 1 1 0 1 0 11
abcf 1 1 1 0 0 1 6
abde 1 1 0 1 1 0 4
abdf 1 1 0 1 0 1 10
abef 1 1 0 0 1 1 4
acde 1 0 1 1 1 0 9
acdf 1 0 1 1 0 1 1
acef 1 0 1 0 1 1 8
adef 1 0 0 1 1 1 1
bcde 0 1 1 1 1 0 6
bcdf 0 1 1 1 0 1 10
bdef 0 1 0 1 1 1 5
bcef 0 1 1 0 1 1 2
cdef 0 0 1 1 1 1 1
abcdef 1 1 1 1 1 1 5

# R-Script for Fractional Factorial Experiments for Estimating Main Effects and Two-
factor Interactions  
attach(fractional)
names(fractional)
a=factor(A)
b=factor(B)
c=factor(C)
d=factor(D)
e=factor(E)
18 

 
f=factor(F)
lm1=lm(X~a+b+c+d+e+f+a:b+a:c+a:d+a:e+a:f+b:c+b:d+b:e+b:f
+c:d+c:e+c:f+d:e+d:f+e:f)
anova(lm1)

library(lsmeans)
lsm1=lsmeans(lm1,"a")
lsm1
#All pairs statement are optional
pairs(lsm1)
lsm2=lsmeans(lm1,"b")
lsm2
pairs(lsm2)
lsm3=lsmeans(lm1,"c")
lsm3
pairs(lsm3)
lsm4=lsmeans(lm1,"d")
lsm4
pairs(lsm4)
lsm5=lsmeans(lm1,"e")
lsm5
pairs(lsm5)
lsm6=lsmeans(lm1,"f")
lsm6
pairs(lsm6)
lsm7=lsmeans(lm1,~a:b)
lsm7
pairs(lsm7)
lsm8=lsmeans(lm1,~a:c)
lsm8
pairs(lsm8)
lsm9=lsmeans(lm1,~a:d)
lsm9
pairs(lsm9)
lsm10=lsmeans(lm1,~a:e)
lsm10
pairs(lsm10)
lsm11=lsmeans(lm1,~a:f)
lsm11
pairs(lsm11)
lsm12=lsmeans(lm1,~b:c)
lsm12
pairs(lsm12)
lsm13=lsmeans(lm1,~b:d)
lsm13
pairs(lsm13)
lsm14=lsmeans(lm1,~b:e)
lsm14
pairs(lsm14)

19 

 
lsm15=lsmeans(lm1,~b:f)
lsm15
pairs(lsm15)
lsm16=lsmeans(lm1,~c:d)
lsm16
pairs(lsm16)
lsm17=lsmeans(lm1,~c:e)
lsm17
pairs(lsm17)
lsm18=lsmeans(lm1,~c:f)
lsm18
pairs(lsm18)
lsm19=lsmeans(lm1,~d:e)
lsm19
pairs(lsm19)
lsm20=lsmeans(lm1,~d:f)
lsm20
pairs(lsm20)
lsm21=lsmeans(lm1,~e:f)
lsm21
pairs(lsm21)
library(multcompView)
cld(lsm1,Letters="ab")
cld(lsm2,Letters="ab")
cld(lsm3,Letters="ab")
cld(lsm4,Letters="ab")
cld(lsm5,Letters="ab")
cld(lsm6,Letters="ab")
cld(lsm7,Letters="abcd")
cld(lsm8,Letters="abcd")
cld(lsm9,Letters="abcd")
cld(lsm10,Letters="abcd")
cld(lsm11,Letters="abcd")
cld(lsm12,Letters="abcd")
cld(lsm13,Letters="abcd")
cld(lsm14,Letters="abcd")
cld(lsm15,Letters="abcd")
cld(lsm16,Letters="abcd")
cld(lsm17,Letters="abcd")
cld(lsm18,Letters="abcd")
cld(lsm19,Letters="abcd")
cld(lsm20,Letters="abcd")
cld(lsm21,Letters="abcd") 

20 

 
B.9: Split Plot Design
Datafile: plots in the package library
library(agricolae)
data(plots)
str(plots)
plots[,1] <-as.factor(plots[,1])
# split-plot analysis
model <- aov(yield ~ block + A + Error(plot)+ B + A:B, data=plots)
summary(model)
attach(plots)
b<-nlevels(B)
a<-nlevels(A)
r<-nlevels(block)
dfa <- df.residual(model$plot)
Ea <-deviance(model$plot)/dfa
dfb <- df.residual(model$Within)
Eb <-deviance(model$Within)/dfb
Eab <- (Ea +(b-1)*Eb)/(b*r)
#dfab<-(Ea +(b-1)*Eb)^2/(Ea^2/dfa +((b-1)*Eb)^2/dfb)
# Comparison A, A(b1), A(b2), A(b3)
title1= "CD at 5% for main plot means"
comparison1 <-LSD.test(yield,A,dfa,Ea)
title1
Comparison1
title2="CD at 5% for sub plot means"
comparison2 <-LSD.test(yield,B,dfb,Eb)
title2
comparison2
title3="CD at 5% for sub plot means at same level main plot"
sd3=sqrt(2*Eb/r)
cd3=qt(0.975,dfb)*sd3
title3
cd3
#comparison6 <-LSD.test(yield[A=="a1"],B[A=="a1"],dfb,Eb)
#comparison7 <-LSD.test(yield[A=="a2"],B[A=="a2"],dfb,Eb)
#comparison8 <-LSD.test(yield[B=="b1"],A[B=="b2"],dfab,Eab)
title4= "calculation Main Plot Means at same or different levels of subplot treatment"
ab <- sqrt(2*((b-1)*Eb+Ea)/(b*r))
tval <- ((b-1)*Eb*qt(0.975,dfb)+Ea*qt(0.975,dfa))/((b-1)*Eb + Ea)
title4=
CD4 <- ab*tval
title4
CD4
plots
detach(plots)

21 

 
B.10: Strip Plot Design
Datafile: STRIP.txt
rep A B yield
1 1 1 103.6
1 1 2 126.25
1 1 3 115.39
1 2 1 103.8
1 2 2 119.32
1 2 3 106.4
1 3 1 138.3
1 3 2 132.81
1 3 3 128.9
2 1 1 91.65
2 1 2 103.3
2 1 3 101.56
2 2 1 116.65
2 2 2 125.4
2 2 3 144.65
2 3 1 106.6
2 3 2 129.35
2 3 3 138.3
3 1 1 126.91
3 1 2 119.9
3 1 3 134.19
3 2 1 131.19
3 2 2 119.73
3 2 3 127.11
3 3 1 125.8
3 3 2 113.8
3 3 3 125.35
4 1 1 129.61
4 1 2 118.39
4 1 3 123
4 2 1 120.81
4 2 2 120.26
4 2 3 125.6
4 3 1 104.71
4 3 2 135.6
4 3 3 114.31
5 1 1 128.29
5 1 2 129.4
5 1 3 123.71
5 2 1 131.29
5 2 2 122.85
5 2 3 138.2
5 3 1 123.31
5 3 2 142.71
5 3 3 152.21
6 1 1 121.06

22 

 
6 1 2 112.95
6 1 3 115.91
6 2 1 119.6
6 2 2 122.45
6 2 3 126.61
6 3 1 126.96
6 3 2 130.94
6 3 3 131.7
#R Script for Strip Plot Design

attach(STRIP)
names(STRIP)
block=factor(rep)
A=factor(A)
B=factor(B)
library(agricolae)
model<-strip.plot(block, A, B, yield)
Ea = model$Ea
Eb = model$Eb
Ec = model$Ec
b<-nlevels(A)
a<-nlevels(B)
r<-nlevels(block)
dfa = model$gl.a
dfb = model$gl.b
dfc = model$gl.c

#CD Vertical Plot means

vsed = sqrt(2*Ea/(r*b))
cd1 = vsed * qt(0.975,dfa)

#CD Horizontal Plot means

hsed = sqrt(2*Eb/(r*a))
cd2 = hsed *qt(0.975,dfb)

#Two vertical plot means at same or different levels of horizontal plot means
sd1 = sqrt(2*((b-1)*Ec+Ea)/(r*b))
twb = ((b-1)*Ec*qt(0.975,dfc)+Ea*qt(0.975,dfa))/((b-1)*Ec+Ea)
cd3 = sd1*twb

# Two horizontal plot means at same or different levels of vertical plot means
sd2 = sqrt(2*((a-1)*Ec+Eb)/(r*a))
twa = ((a-1)*Ec+qt(0.975,dfc)+Eb*qt(0.975,dfb))/((a-1)*Ec+Eb)
cd4 =sd2*twa
title1 = "CD for vertical plot means"
title1
cd1
title2 = "CD for horizontal plot means"
title2

23 

 
cd2
title3 = "CD two vertical plot means at the same or different levels of horizontal plot means"
title3
cd3
title4 = "CD for horizontal plot means at the same or different levels of vertical plot means"
title4
cd4
detach(STRIP)

B.11: Groups of Experiments conducted across locations in a block design

datafile: COMINED2.txt
loc rep varn syield
1 1 1 1794
1 1 2 1134
1 1 3 718
1 1 4 1852
1 1 5 2245
1 1 6 1111
1 1 7 1181
1 1 8 1644
1 1 9 1551
1 1 10 1968
1 1 11 2662
1 1 12 1065
1 2 1 2014
1 2 2 1736
1 2 3 764
1 2 4 1551
1 2 5 2361
1 2 6 1065
1 2 7 880
1 2 8 1991
1 2 9 1435
1 2 10 1551
1 2 11 2338
1 2 12 1227
1 3 1 2581
1 3 2 1898
1 3 3 880
1 3 4 1887
1 3 5 2407
1 3 6 1111
1 3 7 1528
1 3 8 2060
1 3 9 1991
1 3 10 2569
1 3 11 3056
1 3 12 1343
2 1 1 2600

24 

 
2 1 2 3289
2 1 3 2756
2 1 4 2600
2 1 5 2689
2 1 6 2578
2 1 7 3178
2 1 8 3244
2 1 9 2444
2 1 10 3156
2 1 11 2667
2 1 12 2689
2 2 1 2444
2 2 2 2667
2 2 3 2511
2 2 4 2444
2 2 5 2422
2 2 6 2400
2 2 7 3044
2 2 8 2911
2 2 9 2222
2 2 10 2978
2 2 11 2267
2 2 12 2444
2 3 1 2711
2 3 2 2889
2 3 3 2400
2 3 4 2222
2 3 5 2444
2 3 6 2222
2 3 7 2889
2 3 8 3111
2 3 9 2667
2 3 10 2756
2 3 11 2111
2 3 12 2289
3 1 1 3286
3 1 2 2518
3 1 3 757
3 1 4 2553
3 1 5 2908
3 1 6 1797
3 1 7 1749
3 1 8 1501
3 1 9 1513
3 1 10 2447
3 1 11 2600
3 1 12 1631
3 2 1 2459
3 2 2 2364

25 

 
3 2 3 993
3 2 4 2388
3 2 5 2482
3 2 6 1560
3 2 7 1537
3 2 8 2317
3 2 9 1608
3 2 10 2459
3 2 11 2884
3 2 12 1466
3 3 1 3286
3 3 2 2364
3 3 3 875
3 3 4 2884
3 3 5 2884
3 3 6 2033
3 3 7 1537
3 3 8 2577
3 3 9 2104
3 3 10 2813
3 3 11 2648
3 3 12 1844
4 1 1 1370
4 1 2 904
4 1 3 858
4 1 4 904
4 1 5 1438
4 1 6 873
4 1 7 848
4 1 8 1668
4 1 9 910
4 1 10 1558
4 1 11 1508
4 1 12 1280
4 2 1 1209
4 2 2 729
4 2 3 942
4 2 4 959
4 2 5 1456
4 2 6 959
4 2 7 639
4 2 8 1770
4 2 9 907
4 2 10 1606
4 2 11 1389
4 2 12 1207
4 3 1 1320
4 3 2 1007
4 3 3 839

26 

 
4 3 4 1155
4 3 5 1695
4 3 6 946
4 3 7 643
4 3 8 1607
4 3 9 1081
4 3 10 1705
4 3 11 1447
4 3 12 1256
5 1 1 2233
5 1 2 2222
5 1 3 2000
5 1 4 2667
5 1 5 2444
5 1 6 1778
5 1 7 1778
5 1 8 3000
5 1 9 1778
5 1 10 3778
5 1 11 3111
5 1 12 2222
5 2 1 2222
5 2 2 2444
5 2 3 1778
5 2 4 3289
5 2 5 2000
5 2 6 1889
5 2 7 1722
5 2 8 2889
5 2 9 1611
5 2 10 3667
5 2 11 3111
5 2 12 2000
5 3 1 2222
5 3 2 2722
5 3 3 1778
5 3 4 3333
5 3 5 2000
5 3 6 1556
5 3 7 1722
5 3 8 3222
5 3 9 1333
5 3 10 3556
5 3 11 3222
5 3 12 2222
6 1 1 1666
6 1 2 1611
6 1 3 1389
6 1 4 1511

27 

 
6 1 5 1644
6 1 6 1833
6 1 7 1788
6 1 8 1644
6 1 9 1889
6 1 10 2000
6 1 11 944
6 1 12 1488
6 2 1 1333
6 2 2 1389
6 2 3 1244
6 2 4 1778
6 2 5 1622
6 2 6 1822
6 2 7 2333
6 2 8 2220
6 2 9 1822
6 2 10 1556
6 2 11 388
6 2 12 1400
6 3 1 2222
6 3 2 1944
6 3 3 2056
6 3 4 1889
6 3 5 1711
6 3 6 2111
6 3 7 1711
6 3 8 2220
6 3 9 2444
6 3 10 1356
6 3 11 722
6 3 12 1356

#R-Script for Groups of Experiments

attach(COMBINED2)
names(COMBINED2)
loc=factor(loc)
levels(loc)
varn=factor(varn)
rep=factor(rep)

#Individual Analysis
out=by(COMBINED2,COMBINED2[,"loc"],function(x)
aov(syield~factor(rep)+factor(varn),data=x))
out=as.list(out)
sapply(out,summary)
lapply(out,TukeyHSD,"factor(varn)")
MSE=sapply(1:6,function(i,out) sum(out[[i]]$residual^2)/out[[i]]$df.residual,out)

28 

 
residfs=sapply(1:6,function(i,out) out[[i]]$df.residual,out)

#Check homogeneity of error variances across locations

bartlett.test(out)

#Transform the observations as variances are heterogeneous

tsyield=unlist(tapply(syield,loc,function(syield,MSE) syield/sqrt(MSE),MSE))

#for combined anova

lm2=lm(tsyield~loc+varn+loc/rep-rep+loc:varn)
anova(lm2)
library(lsmeans)
lsm1=lsmeans(lm2,"varn")
cld(lsm1, Letters="abcdefghijklmn")

#Obtaining AMMI Biplot

library(agricolae)
model<- AMMI(loc, varn, rep, tsyield)
# biplot PC2 vs PC1
model$biplot
plot(model)
detach(COMBINED2)
B.12: Response Surface Methodology
Datafile: rsd.txt
N S yield
0 0 4121.212
0 20 4678.03
0 40 4742.424
0 60 4727.273
50 0 6083.333
50 20 6041.667
50 40 6223.485
50 60 6715.909
100 0 6761.364
100 20 6916.667
100 40 6852.273
100 60 6810.606
150 0 6174.242
150 20 7022.727
150 40 7003.788
150 60 6943.182

# R-Script for Response Surface Methodology

# Package required is "rsm"
/* response surface analysis*/
/* FO = first order model and SO =second order model*/
library(rsm)

29 

 
attach(rsd)
anal= rsm(yield~ SO(N,S), data=rsd)
summary(anal)
detach(rsd)

B.13: Experiments With Mixtures Methodology

Datafile: mixture.txt
x1 x2 x3 Yield
1 0 0 11.2
0.75 0.25 0 12.33
0.75 0 0.25 14.04
0.5 0.5 0 16.41
0.5 0 0.5 18.26
0.5 0.25 0.25 16.89
0.25 0.75 0 18.22
0.25 0.5 0.25 19.42
0 1 0 20.61
0 0.75 0.25 19.93
0 0.5 0.5 20.77

# R-Script for Mixture Experiments

attach(mixture
names(mixture)
fit=lm(Yield~x1+x2+x3+x1:x2+x1:x3+x2:x3)
summary(fit)
coefficients(fit)
confint(fit, level=0.95)
fitted(fit)
residuals(fit)
anova(fit)
vcov(fit)
influence(fit)
detach(mixture)

Note: In analysis of data generated from designed experiments, the R Scripts given above,
makes use of lm and library(lsmeans) and library(multcompView). In these scripts, the
adjusted means for treatment effects are obtained. In case of balanced and orthogonal
designs, the adjusted means are same as original means. For multiple comparison procedure,
the default option used is Tukey's Honest Significant Difference Test at 5% level of
significance. If one is analysing data from balanced and orthogonal designs, then one may use
different options for multiple comparisons in agricolae R Package.

30 

 
C. Non-parametric Tests (For More Details on Examples, please refer to
lecture notes)
C.1. Binomial test
Suppose for example x= 8 and n=38, the test is as follows:
R Script:
binom.test(8, 38, p = 0.5)

C.2. Chi-square Test for Goodness of Fit

A random sample of students enrolled in Statistics 101 at ABC University was taken. It
consists of the following: there are 25 freshman in the sample, 32 sophomores, 18 juniors,
and 20 seniors. Test the null hypothesis that freshman, sophomores, juniors, and seniors are
equally represented among students signed up for Stat 101.

(a) R Script (This is a goodness of fit test with equal expected frequencies):
chisq.test(c(25,32,18,20))
(b) R Script (This is a goodness of fit test with unequal expected frequencies):
ofs <- c(25,32,18,20)
null.probs <- c(1/3,1/3,1/6,1/6)
chisq.test(ofs, p=null.probs)

C.3. Chi-square Test for Independence of Attributes

R-Script:
library(MASS) # load the MASS package
attach(survey)
tbl = table(survey$Smoke, survey$Exer)
tbl # the contingency table

Freq None Some

Heavy 7 1 3
Never 87 18 84
Occas 12 3 4
Regul 9 1 7

chisq.test(tbl)

C.4. Run test

First download and install the package named lawstat .
Then use runs.test(x)

R Script:
y<-c(5.2, 5.5,3.8,2.5,8.3,2.1,1.7,10,10,6.9,7.5,10.6)
runs.test(y)

C.5. Median test

R Script
x1 <- c(1.1, 2.1, 1.7, 1.6, 1.9, 1.3)
x2 <- c(1.0, 1.2, 0.7, 0.6, 0.9, 0.5)
m <- median(c(x1,x2)) # joint median
f11 <- sum(x1>m) # Pop.1 samples above median
31 

 
f12 <- sum(x2>m)
f21 <- sum(x1<=m) # Pop.1 samples below or at median
f22 <- sum(x2<=m)
table <- matrix(c(f11,f12,f21,f22), nrow=2,ncol=2) # 2x2 contingency table
chisq.test(table)

C.6. Wilcoxon Signed Rank Test for Matched Pairs

First load the package named ‘exactRankTests’

R Script:
b<-c(80,80,92,79,92,82,88,89,92,83)
a<-c(86,84,78,90,92,77,89,90,90,86)
wilcox.exact(a,b, paired = TRUE, alternative = "two.sided")

C.7. Kolmogorov-Smirnov Two Sample Test

R Script:
a<-c(40,30,40,45,55,30 )
b<-c(50,50,45,55,60,40 )
ks.test(a,b)

C.8. Kruskal-Wallis One-Way ANOVA

Import the data saved in Excel into R by loading the packages "xlsxjars rjava xlsx".
OR
Import text file into R-studio

Prepare data file as follows: mydata.txt

group response
1 23
1 26
1 51
1 49
1 58
1 37
1 29
1 44
2 22
2 27
2 39
2 29
2 46
2 48
2 49
2 65
3 59
3 66
3 38
3 49

32 

 
 3 56
3 60
3 56
3 62

R Script:
attach(mydata)
fix(mydata)
kruskal.test(response ~ group, data = mydata)
D. Multivariate Techniques
D.1: Principal Component Analysis
Datafile: pca.txt

sn pp ph ngl yld
1 142 0.525 8.2 2.47
2 143 0.64 9.5 4.76
3 107 0.66 9.3 3.31
4 78 0.66 7.5 1.97
5 100 0.46 5.9 1.34
6 86.5 0.345 6.4 1.14
7 103.5 0.86 6.4 1.5
8 155.99 0.33 7.5 2.03
9 80.88 0.285 8.4 2.54
10 109.77 0.59 10.6 4.9
11 61.77 0.265 8.3 2.91
12 79.11 0.66 11.6 2.76
13 155.99 0.42 8.1 0.59
14 61.81 0.34 9.4 0.84
15 74.5 0.63 8.4 3.87
16 97 0.705 7.2 4.47
17 93.14 0.68 6.4 3.31
18 37.43 0.665 8.4 1.57
19 36.44 0.275 7.4 0.53
20 51 0.28 7.4 1.15
21 104 0.28 9.8 1.08
22 49 0.49 4.8 1.83
23 54.66 0.385 5.5 0.76
24 55.55 0.265 5 0.43
25 88.44 0.98 5 4.08
26 99.55 0.645 9.6 2.83
27 63.99 0.635 5.6 2.57
28 101.77 0.29 8.2 7.42
29 138.66 0.72 9.9 2.62
30 90.22 0.63 8.4 2
31 76.92 1.25 7.3 1.99
32 126.22 0.58 6.9 1.36
33 80.36 0.605 6.8 0.68
34 150.23 1.19 8.8 5.36
35 56.5 0.355 9.7 2.12

33 

 
36 136 0.59 10.2 4.16
37 144.5 0.61 9.8 3.12
38 157.33 0.605 8.8 2.07
39 91.99 0.38 7.7 1.17
40 121.5 0.55 7.7 3.62
41 64.5 0.32 5.7 0.67
42 116 0.455 6.8 3.05
43 77.5 0.72 11.8 1.7
44 70.43 0.625 10 1.55
45 133.77 0.535 9.3 3.28
46 89.99 0.49 9.8 2.69

# R Script for Principal Component analysis

attach(pca)
names(pca)

#To Remove first variable

mydata=pca[,2:5]

#perform principal component analysis

output=princomp(mydata, cor=FALSE, scores=TRUE, covmat=NULL)
print(output)

#Summary results
summary(output)

#scree plot
plot(output)

#Loadings
output$loadings

#PC scores
output$scores
loadings(output, cuttoff=0.0001)
print(output, digits=4, cuttoff=0.0001)
biplot(output)
detach(pca)
 

D.2: Multivariate Analysis of variance

Datafile: manova.txt
blk trt y1 y2
1 1 722 808
1 2 640 742
1 3 640 910
1 4 936 1105
1 5 990 1185
1 6 995 1206
1 7 1145 1395
34 

 
1 8 1190 1380
1 9 1032 1228
1 10 1250 1490
2 1 532 600
2 2 884 1025
2 3 800 945
2 4 765 900
2 5 835 1005
2 6 1070 1294
2 7 1140 1400
2 8 1040 1215
2 9 1145 1362
2 10 1180 1402
3 1 644 725
3 2 664 770
3 3 943 1120
3 4 893 1050
3 5 1071 1285
3 6 988 1195
3 7 880 1070
3 8 940 1090
3 9 1005 1195
3 10 860 1025
4 1 477 535
4 2 754 874
4 3 838 980
4 4 1052 1242
4 5 1037 1244
4 6 1170 1415
4 7 1075 1310
4 8 1150 1220
4 9 1035 1190
4 10 915 1025

# R Script for MANOVA

attach(manova)
names(manova)
blk=factor(blk)
trt=factor(trt)
lm1=manova(cbind(y1,y2)~blk+trt)
out=summary(lm1)
out
results=aov(lm1)
results
detach(manova)

35 

 
E. Miscellaneous
E.1. Variance Components Estimation
Data:
 

 
Table 1: Insect Damage Data for Example
 

#R-Script
library(varComp)
data<-read.csv(“insect_damage.csv”)
vcf = varComp(Y~., data, ~Variety)
summary(vcf)
E.2. GE interaction and Stability Analysis
Data: Yield data of various genotypes selected from various location available in the package
agrocolae and name of the dataset is “plrv”. Partial data is given below-

Genotype Locality Rep WeightPlant WeightPlot Yield

1 102.18 Ayac 1 0.5100000 5.1000 18.8888889
2 104.22 Ayac 1 0.3450000 2.7600 12.7777778
3 121.31 Ayac 1 0.5425000 4.3400 20.0925926
4 141.28 Ayac 1 0.9888889 8.9000 36.6255144
5 157.26 Ayac 1 0.6250000 5.0000 23.1481481
6 163.9 Ayac 1 0.5120000 2.5600 18.9629630
7 221.19 Ayac 1 0.4960000 2.4800 18.3703704
8 233.11 Ayac 1 1.0100000 10.1000 37.4074074
9 235.6 Ayac 1 0.8250000 8.2500 30.5555556
10 241.2 Ayac 1 0.4880000 4.8800 18.0740741
11 255.7 Ayac 1 0.5800000 2.3200 21.4814815
12 314.12 Ayac 1 0.4100000 1.6400 15.1851852
13 317.6 Ayac 1 1.0057143 7.0400 37.2486772
14 319.20 Ayac 1 0.8644444 7.7800 32.0164609
15 320.16 Ayac 1 0.7066667 6.3600 26.1728395
36 

 
#R-Script:
library(agricolae)
data(plrv)
attach(plrv)  
  model<- AMMI(Locality, Genotype, Rep, Yield)
  detach(plrv)
# biplot PC2 vs PC1
 
plot(model)
  detach(plrv)

E.3. Diallel Analysis:

Data: Example was taken from the package named “plantbreeding” and the name of the data
set is “fulldiallel”. Data is given below-
  FAMILY TRT FAMQC MALE FEMALE REP YIELD
  1 11 NA 1 1 1 104.86
1 11 NA 1 1 2 84.32
  1 11 NA 1 1 3 76.92
1 11 NA 1 1 4 76.48
  2 12 1 1 2 1 88.70
2 12 1 1 2 2 69.10
 
2 12 1 1 2 3 76.80
  2 12 1 1 2 4 88.16
3 13 2 1 3 1 75.28
  3 13 2 1 3 2 124.74
3 13 2 1 3 3 94.56
  3 13 2 1 3 4 114.34
  4 14 3 1 4 1 124.26
4 14 3 1 4 2 132.48
  4 14 3 1 4 3 114.38
4 14 3 1 4 4 105.34
  5 15 4 1 5 1 109.74
5 15 4 1 5 2 99.56
 
5 15 4 1 5 3 110.18
#R-Script: 5 15 4 1 5 4 125.68

library(plantbreeding)
data(fulldial)
out <-diallele1(dataframe = fulldial, male = "MALE", female = "FEMALE", progeny =
"TRT", replication = "REP", yvar = "YIELD" )
print(out)
out$anvout # analysis of variance
out$anova.mod1 # analysis of variance for GCA and SCA effects out$components.model1 #
model1 GCA, SCA and reciprocal components
out$gca.effmat # GCA effects
out$sca.effmat # SCA effect matrix
heatmap(out$sca.effmat, labRow = rownames(out$sca.effmat), labCol =
colnames(out$sca.effmat)) # heatmap plot of SCA matrix out$reciprocal.effmat # reciprocal
effect matrix
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