Comparing

Means

Anova
F-test can be used to determine whether the
expected responses at the t levels of an
experimental factor differ from each other
When the null hypothesis is rejected, it may be
desirable to find which mean(s) is (are) different,
and at what ranking order.

In practice, it is actually not primary interest to

test the null hypothesis, instead the investigators
want to make specific comparisons of the means
and to estimate pooled error

Means comparison

Three categories:
1. Pair-wise comparisons (Post-Hoc Comparison)
2. Comparison specified prior to performing the experiment
(Planned comparison)
3. Comparison specified after observing the outcome of the
experiment (Un-planned comparison)

Statistical inference procedures of pair-wise

comparisons:

Fishers least significant difference (LSD) method

Duncans Multiple Range Test (DMRT)
Student Newman Keul Test (SNK)
Tukeys HSD (Honestly Significantly Different)
Procedure

Pair Comparison
Suppose there are t means

x1 , x2 , , x t
An F-test has revealed that there are
significant differences amongst the t
means
Performing an analysis to determine
precisely where the differences exist.

Pair Comparison

Two means are considered different if the

difference between the corresponding sample
means is larger than a critical number. Then,
the larger sample mean is believed to be
associated with a larger population mean.
Conditions common to all the methods:

The ANOVA model is the one way analysis of

variance
The conditions required to perform the ANOVA are
satisfied.
The experiment is fixed-effect.

Comparing Pair-comparison methods

With the exception of the F-LSD test, there is no

good theoretical argument that favors one paircomparison method over the others.
Professional statisticians often disagree on which
method is appropriate.
In terms of Power and the probability of making
a Type Power
I error, the tests discussed can beHIGHER
ordered
MORE
as follows:
P[Type I Error]
Tukey HSD Test
Student-Newman-Keuls
Test
Duncan Multiple Range
Test
Pairwise comparisons
Fisher LSD
areTest
traditionally considered as
not a priori, if one needs to categorize all comparis
one of the two groups

Fisher Least Significant Different

(LSD) Method

This method builds on the equal variances ttest of the difference between two means.
The test statistic is improved by using MSE
rather than sp2.
It is concluded that i and j differ (at %
significance level if |i - j| > LSD, where

LSD t 2,dfe

1 1
MSE ( )
ni n j

Critical t for a test about equality

Example:
Cassava yields (ton/ha)
Source
of
variati
on

Degrees Sum of
of
Square
Freedo
m

Mena
Square

F
calculat
ed

Treatm
ent

136

45,333

34

Block
Error

3
9

40
12

13,333
1,33

10

F-table:
3,86

Duncans Multiple Range Test

The Duncan Multiple Range test uses different Significant

Difference values for means next to each other along the real
number line, and those with 1, 2, , a means in between the
two means being compared.
The Significant Difference or the range value:

R p r , p , MSE n
where r,p, is the Duncans Significant Range Value with
parameters p
(= range-value) and (= MSE degree-of-freedom), and
experiment-wise alpha level (= joint).

Duncans Multiple Range Test

MSE is the mean square error from the ANOVA

table and n is the number of observations used to
calculate the means being compared.
The range-value is:
2 if the two means being compared are adjacent
3 if one mean separates the two means being
compared
4 if two means separate the two means being
compared

Significant Ranges for Duncans

Multiple Range Test
Critical Points for Duncan's Multiple Range Statistic -- ALPHA = 0.05
Degrees of
freedom
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
30
40
60
100
inf

2
18.00
6.09
4.50
3.93
3.64
3.46
3.35
3.26
3.20
3.15
3.11
3.08
3.06
3.03
3.01
3.00
2.98
2.97
2.98
2.95
2.89
2.86
2.83
2.80
2.77

3
18.00
6.09
4.50
4.01
3.74
3.58
3.47
3.39
3.34
3.30
3.27
3.23
3.21
3.18
3.16
3.15
3.13
3.12
3.11
3.10
3.04
3.01
2.98
2.95
2.92

4
18.00
6.09
4.50
4.02
3.79
3.64
3.54
3.47
3.41
3.37
3.35
3.33
3.30
3.27
3.25
3.23
3.22
3.21
3.19
3.18
3.12
3.10
3.08
3.05
3.02

5
18.00
6.09
4.50
4.02
3.83
3.68
3.58
3.52
3.47
3.43
3.39
3.36
3.35
3.33
3.31
3.30
3.28
3.27
3.26
3.25
3.20
3.17
3.14
3.12
3.09

6
18.00
6.09
4.50
4.02
3.83
3.68
3.60
3.55
3.50
3.46
3.43
3.40
3.38
3.37
3.36
3.34
3.33
3.32
3.31
3.30
3.25
3.22
3.20
3.18
3.15

p
7
18.00
6.09
4.50
4.02
3.83
3.68
3.61
3.56
3.52
3.47
3.44
3.42
3.41
3.39
3.38
3.37
3.36
3.35
3.35
3.34
3.29
3.27
3.24
3.22
3.19

8
18.00
6.09
4.50
4.02
3.83
3.68
3.61
3.56
3.52
3.47
3.45
3.44
3.42
3.41
3.40
3.39
3.38
3.37
3.37
3.36
3.32
3.30
3.28
3.26
3.23

9
18.00
6.09
4.50
4.02
3.83
3.68
3.61
3.56
3.52
3.47
3.46
3.44
3.44
3.42
3.42
3.41
3.40
3.39
3.39
3.38
3.35
3.33
3.31
3.29
3.26

10
18.00
6.09
4.50
4.02
3.83
3.68
3.61
3.56
3.52
3.47
3.46
3.46
3.45
3.44
3.43
3.43
3.42
3.41
3.41
3.40
3.37
3.35
3.33
3.32
3.29

20
18.00
6.09
4.50
4.02
3.83
3.68
3.61
3.56
3.52
3.48
3.48
3.48
3.47
3.47
3.47
3.47
3.47
3.47
3.47
3.47
3.47
3.47
3.47
3.47
3.47

50
18.00
6.09
4.50
4.02
3.83
3.68
3.61
3.56
3.52
3.48
3.48
3.48
3.47
3.47
3.47
3.47
3.47
3.47
3.47
3.47
3.47
3.47
3.48
3.53
3.61

100
18.00
6.09
4.50
4.02
3.83
3.68
3.61
3.56
3.52
3.48
3.48
3.48
3.47
3.47
3.47
3.47
3.47
3.47
3.47
3.47
3.47
3.47
3.48
3.53
3.67

Student-Newman-Keuls Test

Similar to the Duncan Multiple Range test, the StudentNewman-Keuls Test uses different Significant Difference
values for means next to each other, and those with 1, 2,
, a means in between the two means being compared.
The Significant Difference or the range value for this
test is

K p q , p , MSE n

where q,a, is the Studentized Range Statistic with

parameters p (= range-value) and (= MSE

degree-of-freedom), and experiment-wise alpha

level (= joint).

Student-Newman-Keuls Test

MSE is the mean square error from the ANOVA

table and n is the number of observations used
to calculate the means being compared.
The range-value is:
2 if the two means being compared are
adjacent
3 if one mean separates the two means being
compared
4 if two means separate the two means being
compared

Studentized Range Statistic

Tukey HSD Procedure

The test procedure:
Assumes equal number of observation per
populations.
Find a critical number as follows:

MSE
q (dft , dfe)
ng

dft = treatment degrees of freedom

=degrees of freedom = dfe
ng = number of observations per population
= significance level
q(dft,) = a critical value obtained from the studentized range table

Studentized Range
Statistic

Scheffe
There are many multiple (post hoc)
comparison procedures

Considerable controversy:
I have not included the multiple
comparison methods of Duncan
because I have been unable to
understand their justification

Planned Comparisons or Contrasts

In some cases, an experimenter may know ahead

of time that it is of interest to compare two
different means, or groups of means.
An effective way to do this is to use contrasts or
planned comparisons. These represent
specific hypotheses in terms of the treatment
means suchH as:
0 : 4 5
y4 y5 0
H A : 4 5
H 0 : 1 3 4 5
H A : 1 3 4 5

y1 y3 y4 y5 0

Planned Comparisons or Contrasts

Each contrast can be specified as:

t

C ci yi
i 1

and it is required:

c
i 1

A sum-of-squares can be calculated for a contrast

as

ssC

c yi

i 1 i
t

n c

2
i 1 i

Planned Comparisons

Each contrast has 1 degree-of-freedom, and a

contrast can be tested by comparing it to the
MSE for the ANOVA:
SS c SSE
F (1, dfe)

1 dfe

Un-planned Comparisons or
Contrasts

If more than 1 contrast is tested, it is important

that the contrasts all be orthogonal, that is
t

c d
i 1

Note that It can be tested at most t-1 orthogonal

contrasts.

Contrast orthogonal
examples
Treatm
ent
Adira-4
GH-6
GH-7
Local

Yields (ton/ha)
19
25
18
18

The mean effect of local and high yielding

varieties
The mean effect of high yielding and
promising lines

Orthogonal Polynomials
Special sets of coefficients that test for
bends but manage to remain uncorrelated
with one another.
Sometimes orthogonal polynomials can be
used to analyze experimental data to test
for curves.
Restrictive
assumptions:
Require quantitative factors
Equal spacing of factor levels (d)
Equal numbers of observations at each cell
(rj)
Usually, only the linear and quadratic

Polynomial Examples
Treatment
(Urea
dosage)
kg/ha
50
100
150
200

Yields (ton/ha)

19
25
18
18

Orthogonal Polynomial

The linear regression model y = X

+ is a general model for fitting any
relationship that is linear in the
unknown parameter .
Polynomial regression model:

26

Polynomial Models in One

Variable

A second-order model (quadratic

model):

A second-order model
(quadratic model)

Polynomial Models

Polynomial
models
are
useful
in
situations where the analyst knows that
curvilinear effects are present in the
true response function.
Polynomial models are also useful as
approximating functions to unknown and
possible
very
complex
nonlinear
relationship.
Polynomial model is the Taylor series
expansion of the unknown function.

Choosing order of the model

Theoretical background
Scatter diagram
Orthogonal polynomial test

30

Theoretical background

1.

2.

3.

Can be searched from previous research

or literature
Examples:
The relationship between dosages of nitrogen
application and yield (The law of diminishing
return)
The relationship between pesticide application
and pest mortality (Linear model/probit analysis)
The relationship between population density and
yield (Exponential model/Cob-Douglass Model)

Scatter Diagram

Scatter Diagram

Orthogonal Linear Contrasts for

Polynomial Regression

Orthogonal Linear Contrasts for

Polynomial Regression