ANOVA

• Tells us only if treatment effect is significant or not

Presentation Title Goes
PARTITIONING SUMSHere
OF SQUARES • If treatment effect is significant, does not tell us the
…presentation subtitle. nature of the significance

Violeta Bartolome
Senior Associate Scientist-Biometrics
Crop Research Informatics Laboratory
International Rice Research Institute

2 :: color, composition, and layout

What to do after ANOVA – if treatment Partitioning Sum of Squares (PSS)

effect is significant
PSS breaks the treatment
BlockSS sums of squares into
• Mean comparison – if treatments have no known components.
structure
ErrorSS
• Partition sum of squares – if treatments have a The maximum number of
known structure components is equal to
o Treatments can be grouped TreatmentSS the Treatment df, i.e.
o Treatment levels are quantitative number of treatment levels
minus one.
o Treatments are a combination of 2 or more factors
and at least one factor is partitioned

3 :: color, composition, and layout 4 :: color, composition, and layout

 Three ways of partitioning sums of Group Comparison
squares Example 1: 3 varieties tested:
Traditional variety A
New varieties B and C
• Group Comparison
• Orthogonal Polynomials SV df SS MS F-value

• Factorial Comparison Blocks 3 0.587 0.196

Varieties 2 1.040 0.520 5.84*

Error 6 0.533 0.089

Total 11 2.16

Objective is to compare yield of traditional variety with

average yield of new varieties
H0: µA = ½(µB + µC)

Pairwise comparison will not answer this objective.

5 :: color, composition, and layout 6 :: color, composition, and layout

Group Comparison Group Comparison

To answer objective, we have to do between group To compute sum of squares for each component
and within group comparisons. we have to construct single df contrasts.

Contrast coefficients should be assigned to each level of

SV df SS MS F-value
the treatment factor. Sum of contrast coefficients should
Blocks 3 0.587 0.196 be zero.
Varieties 2 Between
1.040 0.520 group comparison
5.84*
A vs (B and C) 1
Group 1 Group 2
B vs C 1 Within group comparison Components Sum
A B C
Error 6 0.533 0.089

Total 11 2.16 A vs (B & C) 0

B vs C 0
7 :: color, composition, and layout 8 :: color, composition, and layout
 Group Comparison Group Comparison

Components
Group 1 Group 2
Sum
If Treatment SS = Component 1 SS + Component 2 SS
A B C Then contrasts are orthogonal or independent
A vs (B & C) -2 1 1 0
Contrasts are orthogonal if the sum of the products of the
B vs C 0 -1 1 0 corresponding coefficients of any two comparisons is zero.
Contrast coefficients to be assigned to one group should be
Group 1 Group 2
equal to the number of members of the other group. Components Sum
A B C
Assign a negative sign to either of the groups. A vs (B & C) -2 1 1 0
Treatment levels not included in the B vs C 0 -1 1 0
comparison should be assigned a 0 coefficient.
Product 0 -1 1 0

9 :: color, composition, and layout 10 :: color, composition, and layout

Group Comparison
Group Comparison
ANOVA table
To visually check for orthogonality, treatments should SV df SS Total equals
MS Variety SS
F-value
be compared only once. Blocks 3 0.587 0.196
Varieties 2 1.040 0.520 5.84 *
Example:
A vs B&C 1 0.960 0.960 10.70 **
A B C D B vs C 1 0.080 0.080 0.89
A,B vs (C,D) -1 -1 1 1 0 Error 6 0.533 0.089
Total 11 2.16
B vs C 0 -1 1 0 0
Product 0 1 1 0 2 Results indicate that the significant variety effect is
mainly due to the difference in yield of the traditional
and the new varieties.
11 :: color, composition, and layout 12 :: color, composition, and layout
 Group Comparison
Presentation of Results Example 2: Consider a variety trial involving 5 varieties
5.0
and 4 replications laid out in RCB.
a
Varieties:
Variety Mean 4.5

Japonica group V1 V2

Yield (t/ha)
Traditional 4.0 b
4.0 Indica group V3 V4 V5
New 4.6
3.5
Difference 0.6** The following comparisons are of interest :
3.0 Japonica group vs Indica group (V1, V2) vs (V3, V4, V5)
Traditional New

Within Japonica group V1 vs V2

Within Indica group V3 vs V4 vs V5

13 :: color, composition, and layout 14 :: color, composition, and layout

Group Comparison Group Comparison

ANOVA Table Outline

SV df Comparison Contrast V1 V2 V3 V4 V5

Block 3
Japonica vs Indica V1,V2 vs V3,V4,V5 3 3 -2 -2 -2
Variety 4
(V1, V2) vs (V3, V4, V5) (1) Within Japonica group V1 vs V2 -1 1 0 0 0
V1 vs V2 (1)
V3 vs V4,V5 0 0 -2 1 1
V3 vs V4 vs V5 (2)
Within Indica group
Error 12 V4 vs V5 0 0 0 -1 1
Total 19

15 :: color, composition, and layout 16 :: color, composition, and layout

 Table of means for grain yield (t/ha) When treatments are quantitative
(Ave. of 3 reps)
• Interest usually is not to compare treatment means
N-rate (kg/ha) Mean
• Most often the interest is to estimate an optimum rate
0 4.306
• To estimate an optimum, a response curve between
60 5.982 dependent variable and the treatment should be
estimated
90 6.259
• Partitioning the treatment sums of squares into
120 6.895 orthogonal polynomials will guide us on the
appropriate relationship to use to estimate the
If the interest is to estimate the optimum N-rate, response curve
would a pair wise comparison answer this objective?

17 :: color, composition, and layout 18 :: color, composition, and layout

Orthogonal Polynomials Orthogonal Polynomials

Table of coefficients for equally spaced factors

• Seeks the lowest degree polynomial that can No. of

adequately represent the relationship Levels Trend T1 T2 T3 T4 T5
between crop response and treatment 3 Linear -1 0 +1
Quadratic +1 -2 +1
• The coefficients for equally spaced factors 4 Linear -3 -1 +1 +3
can be found in common statistical tables
Quadratic +1 -1 -1 +1
• They are used exactly the same way as in Cubic -1 +3 -3 +1
group comparison 5 Linear -2 -1 0 +1 +2
Quadratic +2 -1 -2 -1 +2
Cubic -1 +2 0 -2 +1
Quartic +1 -4 +6 -4 +1

19 :: color, composition, and layout 20 :: color, composition, and layout

 Orthogonal Polynomials
Orthogonal Polynomials
ANOVA for grain yield (t/ha)
SV df MS F
Trend 0 kg N/ha 60 kg N/ha 90 kg N/ha 120 kg N/ha Sum Rep 2 0.2134 <1
N-rate 3 3.6602 11.07**
Linear -0.760639 -0.084515 0.253546 0.591608 0
Linear (1) 10.6619 32.24**
Quadratic 0.402911 -0.644658 -0.322329 0.564076 0 Quadratic (1) 0 .1869 <1
Cubic (1) 0.1315 <1
Cubic -0.095346 0.572078 -0.762770 0.286038 0
Error 6 0 .3307

21 :: color, composition, and layout 22 :: color, composition, and layout

Presentation of Results
Factorial Partitioning
8

• Involves partitioning both the main effect(s) and the

7
interaction
6
• Partitioning main effects may use either or both the
Yield (t/ha)

group comparison and orthogonal polynomial

5
y = 0.0212x + 4.4265
r = 0.985*

3
0 30 60 90 120
Nitrogen rate (kg/ha)

23 :: color, composition, and layout 24 :: color, composition, and layout

 Factorial Partitioning Factorial Partitioning
Consider a split plot experiment with 6 nitrogen rates as ANOVA Table Outline
mainplot and 4 varieties as subplot replicated 4 times. SV df SV df
Varieties: Block 3 RxV 15
IRRI-released IR5, IR8 Nitrogen Rate (R) 5 LxV (3)

UPLB released C4-63 Linear (1) QxV (3)

Quadratic (1) CxV (3)
Traditional Peta
Cubic (1) Error 12
Error (a) 15 Total 19
For nitrogen, the interest is to estimate the optimum rate Variety (V) 3
so we partition using orthogonal polynomial.

The interaction effect should be partitioned

correspondingly.
25 :: color, composition, and layout 26 :: color, composition, and layout

Orthogonal Polynomial for Nitrogen Partitioning the Interaction effect

• Choose unequally space orthogonal polynomial Could be done easily with CropStat using the interaction
• Partition up to cubic only – it will be biologically partition option.
difficult to explain a relationship more than the third
degree

27 :: color, composition, and layout 28 :: color, composition, and layout

 CropStat Output Graphical presentation
LN SOURCE OF VARIATION DF
SUMS OF MEAN F RATIO PROB ER
SQUARES SQUARES LN
====================================================================
10000 It seems that C4-63 and IR5
C4-63
1 REP 2 .108696E+07 543478. 3.82 0.058 6 IR5 have the same response to
8000
2 NITROGEN 5 .304137E+08 .608275E+07 42.80 0.000 6 IR8 nitrogen.
3 Linear 1 .202550E+08 .202550E+08 142.51 0.000 6 Peta
4 Quadratic 1 .966009E+07 .966009E+07 67.97 0.000 6

yield (kg/ha)
6000
5 Cubic 1 404408. 404408. 2.85 0.120 6 To confirm this observation,
* LF RESIDUAL 2 94282.9 47141.5 0.33 0.729 6
6 NITROGEN*REP 10 .142128E+07 142128. 0.41 0.934 12
4000
we may partition variety into 3
7 VARIETY$ 3 .898847E+08 .299616E+08 85.81 0.000 12
2000
groups: C463,IR5 vs IR8 vs
8 NITROGEN*VARIETY$ 15 .693419E+08 .462279E+07 13.24 0.000 12
9 L x V 3 .607186E+08 .202395E+08 57.97 0.000 12
Peta
10 Q x V 3 .521363E+07 .173788E+07 4.98 0.006 12 0
0 30 60 90 120 150 180
11 C x V 3 980488. 326829. 0.94 0.435 12
Nitrogen rate (kg/ha)
* LF RESIDUAL 6 .242914E+07 404856. 1.16 0.349 12
* RESIDUAL 36 .125691E+08 349143.
----------------------------------------------------------------------
* TOTAL (CORRECTED) 71 .204718E+09 .288335E+07
----------------------------------------------------------------------

29 :: color, composition, and layout 30 :: color, composition, and layout

Factorial Partitioning Group Comparison for Variety

ANOVA Table Outline Always sort factor levels
SV df SV df
Block 3 RxV 15 Comparison Contrast C4-63 IR5 IR8 Peta
Nitrogen Rate (R) 5 LxV1 (2)
Peta vs C4-63, IR5,
Linear (1) LxV2 (1) 1 1 1 -3
C4,63, IR5 vs IR8 vs IR8
Quadratic (1) QxV1 (2) Peta
IR8 vs C4-63, IR5 1 1 -2 0
Cubic (1) QxV2 (1)
Error (a) 15 CxV1 (2) C4-63 vs IR5 1 -1 0 0
Variety (V) 3 CxV2 (1)
V1:C4-63, IR5 vs IR8 vs Peta (2) Error 12

V2: C4-63 vs IR5 (1) Total 19

31 :: color, composition, and layout 32 :: color, composition, and layout

 CropStat Output
LN SOURCE OF VARIATION DF SUMS OF MEAN F RATIO PROB ER Graphical Presentation
SQUARES SQUARES LN
======================================================================== 10000
1 REP 2 .108696E+07 543478. 3.82 0.058 6
2 NITROGEN 5 .304137E+08 .608275E+07 42.80 0.000 6 IR8
y = 23.463x + 4207.2
3 Linear 1 .202550E+08 .202550E+08 142.51 0.000 6 Peta r = 0.992**
4 Quadratic 1 .966009E+07 .966009E+07 67.97 0.000 6 8000
5 Cubic 1 404408. 404408. 2.85 0.120 6 C4, IR5
* LF RESIDUAL 2 94282.9 47141.5 0.33 0.729 6
6 NITROGEN*REP 10 .142128E+07 142128. 0.41 0.934 21
7 VARIETY$ 3 .898847E+08 .299616E+08 85.81 0.000 21 6000
8 V1:C4,I5 vs IR8 vs Peta 2 .867287E+08 .433644E+08 124.20 0.000 21 y = -0.1423x 2 + 40.374x + 3742.6
9 V2:C4 vs IR5 1 .315595E+07 .315595E+07 9.04 0.005 21 R2 = 0.9869**
10 NITROGEN*VARIETY$ 15 .693419E+08 .462279E+07 13.24 0.000 21
11 L X V1 2 .603906E+08 .301953E+08 86.48 0.000 21 4000
12 L x V2 1 328060. 328060. 0.94 0.341 21 y = -0.1764x 2 + 14.615x + 4561.7
13 Q x V1 2 .508911E+07 .254456E+07 7.29 0.002 21 R2 = 0.907*
14 Q x V2 1 124523. 124523. 0.36 0.561 21
15 C x V1 2 918896. 459448. 1.32 0.280 21 2000
16 C x V2 1 61592.0 61592.0 0.18 0.680 21
* LF RESIDUAL 6 .242914E+07 404857. 1.16 0.349 21
* RESIDUAL 36 .125691E+08 349143.
------------------------------------------------------------------------ 0
* TOTAL (CORRECTED) 71 .204718E+09 .288335E+07
0 30 60 90 120 150 180
------------------------------------------------------------------------

33 :: color, composition, and layout 34 :: color, composition, and layout