Analysis of Variance ANOVA

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Analysis of VarianceANOVA

• For more than two groups multiple t tests to find
  differences in means are not appropriate. One in
  twenty will be wrong on average.

2
ANOVA

• Consider three groups

3
ANOVA

• It can be shown that
• Within Group Between Group
  Total
• Variability Variability
  Variability
• And
• gets larger if there are differences between the
  group means
• This is the essence of ANOVA

4
Minitab Output

• One-way ANOVA Yield 1 versus Group
• Source DF SS MS F P
• Group 2 40.033 20.017 188.24 0.000
• Error 12 1.276 0.106
• Total 14 41.309
• S 0.3261 R-Sq 96.91 R-Sq(adj) 96.40
• Individual 95 CIs For
  Mean Based on
• Pooled StDev
• Level N Mean StDev ----------------------
  --------------
• 1 5 4.0600 0.3362 (---)
• 2 5 5.9600 0.3050 (---)
• 3 5 8.0600 0.3362
  (---)
• ----------------------
  --------------
• 4.8 6.0
  7.2 8.4

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The Model

• The model can be written as
• where
• z1 is 1 for group 2 and 0 elsewhere
• z2 is 1 for group 3 and 0 elsewhere
• b1 and b2 are then differences from group 1
• Note we could do this as a regression with two
  variables z1 and z2

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So What??

• We have carried out a test of significance F
  188.24, p 0.000
• But what was the Null Hypothesis?
• H0 moverall m1 m2 m3
• HA One or more of the pairs of means are not
  equal
• But this is not very useful
• We are now back to the original problem of lots
  of pairwise tests but at least we know with 95
  confidence that there is a real effect that we
  are looking for.

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Post Hoc Multiple Comparisons

• Dear ChrisThis is a  deep philosophical
  debatable issue about what are appropriate
  inference  procedures  if you really do want to
  test for differences between all possible pairs
  simultaneously  -- as you say 120,000  contrasts
  at the same time.The 'bad apples' ( or the
  excellent juicy ones) may of course be more
  simply done by evaluating whether residual 
  estimates are compatable with zero random effect
  ( i.e  that schools do not differ from the
  average)-- in which case there are only 500
  possible comparisons.If indeed you do want an
  appropriate multiple testing procedure  and
  practically in my view there would be some
  question concerning what this would really tell
  you and whether it is at all necessary beyond
  standard caterpillar diagrams  -- then indeed
  some sort of Bonferroni idea would be appropriate
  to account for  the multiple testing procedure .
  You rightly point out the difficulty concerned
  with Bonferroni when there are a multiplicity of
  tests . It can set the right Type 1 error level
  but its Power is really extremely weak.
• An article which develops more powerful
  procedures based on concepts which are called
  Family wise error rates and /or False Discovery
  proportions will shortly be published in JRSS
  Series A of which I am joint editor--
• Antony FieldingProfessor of  Social and
  Educational StatisticsDepartment of
  EconomicsUniversity of Birmingham ,United
  Kingdom

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• A number of possibilities have been suggested
• Bonferroni
• Tukey
• Duncan
• Etc.
• They all work by adjusting the acceptance
  probability in some way.

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Assumptions in ANOVA

• The samples are
• Random
• Independent
• From Normally distributed populations
• Variance of populations is constant

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More than one Factor

• Two Factors - This commonly occurs in blocked
  experiments
• Treatment
• Block
• Remember back to the experimental design
  lectures. I described an experiment with 5
  paddocks and 3 management regimes.

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The data looked like
12
The one way ANOVA
One-way ANOVA Yield versus TrtNo Source DF
SS MS F P TrtNo 2 308846
154423 8.44 0.005 Error 12 219531
18294 Total 14 528377 S 135.3 R-Sq
58.45 R-Sq(adj) 51.53
Individual 95 CIs For Mean Based on Pooled
StDev Level N Mean
StDev ------------------------------------
1 5 1408.7 151.0 (--------------) 2
5 1531.8 132.0
(---------------) 3 5 1755.4 121.1
(---------------)
-------------------------------
----- 1280 1440
1600 1760 Pooled StDev 135.3
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BUT Including the Block Information
Two-way ANOVA Yield versus TrtNo, BlkNo Source
DF SS MS F P TrtNo 2
308846 154423 149.82 0.000 BlkNo 4 211285
52821 51.25 0.000 Error 8 8246
1031 Total 14 528377 S 32.10 R-Sq
98.44 R-Sq(adj) 97.27
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Individual 95 CIs For Mean Based on
Pooled StDev TrtNo Mean
------------------------------------ 1
1408.75 (---) 2 1531.76
(---) 3 1755.39
(---) -----------------------
------------- 1440 1560
1680 1800 Individual
95 CIs For Mean Based on Pooled
StDev BlkNo Mean -------------------------
----------- 6 1741.14
(-----) 9 1397.45 (-----) 11
1559.46 (------) 16 1639.38
(-----) 17 1489.07
(-----) ----------------------
-------------- 1440
1560 1680 1800
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A More Complicated Model

• Data were collected on the length of time
  patients were in hospital, which one of three
  medicines they were treated with, and which one
  of three vitamin supplements they were given.
• 36 patients were used and they were randomly
  assigned to medicines and vitamins in 9 groups of
  4

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A graph of the data
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The Simple ANOVA
One-way ANOVA Days versus Medicine Source
DF SS MS F P Medicine 2
72.00 36.00 3.69 0.036 Error 33 322.00
9.76 Total 35 394.00 S 3.124 R-Sq
18.27 R-Sq(adj) 13.32
Individual 95 CIs For Mean Based on
Pooled StDev Level N Mean
StDev ------------------------------------ 1
12 7.000 2.594 (----------------) 2
12 10.000 4.243
(----------------) 3 12 10.000 2.132
(----------------)
------------------------------------
6.0 8.0 10.0
12.0 Pooled StDev 3.124
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One-way ANOVA Days versus Vitamin Source DF
SS MS F P Vitamin 2 24.0 12.0
1.07 0.355 Error 33 370.0 11.2 Total 35
394.0 S 3.348 R-Sq 6.09 R-Sq(adj)
0.40 Individual 95
CIs For Mean Based on Pooled
StDev Level N Mean StDev
------------------------------------ 1
12 8.000 3.015 (------------------------) 2
12 9.000 2.594
(------------------------) 3 12 10.000
4.221 (------------------------)
------------------
------------------ 6.0
7.5 9.0 10.5 Pooled StDev
3.348
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2 way ANOVA
Two-way ANOVA Days versus Medicine, Vitamin
Source DF SS MS F
P Medicine 2 72 36.0000 3.74 0.035 Vitamin
2 24 12.0000 1.25 0.301 Error 31 298
9.6129 Total 35 394 S 3.100 R-Sq
24.37 R-Sq(adj) 14.61
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With the Interaction
Two-way ANOVA Days versus Medicine, Vitamin
Source DF SS MS F
P Medicine 2 72 36.0000 7.04
0.003 Vitamin 2 24 12.0000 2.35
0.115 Interaction 4 160 40.0000 7.83
0.000 Error 27 138 5.1111 Total
35 394 S 2.261 R-Sq 64.97 R-Sq(adj)
54.60
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Individual 95 CIs For Mean Based on
Pooled StDev Medicine Mean
------------------------------------ 1
7 (----------------) 2 10
(----------------) 3 10
(----------------)
------------------------------------
6.0 7.5 9.0 10.5
Individual 95 CIs For Mean Based
on Pooled StDev Vitamin Mean
------------------------------------ 1
8 (--------------------) 2 9
(--------------------) 3 10
(--------------------)
------------------------------------
7.2 8.4 9.6 10.8
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Individual 95 CIs For Mean
Based on Pooled StDev Medicine
Mean ------------------------------------ 1
7 (----------------) 2 10
(----------------) 3 10
(----------------)
------------------------------------
6.0 8.0 10.0 12.0
Individual 95 CIs For Mean Based on
Pooled StDev Vitamin Mean
------------------------------------ 1
8 (-----------------------) 2 9
(----------------------) 3 10
(-----------------------)
------------------------------------
7.5 9.0 10.5 12.0
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Interaction Plot