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what it is
how you do it
variance components
power and optimal allocation of replication
Nested ANOVA
designs with subsamples nested within replicates
if the nesting is not acknowledged, these designs are
pseudoreplicated
nesting is usually spatial, but can be temporal
Factor B
1
2
3
4
5
6
7
8
9
Not Nested: A x B
Factor A
A
A
A
B
B
B
C
C
C
Factor B
1
2
3
1
2
3
1
2
3
Examples of Nesting
creeks (tributaries) are unique to each river
multiple samples of a single tissue type within a rat
subsamples in time (if sampled w/o replacement) can only
be sampled at one time and not another
Factor A - fixed
sea urchin density
four levels:
Factor B - random
randomly chosen patches
4 within each treatment
n = 5 quadrats / patch
Density:
Patch:
Reps:
100%
66%
1 2 3 4
5 6 7 8
etc.
n = 5 in each of 16 cells
p = 4 densities, q = 4 patches
Linear model
yijk = + i + j(i) + ijk
where
i
i(i)
ijk
overall mean
effect of factor A (i - )
effect of factor B within each level of A
(ij - i)
unexplained variation (error term) variation within each cell
Effects
Main effect:
effect of factor A
i.e., variation among factor A group means
Null hypotheses
H0: Factor A: No difference in mean amount of filamentous algae
between the four sea urchin density treatments
H0: Factor B: No difference in the mean amount of filamentous algae
between all possible patches in any of the treatments
Factor A:
H0: no difference among means of factor A (= no
difference among means of urchin density treatments)
1 = 2 = = i =
is equivalent to
Null hypotheses
Factor B(A)
H0: no difference among means of factor B within any level of
factor A
(no difference among patches in mean filamentous algae
cover within any urchin density treatment)
11 = 12 = = 1j
21 = 22 = = 2j
etc.
H0: no variance among levels of nested random factor B
within any level of factor A
(no variance among patches within each density treatment):
2 = 0
SSB(A) +
SSResidual
Source
SS
df
MS
Factor A
SSA
p-1
SSA/(p-1)
Factor B(A)
SSB(A)
p(q-1)
SSB(A)/(p(q-1))
Residual
SSResidual
pq(n-1)
SSResidual/(pq(n-1))
A fixed, B random:
MSA
MSB(A)
MSResidual
parameters
if no effect of nested
random factor B(A):
MSResidual
4 possible outcomes
H0: true; no variation among A
patches dont differ
A1
patches do differ
B1
B2
Bj
B1
Ai
B2
Bj
Bjs=0
Bjs0
Ais=0
Bjs=0
Bjs0
Ais0
df
MS
var. comp.
Density
4810
2.72
0.09
5.93
<0.001
Patches(Density)
12
1770
Residual
64
299
Total
79
294
49.6%
299
50.4%
Additional Tests
Main effect:
planned contrasts & trend analyses as part of design
unplanned multiple comparisons if main F-ratio test
significant
Nested effect:
usually random factor
usually of little interest in further tests
often can provide information on the characteristic
spatial signal of a population
ANOVA output
Analysis of Variance
Source
Sum-of-Squares
df
Mean-Square
F-ratio
SCHOOL$
156.50000
78.25000
11.17857
0.00947
TEACHER(SCHOOL$)
567.50000
189.16667
27.02381
0.00070
42.00000
7.00000
Error
Sum-of-Squares
df
Mean-Square
F-ratio
SCHOOL$
156.50000
78.25000
11.17857
0.00947
TEACHER(SCHOOL$)
567.50000
189.16667
27.02381
0.00070
42.00000
7.00000
Error
After:
Test of Hypothesis
SS
df
MS
Hypothesis
Source
156.50000
78.25000
0.41366
Error
567.50000
189.16667
0.69397
No effect of school!
Power
more replication always gives you more power
but in nested ANOVA, there is replication at
various levels
where does your power come from?
if you have nested factors within your treatments,
you need to replicate the nested factor, not the
subsamples
Locations
Region 1
Transects
Regions
Region 2
Locations(Regions)
Sites(Locations(Regions))
Transects(Sites(Locations(Regions)))
Region 3
Source
df
MS
Region
6658
10.4
247 (42)
Location(Region)
638
2.43
71 (12)
Site(Location(Region))
18
263
1.40
88 (14)
54
187
187 (32)