Experimental Design

Four Classes of Experimental and

Sampling Designs
 ANOVA Designs
•  If you response variables are continuous and
your predictor variables are categorical
(ordered or unordered)

•  The term ANOVA applies to both the Design

and the Statistical Analysis of such designs
 ANOVA Terminology
Treatment: Different categories of the predictor
variables that are used. In an experiment it refers
to different manipulations that have been
performed

In observations, it refers to the different groups

that are being compared
 ANOVA Terminology
Replicate: Within each treatment, multiple
observations will be made, and each such
observation is a replicate.

In standard designs, the replicates should be

independent of each other, both statistically and
biologically
 ANOVA Terminology
Single-factor design: When treatments
represent variation in a single predictor
variable or factor.

Each value of the factor that represents a

particular treatment is called a treatment level

E.g., Growth responses of an agricultural crop to 4 different

levels of nitrogen or the growth responses of 5 different
plant species at one fixed level of nitrogen.
 ANOVA Terminology
Multifactor design: Treatments cover two (or
more) factors and each factor is applied in
combination in different treatments.

The different levels for each factor may be

ordered or unordered

E.g., Growth responses of an agricultural crop to 4 different

levels of nitrogen and 4 different levels of phosphorus.

This would entail 4 x 4 = 16 different treatment levels

 ANOVA Terminology
Why Multifactor design? Can two separate
single-factor designs not achieve the same?

Advantages:

1. Efficiency in cost, time, and effort to run a single

experiments

2. More importantly, a two-way design allows you to test

both the main effects as well as interaction effects
 ANOVA Terminology
Main effects: The additive effect of each level
of one treatment averages over all of the
levels of the other treatment.

Interaction effects: Unique responses to

particular treatment combinations that
cannot be predicted simply from knowing the
main effects
E.g., The growth of plants at high levels of N and P may be
synergistically greater than what would be predicted from
the additive effects of high N and P separately.
 Single-factor ANOVA
The one-way layout: A simple yet powerful
design. To compare means among two or
more treatments or groups. E.g., Recruitment of
Barnacles in an intertidal zone as a function of substrate
(say, slate, granite, and concrete)
 Single-factor ANOVA
Disadvantages:

(1) Does not explicitly incorporate environmental

heterogeneity. This is a problem when environmental
‘noise’ is as strong as the ‘signal’.

(2) Treatments are organized along just one factor.

Typically, other factors are present, and interaction
terms may be important
 Single-factor ANOVA
Randomized-Block Designs: A modification of one-way
ANOVA to include environmental heterogeneity.

Blocks are delineated in which environmental conditions

are relatively homogeneous.

Blocks may be placed randomly, but should be arranged

such that environmental conditions are more similar within
blocks than between them.

Best to place only one replicate of each treatment within

a block
Single-factor ANOVA – Randomized blocks
 Single-factor ANOVA – Randomized blocks

Block Orientation: Eg., for three blocks in an elevation

gradient
 Single-factor ANOVA – Randomized blocks
Disadvantages: (1) Statistical cost. If sample size is
small and block effect is weak, it is less powerful than
a one-way layout

(2) If blocks are too small, you introduce non-

independence due to crowding

(3) If any replicates are lost, data from that entire

block cannot be used

(4) It assumes that there is no interaction between

blocks and treatments
 Single-factor ANOVA – Randomized blocks
Disadvantages:

Therefore some have suggested replication within

blocks. But then that becomes really a two-factor
ANOVA.

Replication does help, but is a lot to invest in studying

an attribute that is not of primary interest.
Single-factor ANOVA
Nested design: Any
design in which there is
sub-sampling within
each of the replicates.
 Single-factor ANOVA – Nested Designs
Nested design: Any design in which there is sub-sampling
within each of the replicates.

Note: This does not increase the number of replicates, but

helps in improving precision of the replicate
measurements

It also allows you test both variation among treatments,

and the variation within treatments.

Such a nested design can be extended to build a

hierarchical sampling design

E.g., subsamples à replicates à intertidal zones à shores

à regions à sub-continents . . .
 Single-factor ANOVA – Nested Designs
Disadvantages: (1) Often analysed incorrectly. When
you treat each sub-sample as independent, for
example, and analyse it as a one-way . . .

(2) Difficult or impossible analyse properly.

(3) Most serious is the ‘misplaced’ sampling effort.

Why invest in sub-sampling when it will not qualify as
an independent replicate? It is better to invest in
getting independent replicates.
 Multifactor ANOVA
Treatments are assigned to two or more factors.
Factors may represent ordered or unordered
treatments

E.g., say in addition to substrate you were interested

in testing the effects of predatory snails on barnacle
recruitment

Predation levels: (1) unmanipulated (2) cage control

(3) predator exclusion (4) predator inclusion

The key element in proper factorial design is to ensure

that the treatments are fully crossed or orthogonal
Multifactor ANOVA
 Multifactor ANOVA
It is critical that all treatment combinations are present.
Else we end up with a ‘confounded design’

There may be natural covariation between factors in

nature. If you can experimentally break up this
covariation, then you can derive powerful inference on
the independent contributions of each factor

The key advantage is the power to tease apart main

effects and interactions between two factors

Interactions measure the extent to which different

treatment combinations act additively, synergistically, or
antagonistically
Multifactor ANOVA
 Multifactor ANOVA
Disadvantage: Treatment combinations can become
too large with adequate replication.

For the Barnacle example, with 10 replicates per

treatment, you have 120 total replicates.

As with one-way, the simple two-way design does not

account for spatial heterogeneity

Here again you can use a simple randomized block

design. If you replicate within blocks, you have a
three-way design!!!!
Environmental Impacts over time: BACI Designs

BACI: Before-After, Control-Impact

A special type of repeated measures design, in which

measurements are taken before and after the
application of a treatment

A powerful layout for assessing environmental impact

and monitoring trajectories.
Environmental Impacts over time: BACI Designs