The Research Proposal

Describes the:
Researchable question itself
Why it's important (i.e., the rationale and significance of your
research)
Propositions that are known or assumed to be true (i.e., axioms
and assumptions)
Propositions that will be tested (i.e., hypotheses or postulates)
Goals and specific objectives of your research activities
Methods you will use to test hypotheses and achieve objectives
Expected results and scope of inference

Steps in the scientific method

Define the researchable question
Develop hypotheses, predictions, and objectives
Develop materials and methods, including replication
Gather data
Analyze the data (contingency plans if things go wrong?)
Draw conclusions (accept, modify, reject the hypothesis)

Hypotheses
General definitions
A new idea
A statement to be tested - an 'educated guess' that needs more
study to be confirmed or disproved
A proposition that explains some phenomenon

Scientific hypothesis - The researchable question restated as a

declarative sentence that is assumed to be true for testing purposes
Stated as what you believe to be true not what you want to
disprove (i.e., not a statistical 'null' hypothesis)
Must be testable (e.g., generate predictions)
The most valuable hypotheses are simple, consistent with what is
already known, and have broad applicability

Methods and expected results

The materials and methods must describe the:
Proposed experiments or investigations
Materials and techniques that you will use, including their feasibility
Statistical techniques and other methods used to analyze the data
Your expected results and interpretations must describe the:
Results that will lead you to conclude that the hypotheses are proved
or disproved
Scope of inference (i.e., to what extent are the results applicable to
other locations, times, or situations?)
Pitfalls that may be encountered
Limitations to the proposed methods

Think it through!

Typical formats
Each hypothesis or objective often has its own set of methods
OBJECTIVES My objectives are to:
Objective 1
Objective 2

HYPOTHESES I hypothesize that:

Hypothesis 1
Hypothesis 2

MATERIALS AND METHODS

Objective 1
Hypotheses - Rationale
Experimental design
Measurements
Data analysis
Expected results
Objective 2
Hypotheses - Rationale
Experimental design
Measurements
Data analysis
Expected results
Pitfalls and limitations (summary)

MATERIALS AND METHODS

Hypothesis 1
Objectives - Rationale
Experimental design
Measurements
Data analysis
Expected results
Hypothesis 2
Objectives - Rationale
Experimental design
Measurements
Data analysis
Expected results
Pitfalls and limitations (summary)

The materials and methods must describe the:

Proposed experiments or investigations
Materials and techniques that you will use, including their feasibility
Statistical techniques and other methods used to analyze the data

Approach
The strategy connecting hypotheses to conclusions
Observational, experimental, modeling?
Connection
between methods
and conclusions
must be clear why are you doing
these things?

Design
Randomization, replication, etc
How do you know replication is sufficient?

Measurements - Response variables

Survey, lab, field?
Have you done these before?
Are you collaborating with someone who has?

Statistical approaches

Expected results and interpretations

The results you expect to see if your hypotheses are true (i.e., the
predictions that flow from your hypotheses)
What will conclude if you do not see your expected results (i.e., if your
predictions are not observed)?

Observations (axioms)

Expected results and interpretations

must describe the:
Researchable question

Hypothesis

Results that will lead you to conclude that

the hypotheses are proved or disproved

deduction
Expected results

Prediction
Reject hypoth.
(deduction)
False

Accept hypoth.
(induction)
Test

True

Materials and methods

Scope of inference
Closely linked

The conditions to which the conclusions from the research will apply:
Scientific Scope of inference
Biological
Geographical
Temporal
Statistical Scope of Inference

Important to consider when you design your research

How broadly do you want to apply your results?

Pitfalls and limitations

Pitfalls

Demonstrates a realistic knowledge of your materials and methods

Which procedures are risky?
What can go wrong?
How will you keep things from going wrong?
What will you do if things go wrong - backup plans?
What are the consequences if things go wrong?

Limitations
Scope of inference limitations
Describe constraints - i.e., resource, time constraints

Evaluation
Are the materials and methods adequate to test the
hypotheses and achieve the objectives?
Is the scope of inference defined, realistic, and adequate?
Are issues of representation, replication, and randomization
appropriate to the proposal and if so, are they addressed?
Is it clear how conclusions will be drawn?
Is the proposed study doable and repeatable?
Are the pitfalls and limitations understood?
Are the experiments novel or creative?

Define the question

Design the study

Carry out the study

Analyze the data

Draw conclusions

The Question of Interest defines

responses to measure
population to which inference is made
groups to compare
Does the foliar boron concentration of seedlings
differ among the nursery grown Douglas-fir
seedlings in western Oregon that receive one
of 4 different fertilizer regimes, the standard
fertilizer with 0 lb/ac of boron, 1 lb/ac of boron,
2 lb/ac of boron, and 4 lb/ac of boron?

Relating the Question of Interest to the

Conclusions in the planning stages
What outcomes are possible?
- Multiple or one?

What are the explanations for the outcomes?

- a priori decide what you will conclude from
potential outcomes

Does an outcome lead to more than one

explanation?
- Not satisfying if an outcome corroborates many
explanations

Replication
Before we accept the existence of an
effect, the effect must be observable
in replicates that represent the range
of variation* over which inference is to
be made.
-Hurlbert (1983)
*The

scope of inference!

Replication
is the repetition of independent
applications of a treatment or
protocol

Experimental Unit - smallest piece of

material that receives an independent
application of the treatment, a replicate
Sampling Unit - smallest piece of material
on which a measurement is made, a subsample.
Doug-Fir
Pine
Pine

Doug-Fir

Boron Fertilizer applied to sections of

nursery beds.
What gets replicated?
How is the fertilizer applied!
What gets an independent application?

a bed?
or a section of a bed?
or a or a seedling?

Effect of Herbicide on Apple weight

Two Orchards, tractor-sprayed herbicide.
Assign each set of two rows to either herbicide or water
treatment.
In each orchard mix up one tank of herbicide and one tank
of distilled water and apply each to assigned rows of trees.

Herb

Herb

water

Effect of fire severity on re-growth of herbaceous cover

Low

Severe

Medium

Low

Compare tree regeneration rate after fires in Douglas-fir and

Pine Stands.
Doug-Fir
Pine
Pine
Doug-Fir
Doug-Fir

Pine

Detecting Differences Accurately

Avoid Confounding
Confound:

To confuse
To mingle so that the elements cannot be
distinguished

Confounding is the state in which 2 or more phenomena

occur together in such a way that the study
cannot separate the effects of one from the
other.

Confounding: an example
Interest in whether bats forage more along streams then
within forest stands.
In August, sample nighttime foraging activity of
bats along streams in the coastal range.
In October, sample nighttime foraging activity of
bats in forest stands in McDonald Dunn Forest
(near Corvallis).
(Note that in the literature it says that nighttime
foraging activity of bats increases with increasing
nighttime temperature)

Confounding: an example
In August, sample nighttime foraging activity of
bats along streams in the coastal range.
In October, sample nighttime foraging activity of
bats in forest stands in McDonald Dunn Forest
(near Corvallis)
To what should you attribute a difference in foraging activity?
Forest type
Nighttime temperature
Other seasonal effects (e.g. day length, seasonally
available food, day or night light levels)

Randomization
What we do:
Randomly select pieces of material to sample.
randomly select
Randomly assign a piece of material to a protocol.
randomly assign
Order items or protocols randomly.
randomly order
Physically place items randomly.
randomly placed

Why do we randomize?
Randomization is somewhat analogous to insurance, in that
it is a precaution against disturbances that may or may not
occur, and that may or may not be serious if they do occur.
Cochran and Cox 1957

Randomization ensures that a particular treatment will not

be consistently favored or handicapped in successive
replications by some extraneous sources of variation, known
or unknown.
Steele and Torrie 1997
The function of randomization is to ensure that we have a
valid or unbiased estimate of experimental error and of
treatment means and the differences among the means.
Steele and Torrie 1997

Randomization
What do we mean by randomization?
Mixed up the order?
Cant repeat a selection or an assignment?
See no pattern in a selection or an assignment?
Cant explain how we did a selection or
assignment?

Randomization
Each replicate unit has a known chance of
being assigned to a treatment.
Or
Each sample has a known chance of being
sampled
The process is definable and repeatable.
Randomization ensures that the effects we estimate are
reasonably believed to be true for the whole set were
interested in, not just for the subset.

Randomly selecting a unit to sample or measure

can insure no systematic difference between units
intended to be replicates

Inferences
Observational studies can only report associations
between responses and groups
Because you dont know and cant be sure that
something unknown is responsible for the difference
you see between your groups
Controlled designed experiments allow you to draw
cause and effect conclusions
Because in theory, all other effects known to affect
the response have been controlled
Note: natural resource studies are commonly a mix of
observational and design studies. It is not easy to have an
natural resource study that can make cause and effect
conclusions!