1. Exam 2 Analysis of Biological Data/Biometrics Dr. Ryan McEwan
Department of Biology
University of Dayton

2. Exam 2 asks you to practically analyze a “real” biological data set.
Physiochemical data were collected based on analysis of the water in 5 streams that each represented a level of invasion by an exotic shrub named Amur honeysuckle:
Aullwood (Reference = no honeysuckle present)
Englewood (Reference = no honeysuckle present)
Charleston Falls (Moderate = some honeysuckle present)
Englewood (Moderate = some honeysuckle present)
Buckeye Trail (Heavy = dense invasion of honeysuckle)

3. Reference site
Moderate Site- some honeysuckle present
Heavy Site- dense honeysuckle present
Here are example stream pictures for you to look at

4. Physiochemical data were collected based on analysis of the water in 5 streams that each represented a level of invasion by an exotic shrub named Amur honeysuckle:
Aullwood (Reference = no honeysuckle present)
Englewood (Reference = no honeysuckle present)
Charleston Falls (Moderate = some honeysuckle present)
Englewood (Moderate = some honeysuckle present)
Buckeye Trail (Heavy = dense invasion of honeysuckle)
In each site, data were collected in 4 locations.
For the purposes of comparing among sites we will treat these as replicates. You might wonder if this design is pseudoreplicated , and you might also wonder why there are 5 sites and not six. Those are good things to ponder, but better to just ignore that for his assignment. Just go forward with the notion that for comparison AMONG STREAMS you want to treat the 4 samples as replicates. That is where you will pool your variation.
The 4 locations are:
Upstream
Plot 4
Plot 3
Plot 1

5. The 4 locations are:
Upstream
Plot 4
Plot 3
Plot 1
Note, we are not interested in stream direction for this analysis, and upstream vs. plots is not interesting. Just treat them as replicates.
Within each location this set of parameters were measured:
NH3
Ortho-P
SRP
NO3
NO2
Hardness
Alkalinity
Temp DO
Conductivity pH
TDS

6. Using these data you have three basic questions you need to answer for the exam:
Are the variables correlated across ALL sites? For the parameters we measured, they may be correlated regardless of sites. We need to know which are correlated. For this analysis, we will use a correlation coefficient cut off of Which are the most strongly correlated?
Test for a linear relationship between Temperature and Dissolved Oxygen. Biologically, in a natural system, water temperature should be a driver of dissolved oxygen. Here you want to test for a linear relationship across all measurements where temperature is the predictor and dissolved oxygen is the response variables. Is this relationship statistically significant? How much of the variation is explained by the linear relationship.
Is there variation among the sites in any of these parameters. For this part, you want to assess for an overall effect and also test for pairwise differences. For instance, do the streams vary in pH? If so, which ones are different from the others?

7. Details
Due: Monday 4/24/2017 – at the start of class
Final Document: <15 pages total. Printed.
This should include a clear explanation of your analyses and also a write-up of what you found. You do not need to present every graph you make, but you should illustrate your findings with clear figures and you should turn in analysis results.
The final page of your document should be a printout of the R code you used.

15. If you are like me and sadly accustomed to the nonsensical English system, you might want to do this

16. You might like to try something like this.

17. Here is a nifty thing- all the correlations at once!