Preliminary Project Proposals and Intro to R (1/26/2015)

Reminders and things to do before Wednesday, January 28th:

  1. Read the three papers for Week 4.
  2. Get R or R Studio installed and working on your computer. Play around with the R script we worked on in class, all the files are in the Dropbox. Check out R for Ecologists website.
  3. Bring your computer to class on Wednesday for some interactive R coding.
  4. Get started working on project proposals with your groups.
  5. Plan our pirate themed potluck party.


We began with each group reporting what they had researched about their given set of topics and questions. I copy/pasted the relevant questions from last Wednesday’s class and added what we discussed in class today.

Leaf Litter: Kiely, Viri

General ideas: How does litter diversity/mixes, algae cover, or presence of macro-species affect leaf litter decomposition?

  • The Arboretum would be ideal for this project because it is closeby and we’re allowed to do experiments in it.
  • Can algae cover be used as a proxy for eutrophication and anthropogenic effects in stream communities?
  • Invertebrates have different leaf preferences, different leaves decompose faster than others.
  • Leaves often fall in the winter, so now that we’re heading into spring it may be too late for this to be ecologically relevant.
  • How does leaf litter from different trees decompose in urban water systems?
  • How does algae cover effect leaf litter decomposition? What is rate of decomposition? What is affect on invertebrates? Different amounts of algae cover?
  • How does the presence of macrospecies affect leaf litter decomposition in streams?

Diversity: Brendan, Philip, Jason

General ideas: How is biodiversity is affected by: nutrient levels, management regimes, and removal of non-natives?

  • How do different management practices (Fire/grazing/seeding) affect different trophic levels (e.g. soil invertebrates, plant pathogens, rodents; things other than the plants they are trying to restore)
  • We could use Russell Ranch; weeding and mowing is allowed but probably not any controlled burning.
  • Different types of soils due to geologic formations; can see this on Google Earth
  • Timing might be difficult because germination has already started.
  • Is biodiversity affected by nutrient availability? Nutrient pulse project.
  • Tying it back to the Intermediate Upwelling Hypothesis (Menge and Menge 2013).
  • We could use airborne fungi, algae, or plants and control the amount of nutrients being added to a system.
  • Nutrient manipulation is definitely feasible within the parameters of our project.

Vernal Pools: Avery, Alec

General idea: How do plants interact with other plants and their environment in vernal pools?

  • Study site: We are allowed to do manipulative experiments in these pools, including excluding, weeding, cutting, and collecting. There is a wide range of grazing intensities and exclosures, and we can install our own depending on our experiment. Lots of possibilities! It is about a 30 minute drive from Davis.
  • Can do both greenhouse and field experiments looking at grazing pressure, competition, inundation period, island effects (because most natives have short dispersal distances), soil composition, effects of native and non-native species, etc…
  • Are invasive grasses outcompeting native in grasslands/vernal pools? Survival of native plants measured.
  • Does grazing in vernal pools inundation period? And does this allow for natives to persist?

Team Tannins: Galls, Mistletoe, Fungi, and Parasites!

The original category was galls and mistletoe, but we quickly decided it would be too hard to study because they are rarely together on the same tree from our observations. So, they combined with Team Fungi to come up with some cool questions.

General ideas: How does the decomposition of tannins in galls affect the surrounding plant community and insect diversity? How does this play into the nutrient cycle? Can we use fungi (specifically oyster mushrooms) as a vehicle for understanding trophic levels and how secondary compounds affect communities?

  • Galls are high in tannins
  • Relatively cheap experiment.
  • Mushrooms, seedlings, and insects would not take that long to rear.
  • Field and lab component

Experimental setup: Grind up oak galls to simulate decomposition below oak trees. Try to grow native plants that normally grow below oaks (7-21 days), as well as in a greenhouse. Measure rates of growth at different levels of gall/tannin concentrations. Grow oyster mushrooms on tannin-rich soil, place outside to attract insects. Bring mushrooms back into the lab, see what insect larvae hatch.

Concerns: How natural is this experiment, and what can it actually tell us about what is happening in nature? Also, autoclaved soil used in greenhouses might present some issues.

Mistletoe: Michael, Kendra

We went into the field to see what we could find on mistletoe. Brought back samples from each sex of mistletoe, some insects, and a whole lot of dirt in case we want to look through the leaf litter.

  • Soapberry bugs, parasitic wasps, and evidence of egg laying/parasitism/something interesting happening on mistletoe leaves
  • Mistletoe is everywhere in Davis, so we have a wide range of study sites to chose from close to our home in Storer.

General idea: Potential to study multi-level trophic interactions, diversity, and parasitism.

One of our resident entomologists, Michael, identified the wasps as parasitic and hypothesized that they might be parasitizing the soapberry bugs we found on the same bunch of male mistletoe. There could be some really cool specific species interactions going on in this system, and there is the potential to think about questions from an evolutionary standpoint. What are these insects doing? Are they helping or hurting the mistletoe?

  • Diversity experiments are possible but timing might be challenging because most previous studies occurred over several years
  • Exclusion/manipulation experiments possible. Ex: use cages/mesh to exclude or contain certain animals based on size. Could place a certain number of animals inside and measure survivorship.


We then voted on our interest in each of these topics.

And the colorful results are….


Introduction to R

Kate and Kara led a crash course in R using data we just generated on project interest.

General tips and tricks:

  • Do not directly copy and past R scripts from sources. There could be hidden things in the code that you can’t see. And you’ll learn better by typing it out anyway.
  • Commas and parentheses are the most common source of error. If you’re getting frustrated with error messages, retype that line of code.
  • Clear your workspace of old variables and data before you begin using rm(list=ls( ))
  • Use the # symbol to write yourself memos about your script. Anything following this key will not be read by R, but you can use it to remind yourself what you’re doing and take notes. Use the $ symbol to denote a certain column you want to look at.
  • Apparently you can only drag and drop files in R, not in R studio
  • Make sure you are using saved files on your own personal computer so the ones on the course Dropbox are ~pristine~
  • You can change the color of your chart to rainbow

There are a few files in the course Dropbox with the script Kate showed us today, as well as the csv file of the data. All of you in the class should play around with the data and script and make sure you understand how it works. Come to the next class with questions or issues you might have.

Project Proposals

~500 word proposals

Proposal structure:

  1. Selling title
  2. Introduction including broader “big picture” concept — A conceptual basis or background for the question, how the project addresses this conceptual basis. Should include at least 3 citations.
  3. Questions and/or hypothesis
  4. Methods – A specific field site and study organism(s). Key factor, response variable(s), techniques used.
  5. Expected results – The potential outcome(s). Could be supported by a graph.

These proposals will be graded on four things:

  1. Originality (is this a novel contribution to the field of study?)
  2. Importance (justification of the study)
  3. Feasibility
  4. Communication (completeness, presentation, writing)

Post proposals to the blog as individual pages with the title and authors before class on February 2. One proposal per group.


Vernal Pools: Kiely, Avery, Alec

Team Tannins (Fungi): Sonja, Jason, Sean

Team Tannins (Plants): Bonnie, Viri, Jasjeet

Mistletoe: Kendra, Philip, Michael

Brendan will join one of these groups.

Proposed Agenda for Wednesday, January 27

2:00-2:45          Discuss papers (15 min each)

  • Diamond 1986: Kiely
  • Hairston 1989: Sonja
  • Hurlbert 1984: Brendan

2:45-3:05          Experimental/statistical design consideration and discussion

3:05-3:15          Stretch break

3:15-4:30          Explore lab resources

4:30-5:00          R Troubleshooting

And with that, I pass the blogging torch to you, Avery.

One response to “Preliminary Project Proposals and Intro to R (1/26/2015)

  1. Pingback: Experimental Design Workshop (1/28/15) | Ecology 180·

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