Schedule of Events

FOR 692, Spring 2018


Week of

Jan 15  Anastasia had 10 project ideas, Ruth suggested leads for clients

Jan 22  Anastasia had talked to prospective clients and developed her ideas

Jan 29  Anastasia’s 3 project ideas.  Enter Sarah, who already has her project and client

Feb 5  Bibliography (Anastasia, Sarah, Alli sent hers, Sean will later)

Feb 12 Annotated Bibliography. 

Feb 19  Draft Proposal due.  Give Intro presentations

Feb 26 Review Draft Proposal

Mar 5  Final Proposals due.  Time budgets and accounting.  Mid-term feedback

(Spring Break)

Mar 19  (keep working, Ruth out of town)

Mar 26  Check in

Apr 2  …checking in on projects...

Apr 9  Statistical models from Sean and Sarah

Apr 16  Draft Reports due

Apr 23  Review Draft Reports

Apr 30  Final Presentations

Final reports are due on the day scheduled for an exam in our time slot.

May 4  Final Report

Grading scheme

The majority of your grade will be based on your projects:  25% for oral presentations (5% for the Intro and 20% on the Final) and 40% for written reports or other products.  The project proposals are 15% and the remaining 20% is for other assignments such as time and effort accounting, feedback for presenters, and preparing for skill sessions if needed. 

Late assignments will be discounted at the rate of 10%/day.  Assignments required for class participation will be worth 0% after the day we needed them.

Undergraduates are not required to give oral presentations.  Let us know if you want to anyway!

Feb 1

Anastasia’s 3 Project Ideas

1.  City’s wood waste system:  Steve Harris, a lot of ash is getting chipped.

Cosmo Fanizi has a mill in the city.  City Woods.


2.  The new DPW direction was on OCRRA, she is looking into make more of the yard waste.


3.  Urban sugaring.  Management plan or a financial analysis.


How are you going to proceed?  How to narrow it down?

Where is there more of a need?  The City Woods thing is pretty well established.


What would the objective be?

What would the product be?


Time Sheets

previous notes follow 

Check out the collections in google drive and try one or improve on what we have.


Guidelines for Time Sheets

Time entries are in rows, with the most recent at the bottom.

Columns are for categories of tasks, grouped into more general categories.  Examples include: communications, background reading, field work, writing the proposal.  Overhead (not directly related to your project) would include class work like reviewing each other’s proposals or preparing your background presentation.

Show gridlines (if printed), freeze header panes, color optional (especially if printed).

The week starts on Monday and ends on Sunday.

Add a table with weekly project totals.

Time sheets will be due on Monday for the preceding week.

Feb 5: Bibliography


Where did you look, what search terms did you try, what worked and what didn't?

20-30 references (we don't expect that all will be useful). 


Upload your bibliographies by class time, and also send them by email.  Let me know if you have any questions!


Great coverage of subject matter!

Some citations are incomplete.  Can a reader find the reference from the information you provide?

Proofread!  These came in automated:  Ehrlich, John. n.d. (but the date appears later)


 Key words: nitrogen, phosphorous, acid rain, nutrient amendment, light regime, light attenuation, biomass allocation, allometric, twig density, leaf anatomy, macronutrients, calcium, mesophyll length, hardwood, sugar maple, cations.


            In my search, I found literature that discussed the response of hardwood trees to atmospheric nitrogen deposition. Many papers reported that an increase in nitrogen displaces cations in the soil, thus acidifying the soil and mobilizing iron and aluminum. The mobilization of iron and aluminum in the soil can make phosphorous inaccessible to the trees and can increase soil toxicity. The excess of nitrogen may also lead to a lower C:N ratio in soil and foliage and decreased efficiency of organic matter mineralization in forests. It has even been suggested that the increase in nitrogen availability may lead to a shift towards phosphorous limitation in northeast hardwood forests.

            I found it difficult to find literature on differences in the vertical stratification of biomass allocation in the tree canopy. Although this study is examining differences between individual trees, considering a subset of factors within the tree will attempt to highlight any bias in the data. This includes the light regime, differences in twig density, and the movement of nutrients from the top of the canopy to the lowest available foliage. I also realized there are many other factors to be considered outside the individual trees, such as mycorrhizal associations and their relationship with nutrient acquisition. I would like to further explore the mycorrhizal relationships with sugar maple and assess how this may affect the availability of nutrients in this study.



Cost analysis, check citations: include URL, date, organization, etc.

Star system 0-5, 0 being irrelevant, 5 being great


Source comments:



... great sources!...

Denig: maybe talk to city, could be valuable

King: invasive species regulations

*find regulations that could pertain to syracuse

Matheny: “lower stars”

Mitchell: should find out how title is relevant

Nowak & O’Connor: good for syracuse

Plumb: may not be relevant: “woody green waste”

Conference may be very helpful (who hosted it, is there more information outside this conference)

Are there more recent national surveys of urban tree residues?

Feb 12: Annotated Bibliography

Annotated bibliographies


Sarah found some 10-star (very relevant) papers.  Need to figure out “leaf mass area” and how it relates to what you will measure (specific leaf area).  There are a lot of papers about vertical stratification of leaf mass, which we don’t have (did they cut down the tree?).  But shade leaves and sun leaves are super relevant, even if they don’t report the height in the canopy (sun above shade).


Anastasia already had good sources last time.  She needs to know how to develop a wood utilization plan--involving stakeholders sounds challenging.  She found examples from other cities.  Some had good cost information.  She found some specific to emerald ash borer.

It would be easiest to develop something for mulching or composting.  Using sawlogs is more challenging.


Aley: Houston’s study reported that one of the fungal species comes first, but a review paper says that this is not always the case. Find out when the disease complex arrived at your research site.  There are studies pertaining to nitrogen and phosphorus.  Good!


Sean found papers on nutrient resorption and leaching from leaves, and how N and P additions affect those.  For work from our study site, look at Kara Gonzales’s thesis.  Craig See has a paper in revision on changes during the litterfall season, Kara has two papers in preparation.

We have a study on N and P co-limitation, but not all of you will be providing answers to this topic. 


Pose a question you can answer!  If you later find that your results don’t answer it, change your objectives.


Advice to all: Pick the citation that will be most useful to your readers.  It might not (will usually not) be the first one you read that might support your statement. When you have read widely, you know which are the best papers.

What’s in a Proposal?


We reviewed the review sheet for proposals, which lays out what is expected.

Feb 19:  Intro Presentations


Sara, Sean, and Anastasia gave Intro Presentations (see google folder).  Thanks!


Aley had some project ideas, we asked clarifying questions.

Neonectria is the genus, you identify the species by the length of the ascospores.  So does N or P addition affect the size of the ascospores (i.e. a change in species dominance).

Or, does nutrient addition affect whether the two species co-occur on the same tree?  In the same plot or the same tree?

Whether the age of the stand affects co-occurrence.

Sarah:  For the age of the tree, do you need to know when the disease arrived?

Ruth:  At the scale of the landscape, the disease arrived at all our sites at the same time.  But it takes time for the disease to develop on an individual tree, so little trees will be different than big trees.

Reviewer Assignments

Sarah and Sean review each other’s proposals.  Aley and Anastasia review each other’s proposals.

Check in on timesheets.

Upload them and we’ll talk about them when we meet next.

26: Review Draft Proposals

Send your draft final report to everyone on .... 

Primary reviewers:  (see above)

Upload a written review by class time on Feb 26. 

Secondary reviewers are responsible for reading the proposal but not writing a review.

Secondary reviewers (never mind, everyone should look over all the proposals).



            Start with a general problem statement and funnel us towards the very specific problem that you’re going to answer with your results.  What is known and what knowledge gap you will fill.


Could include testable hypotheses

Methods (what’s needed to meet the objectives)

            Site description

            Field methods

            Sample processing

            Data analysis

Expected results:  Make a graph with imaginary data.  This may help you develop hypotheses!  Then go back and make the case in your Introduction for these expectation.

            Could include broader implications

Budget your time

       Supplies and materials we need to purchase





            Everything that you cite and nothing more

            Use APA or another format that allows us to see the author

            Choose the reference most useful to the reader NOT the one where you first read about this.

Other topics

We discussed the cover page, how much contact information should be included?  Enough for someone to pick up the phone and call you?  Are they going to fax you?

Anastasia’s product will be a proposal (potentially confusing); put the outline of that proposal in the Products section

March 5:  Final Proposals

Final Proposals

I forget who said this was a good timeline, we can adjust.

Sarah finished today, earlier than anticipated.

Sean is checking something with Dan, will finish this weekend or early next week.

Anastasia:  end of this week or beginning of next week.

Paper copies can be delivered to 428 Greenwood Place (end of Avondale, 1 block from Westcott)


Upload and we’ll look at examples and see what works best.

Sean has estimated times, which is the best way to improve your estimation skills.

Sarah has in and out like a time clock.  Use Excel to calculate the time worked.

For adding hours in different categories, you could use labels and an “if” in Excel.

Lookup tables (VLookup or HLookup) are cool, check them out.

Freeze panes so we can see your column and row headings even when we scroll.

Consider Toggl for tracking your time--and tell us how it went.

Project Updates

Sarah’s twigs are going according to Plan.

Sean was held up by school closing.  He wants to finish leaves before spring break.  Lab work will be strictly scheduled.

Anastasia:  Things are moving consistently.  She will have more time over the break.

Course Planning and Improvement

Feedback on the activities to date, and suggestions for the rest of the semester.

10 project ideas

3 project ideas


Review of draft proposals


Future secondary topics (your projects being primary): 

Sarah: Interviews

Anastasia: Team management, etc.

Steps towards grad school.

March 26:  Progress reports

How’s it going?

Sean had questions about statistical models, we will have a session for that on April 9.

Sarah hasn’t started microtome processing yet.  Alex is going to try it and then decide.  So next week we want an update on everyone’s scope of work.

Anastasia sent her proposal (draft report) today.  A lot of people contributed, she’s starting to get numbers.  For her GIS class, she is doing a cost-distance analysis.  The state arborist has a database.  The town of DeWitt keeps track of costs (better than the City of Syracuse).  They use the FEMA schedule of equipment estimates.  This will help compare different options for disposal.  Currently she has three options (including business as usual, what they are doing now).

Timesheet show and tell


Toggl if anyone tried it.

April 2

Sarah will give us a report on the scope of her project:

Twigs will be done on time.  It’s faster now that they have more blocks.

Microtome sectioning has yet to be tested.  It was done in a class, they are looking for materials, like the mounting medium.  Alex is concerned about some aspect of the medium damaging the leaves.


Same for Sean given how much time he has and how to prioritize sample processing for tissue analysis.

Answer:  He will start with C1, and do all the species in one stand.  Then he will do all the yellow birch, since all the stands have yellow birch.  That will mean 99 samples total.  Other students are helping (four students total), for 10 hours of grinding, 3 digestion runs, 8-10 hours.  The ICP is an unknown.  Ruth’s advice is to book in advance!


Anastasia reports that things are going well.  Ruth’s feedback on the proposal was helpful.

We discussed how to cite personal communications and various choices of style guides.

April 9: Statistics Workshop

Sarah, Dan, Sean, David, Alex, Ruth


Factorial NxP or 4 treatments?  Goswami et al. 2018, Ecology uses both.  They tested for an interaction, and then since P had an effect on growth but not N, they tested whether NP was any better than P.

Model:  (factorial)   y~ Ntrt + Ptrt + Ntrt*Ptrt

(each observation is coded as to whether it got N or P)

Model:  (no-factorial)   y~ N + P + NP + Control

 (each observation is coded with one of these treatments)


Fixed vs. random effects:  Are you interested in differences among stands?  If they are replicates, then stand is a random effect.

In the MELNHE study, we have argued about whether site (JB, HB, Bartlett) is a fixed effect, we picked them for contrasting soils.

If they are three samples that characterize the landscape, you could argue that site should be random.


Scope: 3 stand (C7, C8, C9), 4 plots/stand, 1 tree/plot

experimental unit: tree (same as plot)

response variables: foliar chemistry elements (N, and others!), twig length, twig mass, specific twig length, leaf mass, leaf area, specific leaf area.  Ask for more variables if those turn out to be disappointing (chlorophyll a, chlorophyll b, cholorophyll a/b, total carotenoids.

explanatory: height in the canopy, treatment (N,P,NP,C)


Model statement for sla:  sla ~ Ntrmt + Ptrmt + Ntrmt:Ptrmt + dfromtop 

 ---- the above model does not ackowledge that there are three different stands.

model statement for sla (including tree nested within stand):

 sla ~ Ntrmt + Ptrmt + Ntrmt:Ptrmt + dfromtop   + ( 1 |Stand/Tree.ID)


Which is a better predictor, height from the top or height from the bottom?  (These are different because trees were different heights and had different numbers of samples collected at 2-m intervals from the top)  Try also scaling each tree and giving the height a value from 0-1.


experimental unit: tree #

response: specific leaf area, Resorption Efficiency and Proficiency Chemistry (P,Ca,...), leaf mass, and leaf area

explanatory: treatment (N,P,NP,Control, Ca (only C1,C6,C8)), species, stand age, site, DBH?


  1. Scope:  1 stand (C1), 3 species: WB, BE, and PC)

model 1 (NxP! for C1) <- sla ~ Ntrt + Ptrt + species + Ntrt:Ptrt:species + Ntrt:Ptrt

model 2 (Treatment for C1) <- sla ~ Treatment + species + Treatment:species


B. Scope:  1 species (YB), 4 stands: C4, C6, C8, and C9

model 3 (NxP! for other stands for YB only) <- sla ~ Ntrt + Ptrt + Ntrt:Ptrt + (1|StandAge/Stand)

model 4 (Treatment for other stands for YB only) <- sla ~ Treatment + (1|StandAge/Stand)


In one stand (C4), for one species, litter was collected at the plot level, not for each tree.  But those samples are not part of this analysis

Treat Ca and Control separately from factorial design.

Stands will be a random effect in regards to stand treatment but a fixed effect in regards to stand age.

Bartlett granite based soil



Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

chla<-lmer(chla~Ntrmt+Ptrmt+Ntrmt:Ptrmt + dfromtop+(1|Stand/Tree.ID),data=Acerdata)

Response: chlorophyll a

               Chisq Df Pr(>Chisq)   

Ntrmt        13.1205  1  0.0002921 ***

Ptrmt         0.4282  1  0.5128824   

dfromtop    112.4573  1  < 2.2e-16 ***

Ntrmt:Ptrmt   0.0217  1  0.8828385   



sla<-lmer(sla~Ntrmt+Ptrmt+Ntrmt:Ptrmt + dfromtop+(1|Stand/Tree.ID),data=Acerdata)

Response: sla

               Chisq Df Pr(>Chisq)   

Ntrmt         2.0879  1     0.1485   

Ptrmt         0.0784  1     0.7794   

dfromtop    165.1977  1     <2e-16 ***

Ntrmt:Ptrmt   0.3533  1     0.5523    



chlb<-lmer(chlb~Ntrmt+Ptrmt+Ntrmt:Ptrmt + dfromtop+(1|Stand/Tree.ID),data=Acerdata)

Response: chlb

               Chisq Df Pr(>Chisq)   

Ntrmt        11.1752  1   0.000829 ***

Ptrmt         0.7685  1   0.380667   

dfromtop    144.1986  1  < 2.2e-16 ***

Ntrmt:Ptrmt   0.0164  1   0.898245   


April 16: (Draft reports due)

Sean:  Tuesday

Sarah  submitted a draft, but she’s still working on it.  She has some results, will talk to Alex about statistical analysis in R.  Maybe Wednesday.

Anastasia is uploading one but she’s hoping to make a couple more maps.

Authors:  Tell your reviewer if you are planning to make improvements and when, but they are not required to wait and squeeze in a review at the last minute.

Project updates

Sarah is waiting on twig data, Gabriel is supposed to do it.  Ruth suggested she set a meeting time with him, it’s more likely to get done.

Anastasia:  What is the most challenging thing about the project?  Putting numbers together in a way that makes sense.  We suggested stacked bar graphs.


Review abstracts for Spotlight (due April 17)

We did this in a google doc with other abstracts from my lab (including Sean’s)

April 23: Review Draft Reports

Poster review!  Bonus session (optional) at 2:15 

Report review at 3:45

Send your draft final report to everyone, let them know if you are updating it.

Primary reviewers:  Anastasia reviews Sarah reviews Sean reviews Anastasia.

Upload a written review by class time on April 23. 

Secondary reviewers are responsible for reading the report but not writing a review.

Secondary reviewers:  (everyone else)


Anastasia’s review of Sarah’s report.  We started with things we like: opening lines (yes!  It was hard to write a problem statement for this paper), completeness of the methods section, standardized citations, completeness of the data set.

P values should be written out to 0.01 place unless you need more places to get to the first digit.  (P = 0.63 but P = 0.006)  Stop with 1 digit if it’s <0.01.


Sean’s review of Anastasia’s report.  We like the content, the layout, and the reports from important informants.




Let’s discuss the options for tailoring the evaluation form to your projects.  For Sarah and Sean, my rubric for scientific papers might be better.  For Anastasia, what is a Methods section?  Would it be useful to write this up for the class?  Ditto for Project Evaluation, for everyone.  Include this as an Appendix.

April 24:  Spotlight!

Poster boards are 48”, both dimensions? The printer in Baker goes to 36”. 

Commonly 36” x 24” (landscape) or 36” x 48” (portrait)

April 30:  Final Presentations

I reserved 324 Bray, same place as the Intro Presentations.


May 4:  Final Report

Due on the date scheduled for the final exam for our class meeting time.