datasets online

invertebrates

vertebrates

plants

 

 

final views of the ocean, waves, and terrace grasslands

IMG_2481 IMG_2427 IMG_2425

 

final sampling

IMG_2477 IMG_2489 IMG_2501

 

survey locations

sample locations

 

alternative format for paper

Given that everyone in the same group has the same Methods and Results, the main thing we are practicing is the Introduction and Discussion. Consequently, I would like to offer you the opportunity to write an increasingly common format for scientific papers. Many of the top scientific journals use this format now. It is entitled ‘short scientific communication’. Here is an example of the instructions from the journal Nature. In the journal Science, they are termed ‘brief communications’. I love them. The primary objective is to highlight novelty, critical thinking, research gaps, opportunities, or challenges to existing research. We can consider writing up these experiments using this format.

Format for a ‘short scientific communication’

Context. Similar to an Introduction but more shorter and more direct. State the research topic, explain the main purpose of the field of research, state the gaps, then state your hypothesis and predictions that fill this gap. One paragraph only.

Discoveries. Similar to your results. State what you found.  A total of 1-2 figures. One paragraph only.

Implications. Link what you found to the research of this specific topic. State whether hypothesis explained the system and if predictions were supported. Propose a really important implication of the work and suggest a future direction.

Literature Cited is 10-12 papers.

1854008pngu

Marking key

Context: 10

Discoveries: 10

Implications: 10

Literature Cited: 5

Effectively writing: 5

Methods: Just send me one copy for your entire group of exactly what you did. Even just typed up super clear notes, point form, so that I know.

 

 

 

 

 

code complete

the-da-vinci-code

It is not the da vinci but solid.

https://cjlortie.github.io/harding.invasion.networks/

 

Guidelines and instructions for final paper

Research paper is due Monday Sept 26th at 5pm value is 40%

Instructions

(a) Independent submissions BUT Methods and Results (including figures) can be the same. Introduction, abstract, and Discussion must be individual.

(b) Structure is as follows:

Title page: Title, author list listing all authors but with your name first, your email address.

Abstract: No more than 300 words total, and use single spacing. State the purpose, what you found, and identify at least one major of implication of this research.

Introduction: Two short paragraphs only. Paragraph 1. Introduce big picture of invasion, grasslands, and then your target taxa. Paragraph 2. Topic sentence, state hypothesis and predictions, then one sentence suggesting why the research is important.

Methods: Three paragraphs. Paragraph 1. Field site description. Paragraph 2. Sampling designs. Paragraph 3. Stats you did and link to your dataset online.

Results: Two paragraphs. Paragraph 1. State main findings. Paragraph 2. Were any covariates important?

Discussion: Two paragraphs. Paragraph 1. Restate hypothesis and state whether it was supported by the evidence you collected to test the predictions. Paragraph 2. Interpret the main finding and suggest implications (i.e. why someone should care what you found).

Figures: Likely two total. Main findings and perhaps one interesting covariate or side-pattern you found.

Literature Cited: At least 10 references to scientific papers on the topic (that you also cite in the main body of your paper).

Rubric/marking key

Introduction/10

Methods & Results/10

Discussion/10

Abstract/Lit cited/10

Guidelines

Once you submit your papers individually, I suggest you share your papers with each other, pick the best bits, then submit the final, single paper to PeerJ listing all authors and state that each contributed equally.

 

 

 

foggy day in paradise

A good day for coding.

fog

 

Guidelines and instructions for data submission

Dataset with meta-data published on figshare.com or knb.ecoinformatics.org Friday September 2nd by 230pm. Value 10%

Instructions
1. Back up/copy ALL data to the 2TB external HD in classroom. This includes the following data: (i) main data frames as .csv, (ii) covariate data, (iii) working data with ALL data including the nested/pseudo-replicates, and (iv) all videos and imagery captured.

2. Back up/copy the (i) main data frame and (ii) covariate data to the ‘dataset’ folder I set up on our class google drive.  Do NOT back up images or videos (no room).

3. I will mark ONLY the final dataframe with meta-data published on figshare or knb. However, I will need to see the working dataframes and covariate data frames too please to ensure accuracy.

TO submit: ONE file per group, email me the link to the main dataframe on figshare or knb.

Marking key

Data: Are the data correctly translated from the working data frame (i.e. is the mean of 6 or 8 cams correct, did the number of plant species from working plant samples translate across)? /5

Meta-data: Is the sampling well described and the column headings explained? The basic question is ‘can someone else not familiar with what you did understand and use the data’? /5

Tags: Are the tags, title for dataset, and subject area all correct?  See other blog post on tags. Ensure you list ALL members of your group as co-authors.

Summary
I need one email from each group with a link to the final data frame published online.
I will then check the google folder for the supporting data files and ensure it all connects correctly.

 

Open science products

Open science makes YOU look good.  It is also critical that scientists share what they produce and collect.

Best experimental design products – get them online! I enjoyed them all.

Figures, tables, and infographics : publish on figshare

Single slides, slide decks, and infographics: slideshare

Ten simple rules and papers: PeerJ preprints

Datasets on figshare or knb (if you have diversity data)

All these sites have the products online for anyone to find in the world.

Always use tags and identify the subject area.

Tags for experimental design:

Lortie (so I can find them)

experimental design

OUFB

best practices

environmental science

ecology

general science

ecodreamers (why not)

UCNRS

Kenneth S. Norris Rancho Marino Reserve

Tags for your datasets that are collecting this week:

Lortie

OUFB

ecology

UCNRS

Kenneth S. Norris Rancho Marino Reserve

Fiscalini Ranch Preserve

California

grassland

invasion

ecodreamers

then whatever your group was: plants, vertebrate animals, invertebrates

 

Get credit for ALL the work you did during this course and also list the link to these products on your resume and CVs!

a. experimental design summary

b. dataset

c. the paper on PeerJ (one ‘compiled’ paper with all papers AFTER you write your individual ones).

This is three awesome scientific outcomes you deserve recognition for.

Please send me the link to them once you publish, and I will share for you too.

3021307-inline-fb-thumbsup-printpackaging

 

r stats

great intro!

http://rforcats.net

programmer

 

amazing pics from the bus driver

everybody loves Cali!

001 002 003 004 005 007 008 009 010

 

Harding Grass

Oh Harding, what have you done!
IMG_2407 IMG_2406

We will find out Friday once we crunch the numbers.

 

bus departure at 545am

Frank will be our driver again Saturday. He will be here at 545am to load and be ready to depart at 6am.

 

 

meeting to do list

Excellent discussions last night.  Here is the list of final meetings before the course completion on Saturday.

  1. One workshop with each group to discuss hypothesis, predictions, and statistics.
  2. Guidelines on final paper.
  3. Discussion of open science products.

cranking

[still cranking at 1015pm]

 

Tips on making H & P’s

-Start by writing down an observation that interests you.

-Ask a few questions about your observation.

-A hypothesis should include an attempt to provide a mechanism that explains the phenomenon you observe.

– 2-3 predictions for each hypothesis is a good goal.

-Predictions are more of a simple statement than anything else. If there is more than 1 sentence in your prediction, make sure the additional sentences are absolutely necessary.

You guys are awesome. Good luck!

 

 

sample code and approach to data science, EDA, and stats

https://cjlortie.github.io/harding.invasion.networks/

rstats

 

common variable names and data frames

Variables, be not so.

all lower case.

final sheet.

site

management

transect

rep.day

harding.cover

exotic.plant.cover

bare.cover

animal.sign

taxa

abundance

diversity

sample.time

final, aggregated templates

note: you will need working files to get to this point too. still use common variable names.

invertebrates

plants

vertebrates

plants.fine

 

data collection

olympic data collection begins.

IMG_2389 IMG_2387 IMG_2388 IMG_2381 IMG_2376 IMG_2377

 

good food

the healthiest field course ever.

IMG_2367IMG_2368

 

grades for hypothesis & predictions

test-hypothesis

Everyone got 18/20 for the actual designs. EXCELLENT work in brainstorming and working so hard on datasheets, workflows, and structure of experiments.

The remaining 10 points was for H & P. It is a challenge to do these. Practice. The point of the field course.

Percent out of 30 points.

All groups got >80%. Eli and I will discuss in person to facilitate further before the final paper.

 

data science is open science

tidy data help.

Here is the review of a super useful data science book.

A review of ‘R for Data Science’ book @hadleywickham #rstats #openscience

 

Best experimental design outcomes summary

Here is the link to the summary analyses including r-code.

https://cjlortie.github.io/best.designs/

Mean: 80.029%

All dimensions of measure worked equally well.

No real differences between type of summary were evident (but did not have sufficient replication of alternatives to ten simple rules).

percents

 

The Wild Trees: A Story of Passion and Daring

A reading to follow up on your day today!
Recommendation from Don.

 

61BybiYkqYL._SX322_BO1,204,203,200_

 

outdoor classroom

IMG_2312 IMG_2318

 

dunes, the tide, salt marshes and our kayaks

IMG_2231 IMG_2232 IMG_2243 IMG_2254 IMG_2259 IMG_2264 IMG_2293 IMG_2295 IMG_2324 IMG_2340 IMG_2342

 

animal trackers

IMG_2077 IMG_2085 IMG_2094 IMG_2109

 

calpoly pier and boat

IMG_2121 IMG_2128 IMG_2129 IMG_2133 IMG_2156 IMG_2190 IMG_2197 IMG_2212

 

Dune research

IMG_2324Camila Castanho is an expert on dune ecology and interactions. Here is a nice synthesis paper on dune interaction research to date.

Estelle Forey is the dune ecologist expert from France.  Here is a spatial analysis of dune research and another on disturbance.

 

 

 

 

 

Just underneath where we were today!

http://www.belowmorrobay.com

 

Hello and see you soon!

Greetings Field Biologists!

I hope you’re amazing adventures on the central coast have been a great learning experience thus far. My name is Eli Swanson and I’m a Ph.D candidate up at Oregon State University. I’ll be helping you get your research surveys and questions set up next week and am really looking forward to it! I’ll be joining you on your ranch tour Saturday with Don and we can start to talk about your research ideas then. We’ll be using the following research protocol as a framework for your own investigations. Give it a brief look and we’ll talk about it in detail Monday morning. SamplingProtocolBiology3001

On Tuesday evening I’ll also be talking with you about some of the broader topics related to natural resource management and ecological disturbance and succession. As you are learning this week and seeing all these fantastic places on the central coast that attract ecotourists, be thinking about how all these great natural resources are managed, the environmental impacts from people and what ecological processes are important to consider in these coastal areas where social, economic and ecological pillars are so tied together. In prep for Tuesday, please read the following essay (its an easy and fun read) by Aldo Leopold. Whether you pursue a career in an ecological field or not, the tenets discussed in this paper are fundamental and useful to know. Leopold Conservation Ethic

Enjoy and see you soon!

Eli.

 

Marking key for experimental design heuristic

Philosophy

Research and teaching should be aligned. I applied the field notebooks workflow to this experimental design product. You will make key observations on the experimental design readings and use your notebook as a mechanism to explore structured thinking. I will then make key observations on the heuristic you provide, ask questions, and turn this into data (i.e. your grades are the data as a mechanism to describe/estimate how effectively your internalized best experimental design principles for ecology).

Marking key 

Likert scale from 1 to 5 (1 is low and 5 is awesome) to answer each question.
Score of 1 to 5 each, total is then 20% for assignment.

(1) Did you provide sufficient evidence you processed the readings?

(2) Is the heuristic you provided useful in designing experiments for ecology?

(3) Is the product (flowchart, table, decision tree, ten simple rules, etc) clear and direct?

(4) Is the case study example with hypothesis and predictions precise and linked to design?

The data structure from asking these questions is thus the marking key and then a spreadsheet with name, and a column for each question with a score of 1-5.

likert-scale

 

 

 

checking in on third morning youtube

 

best experimental design

First assignment: Critical analysis essay of research papers (Week 1).                          20%

Learning outcome
To be able to cogently summarize effective experimental design.

Rationale
Internalize best practices from reading about experimental design before we practice it next week. The goal is to get as much as you can from the learning of other people on how to best design experiments.

Products you can generate worth 20%
Summary of reading with a focus on critical thinking – mini-essay 2 pages long describing what  was proposed in papers but including your critical analysis of limitations of solutions.

Flowchart of best experimental design principles (ensure you show and cite the papers you read)

Table of challenges and solutions proposed in the papers (cite the papers and describe table very briefly)

Decision tree (show how you decide what level of sample unit to work on, handle design, or make best possible decisions).

Ten simple rules for best experiment design in ecology.

Here is the one I wrote for fun about rapid talk formats:
https://peerj.com/preprints/2326/

I have been wanting to write one for experimental design too, so go for it if you want. Ensure you each have your own rules, at least some at least.

Here is the ten simple rules for simple rules. haha. http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003858

In all instances, provide a short paragraph made-up example/case-study to show what you developed/criticized worked. In doing this, list your hypothesis, predictions, and then the design.
Nice example of a visual experimental design from a notebook.

 

Overview-of-the-experimental-design-At-the-experiment-endpoints-total-RNA-and.png

 

 

field notebooks

The field notebook is a critical tool in many subdomains of ecology. Here are three elements that I have found really useful for synthesis, discovery, and recovery of ideas from experiences outside.

  1. Summary of key observations. I try to capture at least 3-5 patterns or changes evident within a system.
  2. Questions. This is the most important element. Discovery happens from asking questions and practice
  3. Visual, qualitative, and quantitative data. Draw, record, write down what you see. Use this process to explore structure of the final data you will collect.

Here is a nice example of ten simple rules for similar notebooks: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004385

butek1_fn-1

 

happy hill

short hike through grasslands with different geomorphology and different management practices.

IMG_2022 IMG_2030 IMG_2046

We did jump into the ocean again at the end of hike – not warm.

http://www.nodc.noaa.gov/dsdt/cwtg/cpac.html

 

adventure this afternoon: happy hill and novel beaches and coastlines

IMG_1946

 

friendly goats

kept us company on walk.IMG_2011

 

low tide adventures

IMG_1964 IMG_1974 IMG_1983 IMG_2001 lSQpl

IMG_1992 IMG_1985

 

South-to-North

Carpinteria to Cambria (South-Central Coast to beginning of Big Sur Coastline).

IMG_1906

IMG_1918

tent point

camping

 

Welcome to Ontario Universities Program in Field Biology Course for California

This particular offering is going to be a really exceptional year. We have met more local people and organized more time on the water and more time exploring. Everything you need to know is in the tabs above. Dig in and see you soon.

Chris.

Note: Home for the week, camping, is at the University of California Rancho Marino Reserve. All key contact information to provide to your friends and family back home including phone numbers are on the website. Bathrooms, electricity, wifi, and a classroom are available at the field station. However, bring a tent for sleeping.