Review journals or journals with synthesis format contributions in EEB

Colleagues and I were checking through current journal listings that either explicitly focus on synthesis such as systematic reviews or include a section that is frequently well represented with synthesis contributions. Most journals in ecology, evolution, and environmental science that publish primary standard, research articles nonetheless also offer the opportunity for these papers too, but it can be less frequent or sometimes less likely to accept different forms of synthesis (i.e. systematic reviews in particular versus meta-analyses).


Diverse synthesis contributions very frequent
Conservation Letters (Letters)
Perspectives in Science
Perspectives in Plant Ecology, Evolution and Systematics
Diversity & Distributions
Ecology Letters
Biological Reviews
Annual review of ecology, evolution, systematics
Letters to Nature
Frontiers in Ecology and the Environment
PLOS ONE (many systematic reviews)
Environmental Evidence
Biology Letters
Quarterly Review of Biology

Frequent synthesis contributions with some diversity in formats
Global Ecology and Biogeography
Annals of Botany
New Phytologist
Ecological Applications
Functional Ecology
Proceedings of the the Royal Society B
Ecology and Evolution



A set of #rstats #AdventureTime themed #openscience slide decks


I recently completed a set of data science for biostatistics training exercises for graduate students. I extensively used R for Data Science and Efficient R programming to develop a set of Adventure Time R-statistics slide decks. Whilst I recognize that they are very minimal in terms of text, I hope that the general visual flow can provide a sense of the big picture philosophy that R data science and R statistics offer contemporary scientists.

Slide decks

  1. WhyR? How tidy data, open science, and R align to promote open science practices.
  2. Become a data wrangleR. An introduction to the philosophy, tips, and associated use of dplyr.
  3. Contemporary data viz in R. Philosophy of grammar of graphics, ggplot2, and some simple rules for effective data viz.
  4. Exploratory data analysis and models in R. An explanation of the difference between EDA and model fitting in R. Then, a short preview of how to highlighting modelR.
  5. Efficient statistics in R. A visual summary of the ‘Efficient R Programming’ book ideas including chunk your work, efficient planning, efficient planning, and efficient coding suggestions in R.

Here is the knitted RMarkdown html notes from the course too, and all the materials can be downloaded from the associated GitHub repo.

I hope this collection of goodies can be helpful to others.



A common sense review of @swcarpentry workshop by @RemiDaigle @juliesquid @ben_d_best @ecodatasci from @brenucsb @nceas

This Fall, I am teaching graduate-level biostatistics. I have not had the good fortune of teaching many graduate-level offerings, and I am really excited to do so. A team of top-notch big data scientists are hosted at NCEAS. They have recently formed a really exciting collaborative-learning collective entitled ecodatascience. I was also aware of the mission of software carpentry but had not reviewed the materials. The ecodatascience collective recently hosted a carpentry workshop, and I attended. I am a parent and use common sense media as a tool to decide on appropriate content. As a tribute to that tool and the efforts of the ecodatascience instructors, here is a brief common sense review.


ecodatascience software carpentry workshop
spring 2016





sw carpentry review

You need to know that the materials, approach, and teaching provided through software carpentry are a perfect example of contemporary, pragmatic, practice-what-you-teach instruction. Basic coding skills, common tools, workflows, and the culture of open science were clearly communicated throughout the two days of instruction and discussion, and this is a clear 5/5 rating. Contemporary ecology should be collaborative, transparent, and reproducible. It is not always easy to embody this. The use of GitHub and RStudio facilitated a very clear signal of collaboration and documented workflows.

All instructors were positive role models, and both men and women participated in direct instruction and facilitation on both days.  This is also a perfect rating. Contemporary ecology is not about fixed scientific products nor an elite, limited-diversity set of participants within the scientific process. This workshop was a refreshing look at how teaching and collaboration have changed. There were also no slide decks. Instructors worked directly from RStudio, GitHub Desktop app, the web, and gh-pages pushed to the browser. It worked perfectly. I think this would be an ideal approach to teaching biostatistics.

Statistics are not the same as data wrangling or coding. However, data science (wrangling & manipulation, workflows, meta-data, open data, & collaborative analysis tools) should be clearly explained and differentiated from statistical analyses in every statistics course and at least primer level instruction provided in data science. I have witnessed significant confusion from established, senior scientists on the difference between data science/management and statistics, and it is thus critical that we communicate to students the importance and relationship between both now if we want to promote data literacy within society.

There was no sex, drinking, or violence during the course :). Language was an appropriate mix of technical and colloquial so I gave it a positive rating, i.e. I view 1 star as positive as you want some colloquial but not too much in teaching precise data science or statistics. Finally, I rated consumerism at 3/5, and I view this an excellent rating. The instructors did not overstate the value of these open science tools – but they could have and I wanted them to! It would be fantastic to encourage everyone to adopt these tools, but I recognize the challenges to making them work in all contexts including teaching at the undergraduate or even graduate level in some scientific domains.

Bottom line for me – no slide decks for biostats course, I will use GitHub and push content out, and I will share repo with students. We will spend one third of the course on data science and how this connects to statistics, one third on connecting data to basic analyses and documented workflows, and the final component will include several advanced statistical analyses that the graduate students identify as critical to their respective thesis research projects.

I would strongly recommend that you attend a workshop model similar to the work of software carpentry and the ecodatascience collective. I think the best learning happens in these contexts. The more closely that advanced, smaller courses emulate the workshop model, the more likely that students will engage in active research similarly. I am also keen to start one of these collectives within my department, but I suspect that it is better lead by more junior scientists.

Net rating of workshop is 5 stars.
Age at 14+ (kind of a joke), but it is a proxy for competency needed. This workshop model is best pitched to those that can follow and read instructions well and are comfortable with a little drift in being lead through steps without a simplified slide deck.


A #scicomm resource guide to video abstracts

I just discovered video abstracts last week thanks to a scientific communication seminar by SciFund founder Jai Ranganathan. Lacking shame, I decided to try one because I just had a paper come out that week. Here was my first attempt at the process.

Of course, I had really no idea what I was doing but did some solid scientific-communication learning.

Personal Discoveries
1. Eyes. Look directly at the camera.
2. Plan. Do not script but think about what you want to say in advance.
3. Do not read. Having the abstract available to read is useful, but watching someone else read it is not that fun and quite distracting (mid-way through you can see me reading it).
4. Personal motivation. Describe your personal reason for doing the paper not listed in the actual abstract.
5. Audience effect. Going public and posting it feels much different than recording and watching on your machine.

A relatively empty niche for ecologists
Excluding kittens, we have an opportunity here. Doing the research now, I checked my two fav ecoblogs (The Oikos Blog and The Journal of Ecology Blog) that are directly associated with journals. I did not see any video content. Loads of great pictures, but no other media.  I also checked the blog provided by Ecography too. Similarly, I could not locate any videos. I then checked the facebook pages for these journals to no avail.  Using the youtube search bar directly, I did find some excellent videos by The Journal of Animal Ecology and Functional Ecology. However, these offerings were not quite the video abstract format I was expecting – author describing a recent paper in brief. If there are loads of them out there for ecology, they are not that easy to find. Consequently, I propose we have an opportunity to do some potentially compelling or at least more personal scientific communication about our research. There are numerous resources for scientists associated directly with video abstracts.

Video abstract resources
1. The scientist videographer blog has a post on how to make a video abstract for your next journal article.  Good introduction.

2. The guidelines provided by the New Journal of Physics for video abstracts are fantastic.

3. Cell also has specific guidelines that are more technical in nature, but the sample videos on the side bar are amazing.

4. To round out your education on the topic, check the out the video abstracts for the Journal of Number Theory.

5. Finally, the simple rules for good oral presentations still apply.

I propose ecologists fire up those webcams built right into the laptops (but use an external mic). We have audience (at least we can share with each other, i.e. ecolog-L has over 10,000 members) and outcomes could include better recognition of one another and appreciation of the inspirations and motivations that drive us to study natural systems.

In a nutshell, plan, be brief (< 4 mins), check audio, minimize distractions, be personable, and view as a mini-story (somewhere between elevator pitch & actual abstract).


A legal workaround idea for non #openaccess ecology articles – university library #openpaper #outreach days

The access paywall of many scientific journals is a significant barrier to a rapid, efficient process of securing many peer-reviewed ecology and science articles. Recently, I needed to assess the state-of-the-art for animal camera trapping in wildlife ecology. I used google scholar and web of science to populate a list of papers to read. I was ‘behind the paywall’ at a university IP address. Even with this barrier removed, it was a challenge.  I wanted to pull down a total of 20 papers, and only 60% of these were readily available because even with the exorbitant subscription fees the university library pays, some journals were not included. I realized that few wildlife ecologists and managers have even the limited level of access that I had to these very applied papers. This is a problem if we want evidence-based conservation and management of natural systems to prevail. There are numerous solutions of course including contacting the authors directly, searching for it online and hoping you get lucky to find it posted somewhere, checking researchgate, and joining a few other similar access author-based portals. There are two other simple solutions of course to engage managers – share with them directly when it is in print and encourage them to join a service like researchgate. Identifying managers interested in our work and sending it to them is a form of scientific communication and outreach. We need to do it. However, I had an even more broad public outreach idea – use university libraries as public access research portals.

University libraries pay subscription fees to many publishers. Leverage this access to run open science or open paper days.  In my experience, even with a temporary guest ID on wifi at most university campuses, one is able to access their full offerings of peer-reviewed publications. Universities could use this access and do even more – educate on peer review and show off all the incredible research that more often than not taxpayer dollars fund.

University-library solutions
1. DayUse Research-IDs. University libraries are increasingly digital repositories of information. Show this off to the public, the parents, and local applied researchers by offering guest-research IDs for a day at time for the public to browse holdings.
2. Notifications for digital research content. University libraries are increasing more like digital cafes than physical holdings of books. Advertise the resources that are available behind this paywall to all users, regularly, when they are online. Notifications/alerts, additional linking to primary research from courses and less on textbooks, and potential (non-obtrusive) pop-ups within the network for students on new research developments.
3. Open-paper public days. University libraries should run access days to teach the public about modern bibliometric search tools, explain the peer-review process, explain the publishing process, and show/allow folks to look up primary research that interests them. There will always be a topic someone needs to know about and a journal for it. Most importantly, these days will promote scientific literacy and also potentially provide fuel to new pay models or even better different profit models for academic publishers. If non-academics that pay taxes fully comprehended how much awesome research is out there in this academic stream that they never get to see, access, and pay for through tax dollars, it is hard not to imagine they would not want to see big changes.

The function of a university library
University libraries can still look like this.


More often that not university libraries instead look like massive digital cafes or computer labs.


The problem with all the information in the ether and behind these paywalls is that this intangibility hides the depth of the resource and extent that information could and should be available more broadly.  I love the ‘learnings common’ philosophy that is evolving in many university libraries. I am just concerned that it is not reaching far enough out – at least to the parents of the students that attend the university.

University library websites have improved dramatically and feel more contemporary. However, there is a limited signal of the extent of the digital research that are held and no indication of how the public might access even a tiny bit of this infrequently to learn. I recognize public libraries and university libraries are not quite the same thing, but why do they have to be so different. Can they partner, co-evolve, and reduce the paywall limitation to the research that matters for better decisions at least for health and the environment?


My best guess is that university libraries thus provide three significant functions in this domain.
1. Provide access to research.
2. Provide a space to access and do research.
3. Train and educate on how to do research.

As a researcher, the first is the most critical to me. As an educator, all three are important to my students.

I recognize all of this misses the point – research should be open. Primary researchers should strive to be OA all the time with our work, but I recognize that there are reasons why we can not necessarily achieve this goal quite yet. Journals can also work towards this end too.

In interim, much of research needed to make the best possible decisions is out there now – i.e. where and how to deploy animal cameras for conservation this field season for my team – and the natural now is changing rapidly.
I want science to help. To do so, we need to be able to see it. Now.