GEB adds unlimited data references section to papers
In a big step forward for allowing proper credit to be provided to all of the awesome folks collecting and publishing data, the journal Global Ecology & Biogeography has just announced that they will start supporting an unlimited set of references to datasets used in a paper.
A growing concern in the macroecological community has been that many papers whose data are used in meta-analyses or data-compilation papers have not been getting citation credit because most journals require these papers to only be listed in the supplemental material (which is not indexed by most indexing services). GEB is proud to support the inclusion of a second list of references within the main paper for all data papers used… To our knowledge, GEB is the first journal in the ecological field to do this. And we’ll be working with Wiley to further improve options in this area.
These references will be included immediately following the traditional references section in both the html and pdf versions of the paper. You can see an example in Olds et al. (2016).
What this means is that when you combine data from dozens or hundreds of studies to conduct a synthetic analysis, you can cite all of the sources in a way that will provide citation credit to those collecting the data1. It also means that scientists using large data compilations can cite the original data sources as well as the compilation itself2.
This is important for encouraging the publication of data, since one of the common reasons that scientists don’t publish data is a lack of credit, and citation only in non-indexed supplementary materials sections is a common concern.
Facilitating proper citation of all data sources is something the community has been requesting and it’s great to see GEB taking the lead in this area. Since Wiley, the publisher of GEB, is the largest publisher of ecology journals, it should be straightforward to implement this new approach widely. If other journals follow GEB’s lead, we will enter a new era where citation of data can be as complete as possible, allowing proper credit to everyone who collects and publishes data.
1GEB will need to make sure that this section gets properly picked up by the indexers, and tweak the presentation as necessary if it isn’t.
2Provided that the compilation provides a method for compiling a citation list of all associated sources.
Thoughts on preprints and citations
A couple of months ago Micah J. Marty and I had a twitter conversation and subsequent email exchange about how citations worked with preprints. I asked Micah if I could share our email discussion since I thought it would be useful to others and he kindly said yes. What follows are Michah’s questions followed by my responses.
Right now, I am finishing up a multi-chapter Master’s thesis and I plan to publish a few papers from my work. I may want to submit a preprint of one manuscript but before I propose this avenue to my advisor, I want to understand it fully myself. And I have remaining questions about the syntax of citing works when preprints come into play. What happens to a citation of a preprint after the manuscript is later published in a peer reviewed venue?
At the level of the journal nothing happens. So, if you cite a preprint in a published ms, and that preprint is later published as a paper, then the citation is still to the preprint. However, some of the services indexing citations recognize the relationship between the preprint and the paper and aggregate the citations. Specifically, Google Scholar treats the preprint and the published paper as the same for citation analysis purposes. See the citation record for our paper on Best practices for scientific computing which has been cited 49 times, but the vast majority of those are citations to the preprints.
Here’s an example with names we can play with: Manuscript 1 (M1) may require some extra analysis, but it presents some important unexpected results that I would like to get out on the table as soon as possible. M1 is submitted to PeerJ Preprints and accepted (i.e., published online as a preprint with a DOI). M2 is submitted to Marine Ecology Progress Series (MEPS) for peer review, and M2 cites the PeerJ Preprint M1.
Just a point related to vocabulary, I wouldn’t typically think of the preprint as being “accepted”. Any checking prior to posting is just a quick glance to make sure that it isn’t embarrassingly bad, so as long as it’s reasonably written and doesn’t have a title like “E is not equal to mc squared” it will be posted almost immediately (within 48 hours on most preprint servers).
1) Are preprints considered “grey literature”? That is, is it illegitimate for M2 to cite a work that has not been peer reviewed?
Yes, in the sense that they haven’t been formally peer reviewed prior to posting they are similar to “grey literature”. Whether or not they can be cited depends on the journal. Some journals are happy to allow citing of preprints. For example, this recent paper in TREE cites a preprint of ours on arXiv. Their paper was published before ours was accepted, so if it wasn’t for the preprint it couldn’t have been cited.
2) Is there a problem if M1 is eventually published in a peer reviewed journal but the published article of M2 cites only the PeerJ Preprint of M1?
I would say no for two reasons. First, assuming that M2 is published before M1 then the choice is between having a citation to something that people can read, science can benefit from, and that can potentially be indexed (giving you citation credit) vs. a citation to “Marty et al. unpublished data”, which basically does nothing. Second, all preprint servers provide a mechanism for linking to the final version, so if someone finds the preprint via a citation in M2 then that link will point them in the direction of the final version that they can then read/cite/etc.
In short, I think as long as you aren’t planning on submitting to a behind the times journal that doesn’t allow the submission of papers that have been posted as preprints (and the list of journals with this policy is shrinking rapidly) then there is no downside to posting preprints. In the best case scenario it can lead to more people reading your research and citing it. The worst case scenario is exactly the same as if you didn’t post a preprint.
Ecology Letters now allows preprints; and why this is a big deal for ecology
As announced by Noam Ross on Twitter (and confirmed by the Editor in Chief of Ecology Letters), Ecology Letters will now allow the submission of manuscripts that have been posted as preprints. Details will be published in an editorial in Ecology Letters. I want to say a heartfelt thanks to Marcel Holyoak and the entire Ecology Letters editorial board for listening to the ecological community and modifying their policies. Science is working a little better today than it was yesterday thanks to their efforts.
For those of you who are new to the concept of preprints, they are manuscripts, that have not yet been published in peer reviewed journals, which are posted to websites like arXiv, PeerJ, and bioRxiv. This process allows for more rapid communication of scientific results and improved quality of published papers though more expansive pre-publication peer-review. If you’d like to read more check out our paper on The Case for Open Preprints in Biology.
The fact that Ecology Letters now allows preprints is a big deal for ecology because they were the last of the major ecology journals to make the transition. The ESA journals began allowing preprints just over two years ago and the BES journals made the switch about 9 months ago. In addition, Science, Nature, PNAS, PLOS Biology, and a number of other ecology journals (e.g., Biotropica) all support preprints. This means that all of the top ecology journals, and all of the top general science journals that most ecologists publish in, allow the posting of preprints. As such, there is not longer a reason to not post preprints based on the possibility of not being able to publish in a preferred journal. This can potentially shave months to years off of the time between discovery and initial communication of results in ecology.
It also means that other ecology journals that still do not allow the posting of preprints are under significant pressure to change their policies. With all of the big journals allowing preprints they have no reasonable excuse for not modernizing their policies, and they risk loosing out on papers that are initially submitted to higher profile journals and are posted as preprints.
It’s a good day for science. Celebrate by posting your next manuscript as a preprint.
Which preprint server should I use?
Preprints are rapidly becoming popular in biology as a way to speed up the process of science, get feedback on manuscripts prior to publication, and establish precedence (Desjardins-Proulx et al. 2013). Since biologists are still learning about preprints I regularly get asked which of the available preprint servers to use. Here’s the long-form version of my response.
The good news is that you can’t go wrong right now. The posting of a preprint and telling people about it is far more important than the particular preprint server you choose. All of the major preprint servers are good choices.Of course you still need to pick one and the best way to do that is to think about the differences between available options. Here’s my take on four of the major preprint servers: arXiv, bioRxiv, PeerJ, and figshare.
arXiv is the oldest of the science preprint servers. As a result it is the most well established, it is well respected, more people have heard of it than any of the other preprint servers, and there is no risk of it disappearing any time soon. The downside to having been around for a long time is that arXiv is currently missing some features that are increasingly valued on the modern web. In particular there is currently no ability to comment on preprints (though they are working on this) and there are no altmetrics (things like download counts that can indicate how popular a preprint is). The other thing to consider is that arXiv’s focus is on the quantitative sciences, which can be both a pro and a con. If you do math, physics, computer science, etc., this is the preprint server for you. If you do biology it depends on the kind of research you do. If your work is quantitative then your research may be seen by folks outside of your discipline working on related quantitative problems. If your work isn’t particularly quantitative it won’t fit in as well. arXiv allows an array of licenses that can either allow or restrict reuse. In my experience it can take about a week for a preprint to go up on arXiv and the submission process is probably the most difficult of the available options (but it’s still far easier than submitting a paper to a journal).
bioRxiv is the new kid on the block having launched less than a year ago. It has both commenting and altmetrics, but whether it will become as established as arXiv and stick around for a long time remains to be seen. It is explicitly biology focused and accepts research of any kind in the biological sciences. If you’re a biologist, this means that you’re less likely to reach people outside of biology, but it may be more likely that biology folks come across your work. bioRxiv allows an array of licenses that can either allow or restrict reuse. However, they explicitly override the less open licenses for text mining purposes, so all preprints there can be text-mined. In my experience it can take about a week for a preprint to go up on bioRxiv.
PeerJ Preprints is another new preprint server that is focused on biology and accepts research from across the biological sciences. Like bioRxiv it has commenting and altmetrics. It is the fastest of the preprint servers, with less than 24 hours from submission to posting in my experience. PeerJ has a strong commitment to open access, so all of it’s preprints are licensed with the Creative Commons Attribution License. PeerJ also publishes an open access journal, but you can post preprints to PeerJ Preprints with out submitting them to the journal (and this is very common). If you do decide to submit your manuscript to the PeerJ journal after posting it as a preprint you can do this with a single click and, should it be published, the preprint will be linked to the paper. PeerJ has the most modern infrastructure of any of the preprint servers, which makes for really pleasant submission, reading, and commenting experiences. You can also earn PeerJ reputation points for posting preprints and engaging in discussions about them. PeerJ is the only major preprint server run by a for-profit company. This is only an issue if you plan to submit your paper to a journal that only allows the posting of non-commercial preprints. I only know of only one journal with this restriction, but it is American Naturalist which can be an important journal in some areas of biology.
figshare is a place to put any kind of research output including data, figures, slides, and preprints. The benefit of this general approach to archiving research outputs is that you can use figshare to store all kinds of research outputs in the same place. The downside is that because it doesn’t focus on preprints people may be less likely to find your manuscript among all of the other research objects. One of the things I like about this broad approach to archiving anything is that I feel comfortable posting that isn’t really manuscripts. For example, I post grant proposals there. figshare accepts research from any branch of science and has commenting and altmetrics. There is no delay from submission to posting. Like PeerJ, figshare is a for-profit company and any document posted there will be licensed with the Creative Commons Attribution License.
Those are my thoughts. I have preprints on all three preprint servers + figshare and I’ve been happy with all three experiences. As I said at the beginning, the most important thing is to help speed up the scientific process by posting your work as preprints. Everything else is just details.
UPDATE: It looks like due to a hiccup with scheduling this post than an early version went out to some folks without the figshare section.
UPDATE: In the comments Richard Sever notes that bioRxiv’s preprints are typically posted within 48 hours of submission and that their interpretation of the text mining clause is that this is covered by fair use. See our discussion in the comments for more details.
British Ecological Society journals now allow preprints
The British Ecological Society has announced that will now allow the submission of papers with preprints (formal language here). This means that you can now submit preprinted papers to Journal of Ecology, Journal of Animal Ecology, Methods in Ecology and Evolution, Journal of Applied Ecology, and Functional Ecology. By allowing preprints BES joins the Ecological Society of America which instituted a pro-preprint policy last year. While BES’s formal policy is still a little more vague than I would like*, they have confirmed via Twitter that even preprints with open licenses are OK as long as they are not updated following peer review.
Preprints are important because they:
- Speed up the progress of science by allowing research to be discussed and built on as soon as it is finished
- Allow early career scientists to establish themselves more rapidly
- Improve the quality of published research by allowing a potentially large pool reviewers to comment on and improve the manuscript (see our excellent experience with this)
BES getting on board with preprints is particularly great news because the number of ecology journals that do not allow preprints is rapidly shrinking to the point that ecologists will no longer need to consider where they might want to submit their papers when deciding whether or not to post preprints. The only major blocker at this point to my mind is Ecology Letters. So, my thanks to BES for helping move science forward!
*Which is why I waited 3 weeks for clarification before posting.
How I remember the positive in science and academia: My Why File
Doing science in academia involves a lot of rejection and negative feedback. Between grant agencies single digit funding rates, pressure to publish in a few “top” journals all of which have rejection rates of 90% or higher , and the growing gulf between the number of academic jobs and the number of graduate students and postdocs , spending even a small amount of time in academia pretty much guarantees that you’ll see a lot of rejection. In addition, even when things are going well we tend to focus on providing as much negative feedback as possible. Paper reviews, grant reviews, and most university evaluation and committee meetings are focused on the negatives. Even students with awesome projects that are progressing well and junior faculty who are cruising towards tenure have at least one meeting a year where someone in a position of power will try their best to enumerate all of things you could be doing better . This isn’t always a bad thing  and I’m sure it isn’t restricted to academia or science (these are just the worlds I know), but it does make keeping a positive attitude and reasonable sense of self-worth a bit… challenging.
One of the things that I do to help me remember why I keep doing this is my Why File. It’s a file where I copy and paste reminders of the positive things that happen throughout the year . These typically aren’t the sort of things that end up on my CV. I have my CV for tracking that sort of thing and frankly the number of papers I’ve published and grants I’ve received isn’t really what gets me out of bed in the morning. My Why File contains things like:
- Email from students in my courses, or comments on evaluations, telling me how much of an impact the skills they learned have had on their ability to do science
- Notes from my graduate students, postdocs, and undergraduate researchers thanking me for supporting them, inspiring them, or giving them good advice
- Positive feedback from mentors and people I respect that help remind me that I’m not an impostor
- Tweets from folks reaffirming that an issue or approach I’m advocating for is changing what they do or how they do it
- Pictures of thank you cards or creative things that people in my lab have done
- And even things that in a lot of ways are kind of silly, but that still make me smile, like screen shots of being retweeted by Jimmy Wales or of Tim O’Reilly plugging one of my papers.
If you’ve said something nice to me in the past few years be it in person, by email, on twitter, or in a handwritten note, there’s a good chance that it’s in my Why File helping me keep going at the end of a long week or a long day. And that’s the other key message of this post. We often don’t realize how important it is to say thanks to the folks who are having a positive influence on us from time to time. Or, maybe we feel uncomfortable doing so because we think these folks are so talented and awesome that they don’t need it, or won’t care, or might see this positive feedback as silly or disingenuous. Well, as Julio Betancourt once said, “You can’t hug your reprints”, so don’t be afraid to tell a mentor, a student, or a colleague when you think they’re doing a great job. You might just end up in their Why File.
What do you do to help you stay sane in academia, science, or any other job that regularly reminds you of how imperfect you really are?
 This idea that where you publish not what you publish is a problem, but not the subject of this post.
 There are lots of great ways to use a PhD, but unfortunately not everyone takes that to heart.
 Of course the people doing this are (at least sometimes) doing so with the best intentions, but I personally think it would be surprisingly productive to just say, “You’re doing an awesome job. Keep it up.” every once in a while.
 There is often a goal to the negativity, e.g., helping a paper or person reach their maximum potential, but again I think we tend to undervalue the consequences of this negativity in terms of motivation [4b].
[4b] Hmm, apparently I should write a blog post on this since it now has two footnotes worth of material.
 I use a Markdown file, but a simple text file or a MS Word document would work just fine as well for most things.
New journals that are changing the way we publish
Academic publishing is in a dynamic state these days with large numbers of new journals popping up on a regular basis. Some of these new journals are actively experimenting with changing traditional approaches to publication and peer review in potentially important ways. So, I thought I’d provide a quick introduction to some of the new kids on the block that I think have the potential to change our approach to academic publishing.
PeerJ is in some ways a fairly standard PLOS One style open access journal. Like PLOS One they only publish primary research (no reviews or opinion pieces) and that research is evaluated only on the quality of the science not on its potential impact. However, what makes PeerJ different (and the reason that I’m volunteering my time as an associate editor for them) is their philosophy that in the era of the modern web it should it should be both cheap and easy to publish scientific papers:
We aim to drive the costs of publishing down, while improving the overall publishing experience, and providing authors with a publication venue suitable for the 21st Century.
The pricing model is really interesting. Instead of a flat fee per paper PeerJ uses a lifetime author memberships. For $99 (total for life) you can publish 1 paper/year. For $199 you can publish 2 papers/year and for $299 you can publish unlimited papers for life. Every author has to have a membership so for a group of 5 authors publishing in PeerJ for the first time it would cost $495, but that’s still about 1/3 of what you’d pay at PLOS One and 1/6 of what you’d pay to make a paper open access at a Wiley journal. And that same group of authors can publish again next year for free. How can they publish for so much less than anyone else (and whether it is sustainable) is a bit of open question, but they have clearly spent a lot of time (and serious publishing experience) thinking about how to automate and scale publication in an affordable manner both technically and in terms things like typesetting (since single column text no attempt to wrap text around tables and figures is presumably much easier to typeset). If you “follow the money” as Brian McGill suggests then the path may well lead you to PeerJ.
Other cool things about PeerJ:
- Optional open review (authors decide whether reviews are posted with accepted manuscripts, reviewers decide whether to sign reviews)
- Ability to comment on manuscripts with points being given for good comments.
- A focus on making life easy for authors, reviewers, and editors, including a website that is an absolute joy compared to interact with and a lack of rigid formatting guidelines that have to be satisfied for a paper to be reviewed.
We want authors spending their time doing science, not formatting. We include reference formatting as a guide to make it easier for editors, reviewers, and PrePrint readers, but will not strictly enforce the specific formatting rules as long as the full citation is clear. Styles will be normalized by us if your manuscript is accepted.
Now there’s a definable piece of added value.
Faculty of 1000 Research
Faculty of 1000 Research‘s novelty comes from a focus on post-publication peer review. Like PLOS One & PeerJ it reviews based on quality rather than potential impact, and it has a standard per paper pricing model. However, when you submit a paper to F1000 it is immediately posted publicly online, as a preprint of sorts. They then contact reviewers to review the manuscript. Reviews are posted publicly with the reviewers names. Each review includes a status designation of “Approved” (similar to Accept or Minor Revisions), “Approved with Reservations” (similar to Major Revisions), and “Not Approved” (similar to Reject). Authors can upload new versions of the paper to satisfy reviewers comments (along with a summary/explanation of the changes made), and reviewers can provide new reviews and new ratings. If an article receives two “Approved” ratings or one “Approved” and two “Approved with Reservations” ratings then it is considered accepted. It is then identified on the site as having passed peer review, and is indexed in standard journal databases. The peer review process is also open to anyone, so if you want to write a review of a paper you can, no invite required.
It’s important to note that the individuals who are invited to review the paper are recommended by the authors. They are checked to make sure that they don’t have conflicts of interest and are reasonably qualified before being invited, but there isn’t a significant editorial hand in selecting reviewers. This could be seen as resulting in biased reviews, since one is likely to select reviewers that may be biased towards liking you work. However, this is tempered by the fact that the reviewers name and review are publicly attached to the paper, and therefore they are putting their scientific reputation on the line when they support a paper (as argued more extensively by Aarssen & Lortie 2011).
In effect, F1000 is modeling a system of exclusively post-publication peer review, with a slight twist of not considering something “published/accepted” until a minimum number of positive reviews are received. This is a bold move since many scientists are not comfortable with this model of peer review, but it has the potential to vastly speed up the rate of scientific communication in the same way that preprints do. So, I for one think this is an experiment worth conducting, which is why I recently reviewed a paper there.
Oh, and ecologists can currently publish there for free (until the end of the year).
Frontiers in X
I have the least personal experience with the Frontiers’ journals (including the soon to launch Frontiers in Ecology & Evolution). Like F1000Research the ground breaking nature of Frontiers is in peer review, but instead of moving towards a focus on post-publication peer review they are attempting to change how pre-publication review works. They are trying to make review a more collaborative effort between reviewers and authors to improve the quality of the paper.
As with PeerJ and F1000Research, Frontiers is open access and has a review process that focuses on “the accuracy and validity of articles, not on evaluating their significance”. What makes Frontiers different is their two step review process. The first step appears to be a fairly standard pre-publication peer review, where “review editors” provide independent assessments of the paper. The second step (the “Interactive Review phase”) is where the collaboration comes in. Using an “Interactive Review Forum” the authors and all of the reviewers (and if desirable the associate editor and even the editor in chief for the subdiscipline) work collaboratively to improve the paper to the point that the reviewers support its publication. If disagreements arise the associate editor is tasked with acting as a mediator in the conversation. If a paper is eventually accepted then the reviewers names are included with the paper and taken as indicating that they sign off on the quality of the paper (see Aarssen & Lortie 2011 for more discussion of this idea; reviewers can withdraw from the process at any point in which case their names are not included).
I think this is an interesting approach because it attempts to make the review process a friendlier and more interactive process that focuses on quickly converging through conversation on acceptable solutions rather than slow long-form exchanges through multiple rounds of conventional peer review that can often end up focusing as much on judging as improving. While I don’t have any personal experiences with this system I’ve seen a number of associate editors talk very positively about the process at Frontiers.
This post isn’t intended to advocate for any of these particular journals or approaches. These are definitely experimental and we may find that some of them have serious limitations. What I do advocate for is that we conduct these kinds of experiments with academic publishing and support the folks who are taking the lead by developing and test driving these systems to see how they work. To do anything else strikes me as accepting that current academic publishing practices are at their global optimum. That seems fairly unlikely to me, which makes the scientist in me want to explore different approaches so that we can find out how to best evaluate and improve scientific research.
UPDATE: Fixed link to the Faculty of 1000 Research paper that I reviewed. Thanks Jeremy!
UPDATE 2: Added a missing link to Faculty of 1000 Research’s main site.
UPDATE 3: Fixed the missing link to Frontiers in Ecology & Evolution. Apparently I was seriously linking challenged this morning.
An open letter to Ecology Letters and the British Ecological Society about preprints
UPDATE: Both Ecology Letters and the British Ecological Society journals now allow preprints. Thanks to both groups for listening to the community and supporting the rapid and open exchange of scientific ideas.
Dear Ecology Letters and the British Ecological Society ,
I am writing to ask that you support the scientific good by allowing the submission of papers that have been posted as preprints. I or my colleagues have reached out to you before without success, but I have heard through various grapevines that both of you are discussing this possibility and I want to encourage you to move forward with allowing this important practice.
The benefits of preprints to science are substantial. They include:
- More rapid communication and discussion of important scientific results
- Improved quality of published research by allowing for more extensive pre-publication peer review
- A fair mechanism for establishing precedence that is not contingent the idiosyncrasies of formal peer review
- A way for early-career scientists to demonstrate productivity and impact on a time scale that matches their need to apply for postdoctoral fellowships and jobs
I am writing to you specifically because your journals represent the major stumbling block for those of us interested in improving science by posting preprints. Your journals either explicitly do not allow the submission of papers that have preprints posted online or lack explicit statements that it is OK to do so. This means that if there is any possibility of eventually submitting a paper to one of these journals then researchers must avoid posting preprints.
The standard justification that journals give for not allowing preprints is that they constitute “prior publication”. However, this is not an issue for two reasons. First, preprints are not peer reviewed. They are the equivalent of a long established practice in biology of sending manuscripts to colleagues for friendly review and to make them aware of cutting edge work. They simply take advantage of the internet to scale this to larger numbers of colleagues. Second, the vast majority of publication outlets do not believe that preprints represent prior publication, and therefore the publication ethics of the broader field of academic publishing clearly allows this. In particular Science, Nature, PNAS, the Ecological Society of America, the Royal Society, Springer, and Elsevier all generally allow the posting of preprints. Nature even wrote about this policy nearly a decade ago stating that:
Nature never wishes to stand in the way of communication between researchers. We seek rather to add value for authors and the community at large in our peer review, selection and editing… Communication between researchers includes not only conferences but also preprint servers… As first stated in an editorial in 1997, and since then in our Guide to Authors, if scientists wish to display drafts of their research papers on an established preprint server before or during submission to Nature or any Nature journal, that’s fine by us.
If you’d like to learn more about the value of preprints, and see explanations of why some of the other common concerns about preprints are unjustified, some colleagues and I have published a paper on The Case for Open Preprints in Biology.
So, I am asking that for the good of science, and to bring your journals in line with widely accepted publication practices, that you please move quickly to explicitly allow the submission of papers that have been posted as preprints.
[Preprint] Nine simple ways to make it easier to (re)use your data
I’m a big fan of preprints, the posting of papers in public archives prior to peer review. Preprints speed up the scientific dialogue by letting everyone see research as it happens, not 6 months to 2 years later following the sometimes extensive peer review process. They also allow more extensive pre-publication peer review because input can be solicited from the entire community of scientists, not just two or three individuals. You can read more about the value of preprints in our preprint about preprints (yes, really) posted on figshare.
In the spirit of using preprints to facilitate broad pre-publication peer review a group of weecologists have just posted a preprint on how to make it easier to reuse data that is shared publicly. Since PeerJ‘s commenting system isn’t live yet we would like to encourage your to provide feedback about the paper here in the comments. It’s for a special section of Ideas in Ecology and Evolution on data sharing (something else I’m a big fan of) that is being organized by Karthik Ram (someone I’m a big fan of).
Our nine recommendations are:
- Share your data
- Provide metadata
- Provide an unprocessed form of the data
- Use standard data formats (including file formats, table structures, and cell contents)
- Use good null values
- Make it easy to combine your data with other datasets
- Perform basic quality control
- Use an established repository
- Use an established and liberal license
Most of this territory has been covered before by a number of folks in the data sharing world, but if you look at the state of most ecological and evolutionary data it clearly bears repeating. In addition, I think that our unique contribution is three fold: 1) We’ve tried hard to stick to relatively simple things that don’t require a huge time commitment to get right; 2) We’ve tried to minimize the jargon and really communicate with the awesome folks who are collecting great data but don’t have much formal background in the best practices of structuring and sharing data; and 3) We contribute the perspective of folks who spend a lot of time working with other people’s data and have therefore encountered many of the most common issues that crop up in ecological and evolutionary data.
So, if you have the time, energy, and inclination, please read the preprint and let us know what you think and what we can do to improve the paper in the comments section.
UPDATE: This manuscript was written in the open on GitHub. You can also feel free to file GitHub issues if that’s more your style.
UPDATE 2: PeerJ has now enabled commenting on preprints, so comments are welcome directly on our preprint as well (https://peerj.com/preprints/7/).
Some alternative advice on how to decide where to submit your paper
Over at Dynamic Ecology this morning Jeremy Fox has a post giving advice on how to decide where to submit a paper. It’s the same basic advice that I received when I started grad school almost 15 years ago and as a result I don’t think it considers some rather significant changes that have happened in academic publishing over the last decade and a half. So, I thought it would be constructive for folks to see an alternative viewpoint. Since this is really a response to Jeremy’s post, not a description of my process, I’m going to use his categories in the same order as the original post and offer my more… youthful… perspective.
- Aim as high as you reasonably can. The crux of Jeremy’s point is “if you’d prefer for more people to read and think highly of your paper, you should aim to publish it in a selective, internationally-leading journal.” From a practical perspective journal reputation used to be quite important. In the days before easy electronic access, good search algorithms, and social networking, most folks found papers by reading the table of contents of individual journals. In addition, before there was easy access to paper level citation data, and alt-metrics, if you needed to make a quick judgment on the quality of someones science the journal name was a decent starting point. But none of those things are true anymore. I use searches, filtered RSS feeds, Google Scholar’s recommendations, and social media to identify papers I want to read. I do still subscribe to tables of contents via RSS, but I watch PLOS ONE and PeerJ just as closely as Science and Nature. If I’m evaluating a CV as a member of a search committee or a tenure committee I’m interested in the response to your work, not where it is published, so in addition to looking at some of your papers I use citation data and alt-metrics related to your paper. To be sure, there are lots of folks like Jeremy that focus on where you publish to find papers and evaluate CVs, but it’s certainly not all of us.
- Don’t just go by journal prestige; consider “fit”. Again, this used to mater more before there were better ways to find papers of interest.
- How much will it cost? Definitely a valid concern, though my experience has been that waivers are typically easy to obtain. This is certainly true for PLOS ONE.
- How likely is the journal to send your paper out for external review? This is a strong tradeoff against Jeremy’s point about aiming high since “high impact” journals also typically have high pre-review rejection rates. I agree with Jeremy that wasting time in the review process is something to be avoided, but I’ll go into more detail on that below.
- Is the journal open access? I won’t get into the arguments for open access here, but it’s worth noting that increasing numbers of us value open access and think that it is important for science. We value open access publications so if you want us to “think highly of your paper” then putting it where it is OA helps. Open access can also be important if you “prefer for more people to read… your paper” because it makes it easier to actually do so. In contrast to Jeremy, I am more likely to read your paper if it is open access than if it is published in a “top” journal, and here’s why: I can do it easily. Yes, my university has access to all of the top journals in my field, but I often don’t read papers while I’m at work. I typically read papers in little bits of spare time while I’m at home in the morning or evenings, or on my phone or tablet while traveling or waiting for a meeting to start. If I click on a link to your paper and I hit a paywall then I have to decide whether it’s worth the extra effort to go to my library’s website, log in, and then find the paper again through that system. At this point unless the paper is obviously really important to my research the activation energy typically becomes too great (or I simply don’t have that extra couple of minutes) and I stop. This is one reason that my group publishes a lot using Reports in Ecology. It’s a nice compromise between being open access and still being in a well regarded journal.
- Does the journal evaluate papers only on technical soundness? The reason that many of us think this approach has some value is simple, it reduces the amount of time and energy spent trying to get perfectly good research published in the most highly ranked journal possible. This can actually be really important for younger researchers in terms of how many papers they produce at certain critical points in the career process. For example, I would estimate that the average amount of time that my group spends getting a paper into a high profile journal is over a year. This is a combination of submitting to multiple, often equivalent caliber, journals until you get the right roll of the dice on reviewers, and the typically extended rounds of review that are necessary to satisfy the reviewers about not only what you’ve done, but satisfying requests for additional analyses that often aren’t critical, and changing how one has described things so that it sits better with reviewers. If you are finishing your PhD then having two or three papers published in a PLOS ONE style journal vs. in review at a journal that filters on “importance” can make a big difference in the prospect of obtaining a postdoc. Having these same papers out for an extra year accumulating citations can make a big difference when applying for faculty positions or going up for tenure if folks who value paper level metrics over journal name are involved in evaluating your packet.
- Is the journal part of a review cascade? I don’t actually know a lot of journals that do this, but I think it’s a good compromise between aiming high and not wasting a lot of time in review. This is why we think that ESA should have a review cascade to Ecosphere.
- Is it a society journal? I agree that this has value and it’s one of the reasons we continue to support American Naturalist and Ecology even though they aren’t quite as open as I would personally prefer.
- Have you had good experiences with the journal in the past? Sure.
- Is there anyone on the editorial board who’d be a good person to handle your paper? Having a sympathetic editor can certainly increase your chances of acceptance, so if you’re aiming high then having a well matched editor or two to recommend is definitely a benefit.
To be clear, there are still plenty of folks out there who approach the literature in exactly the way Jeremy does and I’m not suggesting that you ignore his advice. In fact, when advising my own students about these things I often actively consider and present Jeremy’s perspective. However, there are also an increasing number of folks who think like I do and who have a very different set of perspectives on these sorts of things. That makes life more difficult when strategizing over where to submit, but the truth is that the most important thing is to do the best science possible and publish it somewhere for the world to see. So, go forth, do interesting things, and don’t worry so much about the details.
UPDATE: More great discussion here, here, here and here. [If I missed yours just let me known in the comments and I”ll add it]
ESA journals will now allow papers with preprints
ESA has just announced that it has changed its policy on preprints and will now allow articles that have been posted on major preprint servers, like arXiv, to be considered for publication in its journals.
I am very excited about this change for two reasons. First, as nicely laid out in INNGE blog post by Philippe Desjardins-Proulx*, there are many positive benefits to science of the preprint culture. They make science more accessible, allow researchers to get feedback from the community prior to peer review, and speed up the scientific process by making ideas available to others as quickly as possible. We should take this opportunity as a community to start developing the kind of vibrant preprint culture that has benefited so many other disciplines. Second, I am encouraged by the rapid response of ESA to the concerns expressed by myself and other members of the community, and take it as a sign that my favorite society is open to making the kinds of changes that are necessary to best facilitate science in the modern era. More work is clearly necessary, but this is a very encouraging start.
UPDATE: Carl Boettiger has posted his very nice letter to Don Strong that played an critical roll in taking this discussion from a bunch of folks talking over social media to something that effected meaningful change.
*See also, posts by GCBias and Titus Brown
Using Google Scholar to keep up with the literature
We have all bemoaned the increasing difficulty of keeping up with the growing body of literature. Many of us, me included, have been relying increasingly on following only a subset of journals, but with the growing popularity of the large open-access journals I know I for one am increasingly likely to miss papers. The purpose of this post isn’t to give you the panacea to your problems (sadly I don’t think there is a panacea to this issue, though I have hopes that someone will come up with something viable in the future). The purpose of this post is to let you know about an interesting addition or alternative (for the brave) to the frantic scanning of the table of contents or RSS feeds: Google Scholar.
Almost everyone at this point knows you can go to Google Scholar and search for key words and it’ll produce a list of papers. Did you also know that you can set up a google profile with your published articles and that Google can use that to find articles that might be of interest to you. How does it do that? I’ll have to quote Google’s Blog because it’s a little like voodoo to me (obviously this is Morgan writing this post, not Ethan): “We determine relevance using a statistical model that incorporates what your work is about, the citation graph between articles, the fact that interests can change over time, and the authors you work with and cite. “ When you go to Google Scholar’s homepage (and you’re logged in as you) it’ll notify you if there are new articles on your suggested list. I actually have been pleasantly surprised by the articles it has identified for me, including some book chapters I would never have seen. For example here’s several things that sound really interesting to me, but I would never have seen:
The importance of body size, abundance, and food-web structure for ecosystem functioning
MC Emmerson – Marine Biodiversity and Ecosystem Functioning: …, 2012 – books.google.com
The Limitations of Hierarchical Organization*
A Potochnik, B McGill – Philosophy of Science, 2012 – JSTOR
On Allometry Relations
D West, J BRUCE – International Journal of Modern Physics B, 2012 – World Scientific
It doesn’t just search published journal articles. For example there are preprints from arXiv and government reports on my list. I don’t know if this would work as well for the young graduate students/postdocs since it uses the citations in your existing papers and our junior colleagues might have less data for Google to work with. However, once you have a profile, you can also follow other people who have profiles, which means you get an email every time scholarly work gets added to their profile. Are you a huge Simon Levin groupie? You can follow him and every time a paper gets added to his profile, you can get an email alerting you about the new paper. I also use this to follow a bunch of interesting younger people because they often publish less frequently or in journals I don’t happen to follow and this way I don’t miss their stuff when my Google Reader hits 1000+ articles to be perused! You can also sign up for alerts when someone you follow has their work cited. (And you can set up alerts for when your own work gets cited as well).
As I said before, I don’t think Google Scholar is a one-stop literature monitoring stop (yet), but I find it useful for getting me out of my high impact factor monitoring rut. The only thing you need to do is set up your Google Scholar profile and the only reason not to do that is if you’re worried it’ll give Google the edge when it finally becomes self-aware and renames itself Skynet (ha ha ha ha….hmmm).