Thoughts on the proposed RCUK policy on Open Access to research outputs

Today is the last day of a consultation by Research Councils UK (RCUK) on its draft policy on Access to Research Outputs [PDF]. The proposals are a clear and strong statement that RCUK-funded research should be made available via open access (OA). It goes far beyond the current OA offerings from some publishers and represents a welcome statement of support for the OA movement. Where the policy is less strident is on open access to research data and related materials.

I copy my email to RCUK below.

Course: Analysing Palaeolimnological Data with R

Update: As of 18 April 2012 the course is now fully subscribed. Should you wish to be placed on a waiting list please contact Steve Juggins.

Analysing Palaeolimnological Data with R

16th — 20th August 2012, University Marine Biological Station Millport, Isle of Cumbrae, Scotland

Steve Juggins and I will be running a 4-day residential R course to coincide with the International Paleolimnology Symposium 2012 this August. The course will be held at the University Marine Biological Station Millport on the Isle of Cumbrae, within easy reach of Glasgow and the IPS2012 venue.

The course costs £300 + VAT and includes food, accommodation and course materials. We have support from PAGES to assist with costs for young researchers from developing countries (see below). Please note that you do not need to register for IPS2012 to attend the R course; it is open to anyone.

The course will cover many topics of particular interest to palaeolimnologists and palaeoecologists. Details can be found on the course website and a detailed programme [PDF] is available.

Registration for the course is now open via Newcastle University.Registration for the course is now closed.

Support for young researchers from developing countries

Thanks to the generous support of PAGES we are able to cover travel, subsistence and course costs (up to £1100) for five young researchers from developing countries. If you would like to apply for PAGES financial support please send a CV and short covering letter outlining
your research interests and why the course will benefit you to both Gavin and Steve (our contact details are on the course website). The deadline for applying for PAGES support is 15th May 2012.

If you have any further questions, please do not hesitate to contact me.

We look forward to seeing you in August.

A better way of saving and loading objects in R

Hadley Wickham (@hadleywickham) this week mentioned on Twitter his preference for saveRDS() over the more familiar save(). Being a new function to me, I thought I’d take a look…

Elsevier on Open Access part 2

Somehow I’m on Elsevier’s author mail-out listing and as such I received the first edition of their “Author’s Update” newsletter. Whilst nowhere near as misrepresentative of Open Access as their recent Editor’s Update issue (that I blogged about recently), it is worth taking a few moments to consider how Elsevier presents Open Access to a largely uninformed audience; us academics.

Elsevier’s Alice Wise (Director of Universal Access) contributed a piece to the newsletter titled “The choice is yours”, where she sets out the various options available to authors wanting to publish Open Access papers or in one of Elsevier’s Open Access journals. Wise outlines the options available to authors and provides links to various pages on the Elsevier website that set out author rights under Elsevier’s open access provisions. She even mentions Elsevier’s policy on self-posting of author manuscripts. To the uninitiated this all sounds great; Elsevier are being “open” and providing the academic with a range of tools that allow them to choose open access for their articles within their current subscription-based business model. That’s great isn’t it? What is there to complain about? Well, a lot actually, and here’s why…

Elsevier on Open Access part 1

In the past few days I’ve come across two advertorials (articles or editorials if I’m being generous) from Elsevier in the context of newsletters sent to editors and authors. Here I consider the one sent to editors that Ross Mounce (@rossmounce) tweeted about earlier today.

The opening paragraph sets the scene and paints Elsevier and similar publishers in a good light as the Guardians of copyright. Ironically, by requesting copyright transfer from authors to Elsevier, they aren’t really protecting the copyright of the author any longer (just their moral rights); the author has signed away their copyright so Elsevier is protecting its own interests and those of its shareholders.

The next paragraph really annoys me! I quote

To all intents and purposes, the fact that journal articles are being made available to all through open access, or to subscribers under the subscription model, should not really affect things.  Issues can arise, however, as there is a common misperception that open access means anyone can do anything with an article  – in fact, the rights in the content must still be understood and upheld. (Tempest, 2011)

Firstly respecting copyright applies just as equally to Open Access articles as it does to those behind publishers’ paywalls. Second, we have a very clear description of Open Access in the form of the Budapest Open Access Initiative definition of Open Access. Some publishers (like Springer) get this and their Open Access offerings are under a Creative Commons CC-BY licence which as long as the original work is attributed you can do what you want with the content. Yet Elsevier have a sorry excuse for an “open access” licence which is somewhat like CC-NC-SA but with extra restrictions; its not “open” if what you can and can’t do with it is controlled to such a degree. Issues can certainly arise if you muddy the waters and don’t follow an accepted standard!

In addition, from an editorial perspective, copyright helps to prevent elements such as plagiarism, multiple submission and fraud in journal articles, and whilst is does not actually detect these elements, it acts as a protective measure to uphold the quality of journals (Tempest, 2011)

I’m not sure what this has to do with “open access”? I can’t imagine Elsevier pays a legion of minions to scour the web and print literature looking for copyright infringement. If they are alerted to any infringement they can bring their lawyers to bare, but an author could do the same (perhaps without the same depth of pocket) or alert journal editors to the plagiarism or fraud.

Elsevier then suggests that

If copyright is retained, then this process [upholding of author rights] remains with the author and, if it is shared, there is a greater risk that fraudulent use may occur, which is why we continue to advocate the transfer of copyright for our journals.(Tempest, 2011)

It really is unclear what they mean by “sharing” copyright but regardless, why should the risk of fraud be greater because the author not Elsevier is the copyright holder?

Tempest claims that Open Access journals, in allowing extra usage rights, introduce confusion over copyright. How exactly is it more confusing if this is an Open Access journal? The only way confusion is increased is if the rights of the user are not clearly indicated at the point of access. Most journals that allow Open Access articles are quite clear about rights granted to the user and use a clear, well-recognised licence like CC-BY. The one publisher I know that obfuscates user rights for “open access” articles, one that spreads confusion not reduces it, is Elsevier.

The advertorial closes with a general comment that the main issues with copyright are a general lack of understanding as to what it is and apathy about it importance. Again, Tempest, I ask you what does this have to do with Open Access?

It is clear that this propaganda piece is designed to play on the poor level of understanding of and apathy towards copyright issues in its pool of journal editors. None of the concerns raised applies solely to Open Access journals or articles; unless you give away your copyright by placing works in the public domain (and even then it may not be possible in some jurisdictions to give up all your rights) copyright applies whether it is the author or Elsevier that holds the copyright¹. By linking Open Access with a murky world of potential or perceived threats arising from the chaos of authors’ retaining their copyrights Elsevier are travelling a well worn path when it comes to vested interests reacting to a threat to their business model; we’ve seen similar strategies in open access software and climate change to name but two.

If Elsevier are as committed to improving access to articles and working for the benefit of authors as they claim they are, they should stop spreading this FUD that can only lead to confusion and uncertainty in the very people they claim to want to help. Ultimately Elsevier will be judged by their actions; to date they have hardly ingratiated themselves with academics. I do wonder when they will realise that in the long run their actions will only harm their business?

¹ In the US unless you register you copyright on a work (for a fee) then potential damages for copyright infringement are reduced. Publishers will register your works on your behalf (well theirs!). But given that the key reason of choosing Open Access is to remove restrictions on use other than attribution, I’m not sure how huge damages/fees apply.

I signed the Elsevier boycott pledge

After a little soul searching I signed the Elsevier boycott, pledging not to do any peer review or editorial work for any of that publishers titles. I have written before about my objections to Elsevier’s practices and have boycotted Wiley for similar reasons. Here I want to briefly outline why it took me so long to sign the pledge to boycott Elsevier.

The cost of subscribing to academic journals

Much has been written about the Research Works Act [you could do a lot worse than read Saurodpod Mike on the subject], academic publishing and the relationship between the scientists who do most of the work and the publishers who then assert somewhat draconian rights over those works. A boycott of the biggest publisher of them all, Elsevier, started to gain a fair degree of traction with almost 8000 scientists having pledge to limit some or all of their interactions with Elsevier and its journals.

One of the allegations levelled at Elsevier is that they charge such exorbitant prices for subscriptions to their journals that they essentially force university libraries to subscribe to so-called “bundles” or “deals” that allow access to huge swathes of titles. Accessing all those titles individually would be prohibitively costly for any institution but by offering bundles, STEM publishers are accused of exploiting the high prices of their most popular titles to foist titles onto users and librarians that have no need for them.

At the time (Elsevier has since withdrawn its support for the RWA though not the spirit of the legislation) there was little concrete information on the interweb about Elsevier’s bundling practices (lots anecdotal!). In order to inform any decision to boycott the publisher I arranged to meet UCL‘s Journals Librarian. I wanted to find out about Elsevier’s bundles and our usage of bundle titles from someone who has to justify the massive outlay on journals to the powers that be in UCL. A bout of flu put paid to the original meeting, but last week I finally managed to spend an hour with UCL’s Journals Librarian and the Geography Subject Librarian.

What I discovered certainly clouds the sometimes clear-cut message that bundling is bad. The meeting was eye-opening in some respects and Elsevier and the other big publishers certainly don’t come out smelling of roses.

TL;DR: Bundling obfuscates high subscriptions prices on the most popular journals. This is due to title bundles being priced such that for large institutions at least it is far more cost-effective to have the bundle than subscribe to exorbitantly priced journals individually, ultimately propagating the high subscription price. Publishers have a near monopoly and they use (abuse?) this position to maximise their profits. But we the scientific community have allowed this situation to arise; funding decisions, academic assessment etc. all depend on publishing in “high impact” journals, so we continue to feed the monsters that are the big STEM publishers in a self-perpetuating cycle. Ultimately it is science and society that suffers. We need to starve the monsters of content and then demand seismic shift in the baseline of academic assessment.

I’m on peer review strike!

There has been a lot of discussion on the interweb about the support for legislation in the US by the major academic publishers that would place stifling restrictions on access to Government-funded science outputs published in their journals. In effect, the Research Works Act would hand these same wealthy publishers a licence to print money on the back of tax payer-funded research and the tax payer-funded efforts of the scientists required to peer review the manuscripts. We the scientists do the research and peer review the manuscripts, the tax payer pays for all of this and yet the academic publishers charge upwards of £30 to access a single article and hundreds to tens of thousands of pounds for individuals and institutions to subscribe to their journals. All the publishers add is

1. the infrastructure that allows them to track papers in peer review (which is largely web-based and rubbish),
2. the typesetting of manuscripts into final journal style form, and
3. the websites and infrastructure allowing people to get access to journals electronically (for the proper fee of course).

The major publishers make 20-30% 30-40% profit-margins on their revenues yet contribute little.

And yet they want more…! I’m not suggesting that the publishers should add their value without monetary reward, but they are being disingenuous when they claim to be adding significant value, which they need to recoup, to the manuscripts we supply.

So from today I am on strike when it comes to performing peer-review for journals from the stables of the major academic publishers. I will only review for journals that release all papers under Open Access frameworks. As such, I will now only be submitting papers to Open Access-only journals.

New version of analogue (0.8-0)

Yesterday I pushed an update of my analogue package to CRAN. The new version is 0.8-0 and contains some new functions, several bug fixes and a major change arising from additions to R 2.14.x requiring all packages to have a namespace. analogue now has its own namespace rather than relying on the one R would automagically generate if it weren’t provided.

0.8-0 is a moderate update to analogue containing some new functionality, some of which is there for testing/experimentation (like the fancy principal components regression). The main user visible changes are:

• crossval() new function to perform leave-one-out, k-fold, n k-fold, and bootstrap cross-validation on transfer function models. A method for wa() models is provided.
• pcr() performs principal components regression. Designed to allow transformations in the spirit of Legendre & Gallagher (2001, Oecologia) that allow PCA to be usefully applied to species data.
• varExpl() and gradientDist() are two new functions that extract the amount or variance explained by ordinations axes and the distances or locations along ordination axes. Methods currently available for cca() and prcurve() objects.
• weightedCor() implements one of the tests from Telford & Birks (2011, QSR) based on the weighted correlation of WA optima and constrained ordination species scores.
• Stratiplot() now handles absolute data better following a few bug fixes and general improvements in the underlying code. panel.Stratiplot() gains new arguments gridh and gridv to allow user control of the grid lines on panel if plotted.
• mat() gains a new argument `kmax` which can be used to limit the number of analogues considered as models when fitting MAT transfer functions. By default, mat() considers models with 1 through to n-1 analogues (n = number of sites). kmax can control this upper limit which will speed up fitting models, especially for large training sets. Invariably one wouldn’t want to average over entire training sets to produce predictions, or even over large numbers of analogues.

AGU Fall Meeting Day 3 (Wednesday)

Day 3 was an easier day for me with fewer talks that I wanted to see so I was able to spend a bit of time thinking about work matters and cogitating a bit more on the talks I was listening to. I also spent a large chunk of time in one of the poster sessions, which was very enlightening; it was like an informal talk session with authors presenting their posters ad hoc and groups discussions taking place about the results. (As I write this I have just come from my own poster session and had the same experience; far better than many poster sessions at other meetings.)