Monthly Archives: August 2009
- If you don’t have an easily accessible RSS feed available (and by easily accessible I mean in the browser’s address bar on your journal’s main page) for your journal’s Table of Contents (TOCs), there is a certain class of readers who will not keep track of you TOCs. This is because receiving this information via email is outdated and inefficient and if you are in the business of content delivery it is, at this point, incompetent for you to not have this option (it’s kind of like not having a website 10 years ago).
- If, for some technophobic reason, you refuse to have an RSS feed, then please, pretty please with suger on top, don’t hide the ability to subscribe to the TOCs behind a username/password wall. All you need is a box for people to add their email addresses to for subscribing and a prominent unsubscribe link in the emails (if you are really paranoid you can add a confirmation email with a link that needs to be followed to confirm the subscription).
- Most importantly. Please, for the love of all that is good and right in the world, DO NOT START AN RSS FEED AND THEN STOP UPDATING IT. Those individuals who track a large number of feeds in their feed readers will not notice that you stopped updating your feed for quite some time. You are losing readers when you do this.
- If you have an RSS feed that is easily accessible (congratulations, you’re ahead of many Elsevier journals) please try to maximize the amount of information it provides. There are three critical pieces of information that should be included in every TOCs feed:
- The title (you all manage to do this one OK)
- All of the authors’ names. Not just the first author. Not just the first and last author. All of the authors. Seriously, part of the decision making process when it comes to choosing whether or not to take a closer look at a paper is who the authors are. So, if you want to maximize the readership of papers, include all of the authors’ names in the RSS feed.
- The abstract. I cannot fathom why you would exclude the abstract from your feed, other than to generate click throughs to your website. Since those of you doing this (yes, Ecology, I’m talking about you) aren’t running advertising, this isn’t a good reason, since you can communicate the information just as well in the feed (and if you’re using website visits as some kind of metric, don’t worry, you can easily track how many people are subscribed to your feed as well).
If this seems a bit harsh, whiny, etc., then keep this in mind. In the last month I had over 1000 new publications come through my feed reader and another 100 or so in email tables of contents. This is an incredible amount of material just to process, let alone read. If journals want readers to pay attention to their papers it is incumbent upon them to make it as easy as possible to sort through this deluge of information and allow their readership to quickly and easily identify papers of interest. Journals that don’t do this are hurting themselves as well as their readers.
During the course of this long volume I have undoubtedly plagiarized from many sources–to use the ugly term that did not bother Shakespeare’s age. I doubt whether any criticism or cultural history has ever been written without such plagiary, which inevitably results from assimilating the contributions of your countless fellow-workers, past and present. The true function of scholarship as a society is not to stake out claims on which others must not trespass, but to provide a community of knowledge in which others may share.
-F. O. Matthiessen, American Renaissance 1941.
Thanks to academhack for pointing me to this great quote. Given the spirit of the quote I don’t think he’ll mind me reposting it. I find this to be a particularly relevant in light of recent discussion about tracking down self-plagarism and how grave an offense it may be. I’m not saying that self, and regular, plagarism aren’t serious issues. I’ve been involved in reporting a case of self-plagarism myself and it’s disturbing when you see it. It’s also clearly bad for science. It clutters the already crowded literature, has a negative influence on broader perceptions regarding the ethics of scientists, and results in undue credit (which presumably influences funding and promotion). That said, I think it’s important to keep the bigger picture in mind. We are, after all, in the business of ideas. Words are important for communicating those ideas, but the ideas themselves are the currency of interest. Our ideas are influenced by everyone we talk to, colored by every paper we’ve ever read and talk we’ve ever seen. The goal of science is (or at least should be) to progress our knowledge as rapidly as possible. I think that conversations surrounding plagarism, and what it means in this new era, should start from this core goal and proceed from there.
Beyond simple histograms there are two basic methods for visualizing frequency distributions.
Kernel density estimation is basically a generalization of the idea behind histograms. The basic idea is to put an miniature distribution (e.g., a normal distribution) at the position of each individual data point and then add up those distributions to get an estimate of the frequency distribution. This is well developed field with a number of advanced methods for estimating the true form of the underlying frequency distribution. Silverman’s 1981 book is an excellent starting point for those looking for details. I like KDE as a general approach. It has the same issues as binning in that depending on the kernel width (equivalent to bin width) you can get different impressions of the data, but it avoids the issue of having to choose the position of bin edges. It also estimates a continous distribution which is what we are typically looking for.
Cumulative distribution functions (CDF for short) characterize the probability that a randomly drawn value of the x-variable will be less than or equal to a certain value of x. The CDF is conveniently the integral of the probability density function, so if you understand the CDF then simply taking it’s derivative will give you the frequency distribution. The CDF is nice because there are no choices that need to be made to construct a CDF for empirical data. No bin widths, no kernel widths, nothing. All you have to do is rank the n observed values of x from smallest to largest (i=1 . . . n). The probability that an observation is less than or equal to x (the CDF) is then estimated as i/n. If all of this seems a bit esoteric, just think about the rank-abundance distribution. This is basically just a CDF of the abundance distribution with the axes flipped (and one of them rescaled). Because of the objectivity of this approach it has recently been suggested that this is the best approach to visualizing species-abundance distributions. I’ve spent a fair bit of time working with CDFs for exactly this reason. The problem that I have run into with this approach is that except in certain straightforward situations it can be difficult/counterintuitive to grasp what a given CDF translates into with respect to the frequency distribution of interest.
The take home message for visualization is that any of the available approaches done well and properly understood is perfectly satisfactory for visualizing frequency distribution data.
I read a handful of experimental ecology papers the other day. I liked some of them and didn’t like some of them. It wasn’t that there was anything inherently wrong with the ones I didn’t like, they just didn’t fit in with my world view.
Yeah, this doesn’t make any sense to me either, but apparently that’s how we’re using this phrase these days.
P.S. I was going to let this one go until Ecotone used the original post to question “the reality (or not) of macroecology as its own discipline.” There’s nothing wrong with creative titles (we enjoy them here at Jabberwocky), but when contrasted with EEB & Flow’s other posts from ESA it’s not surprising that Ecotone took this as being a passive agressive critique of the state of the field. My main concern is that EEB & Flow seems to conflate an important methodological approach with particular interpretations of ecological process resulting from an application of that approach. Just because I disagree with a particular paper using an experiment doesn’t lead me to have “an unsure feeling about this field.” I mean really.