This is an unfinished story of a single manuscript. It started 14 months ago in February of 2012 when after months and months of work my old advisor, Nick Gotelli, and I submitted a manuscript to Science and found out it was going out for review. Going out for review in Science launched my hopes. Back then I was still hopeful I would find a career in academia, and this manuscript seemed like it would be the key. I had recently seen another friend’s career launch with the publication of a manuscript in Nature and I thought: This will be my moment!. All those fears that we all harbor as post-docs: Will I get a job? Will I get a job where I want to work? Will I be trapped in lecturer limbo? Gone with the opinions of just two people.

When I was in college I had a girlfriend who’s dad was an ex-lawyer turned self-proclaimed anarchist scholar. She left me for a guy in his late 30’s who worked in a scarf store, and I was stuck with a stack of anarchist theory books I’d bought to try and impress her at the local used bookstore. while my politics have mellowed a bit in most things, my opninion on scholarly publishing is about in line with what Kropotkin would have made of the situation if he were around today. I got a chance to air my radical views thanks to the wonderful Jarrett Byrnes and his NCEAS colleagues. He is working on a survey, where you can speak your mind and channel Kropotkin, or Karl Rove, or anyone in between. No matter what the most important thing is that you take the survey! So here’s the link to the survey and you can read more about their NCEAS group here.

I’d like to say that I’ve been waiting to give a state of the blog to coincide with the president’s state of the union instead of just being “busy”, but that’s not the case. In fact I wish I were so “busy”, but the truth is that it’s less that I’ve been busy and more that I don’t have much to say. If a blog is going to be successful, it relies on people having to a lot of things to say, so it begs the question: “why don’t I have much to say?” So in many ways this post on the state of the blog is more like a “state of me.”

There’s a saying that goes “it’s not where you are, it’s where you’re at” (A friend told me it was from Mobb Deep, but the original lyrics there is “it ain’t where you from it’s where you at”). The main point being that no matter where you “are” (geographically, professionally, etc…) what matters most is where you’re “at” (mentally, emotionally, spiritually, etc…), because you can never escape yourself. So I want to take stock of where I (and my blog) both “are” and are “at”.

This post is inspired by Jeremy Yoder’s post on the Molecular Ecology blog on “Knowing what I know now” advice for graduate students. He opened it up as a carnival so I wrote this little gem with my own advice for graduate students. Fair warning, I will not be winning any awards for “positive person of the year award” so take this all with a grain of salt. And potential employers, please stop reading here

Get out while you still can: Seriously, that’s what any sane rational person would do. You’re giving up probably 8+ years of earnings potential (Phd and post-doc). Let’s consider a simple case. You decide instead of academia you’ll take that brilliant mind of yours and study something more profitable, like engineering or business. Now at 23 you get a good job and over those 8 years, you manage to sock away $10,000 a year, and invest in a fund that has the minimal annual return rate of 5%. At the end of those 8 years, say around 31-32, you will have around $100k+. What does the scenario look like after grad school and some post-docing? My guess would be debt, a used car and a shitty apartment (I don’t have a shitty apartment for the record). Because when you’re 25 putting a trip to Hawai’i on a credit card and sleeping on the beach sounds like great fun, but at 32 you’re sort of a loser doing that. So why on earth would you go to graduate school, giving up your prime earning years, to spend 8 years training for a job that pays the same salary as an entry level engineering job? Does this sound like the choice of a rational person?

The other night in my office I got into a discussion with my office mate, the brilliant scientist / amazing skier Dr. Thor Veen about how to understand the random effect variance term in a mixed-effects model. Thor teaches the R statistics course here at UBC, and last night a student came to the office to ask a question about how to interpret that returned from a mixed model object (in this case lmer from the package lme4. The question surrounded a dataset where individual stickleback fish had been measured for a trait at different light wavelengths. Because the individual fish had been measured multiple times, a mixed-model was fit with a fixed factor for wavelength and a random effect of individual fish. In this case the random effects variance term came back as 0 (or very close to 0), despite there appearing to be variation between individuals. The quesiton is under what circumstances do we expect that variance to increase, and how do we interpret it vs the residual variance. I’ll illustrate this with two simulated data sets.

Recently we at rOpenSci released our rfigshare package up on cran (or you can check out the most up to date version on github. So what’s so great about being able to create figshare articles through R? For some time now I’ve been advocating the use of a workflow that involves documents written in R using either LaTeX or markdown with code integtated into the manuscript. Then the manuscript is itself a “compilable” file that is formatted and converted into a pdf. Once you’re done with your document, you can run a little script and just upload it to figshare.com. Now your workflow is seemlessly embedded within R. Even better you can use our other packages to actually download your data from within R, write your manuscript in R and then share it with rfigshare. I’ve written up a little tutorial on how to do this and you can see the figshare version or see the raw markdown source version Other uses though could be beyond publishing documents. You could also generate data from simulations and push it to figshare, or even perform various data aggretation or processing on your raw data and then upload it to figshare. Could you do this all via the great figshare web interface? Of course, but we like to think this will make your life a little easier. Many thanks to Carl Boettiger for taking the lead on developing the package and put in the bulk of the development work.

I’m happy to announce that I’ve finally finished my rGtrends package, an interface for the unofficial python Google trends API. It’s a simple function that will allow you to search Google Trends from within R. I haven’t really come up with how this is really relevant to ecology, but it is pretty interesting from a social perspective. For instance you can see trends such as the rise of Honey Boo Boo and the fall of the Jersey Shore)

Which matches the same data from Google.

Have you ever wanted an easy way to generate continuous color pallettes for a discrete factor? I came across a question over on Stackoverflow about how add color to a ggplot figure. I often find myself with lot’s of categories that are discrete when I want a continuous color plot. This can be achieved by writing a quick little function for your colors as:

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gs.pal <- colorRampPalette(c("#FFFFFF","#000000"),bias=.1,space="rgb")

Now you’ve got a function called gs.pal that accepts the number of colors you want evenly spaced between the two hex code, e.g. gs.pal(5) will generate 5 different evenly spaced color codes. Here it goes between black and white, but you could do between any colors you want. You can put in as many colors as you want in your color vector. Bias controls how much spacing happens between your parameters. Here’s low spacing, with your pallete function set as going from red to blue to yellow.gs.pal <- colorRampPalette(c("#AF1E2D","#0147FA","#FFFF00"),bias=.1,space="rgb")

You can get more smoothing (depending on how many different categories you have) by adjusting the bias parameter, here I’ll set it to 1, and you’ll see much better smoothing. `gs.pal <- colorRampPalette(c(“#AF1E2D”,”#0147FA”,”#FFFF00”),bias=1,space=”rgb”)

Ok, I’m calling you out ESA to the meager number of people who read my blog. I’m reading my RSS feeds for journal abstracts on my iPad tonight in my favorite aggrigator reading app, pulse. I think to myself: “Well I know that Ecology doesn’t have abstracts, but Ecosphere must. Why it’s ESA’s new flagship open access, online only journal!” Of course what was I thinking? I forgot that ESA’s online presence is essentially run by people who are frozen in time. I imagine it’s two guys wearing track suits talking about how much they hate that new song “Hit me baby one more time” and marveling at these cool new things called “cascading style sheets”. Ok, I’m being snarky for the sole reason of being able to bring up Britney Spears in a blog post. Truly I have no idea why the ESA website hasn’t changed much from when I looked at when I was still an undergrad a decade ago, but I don’t think it’s due to any lack of technical expertise. But here’s a quick list of technical gripes.

• Seriously, no abstracts in your RSS feed? I pay less attention to your journal because of that.
• No share or tweet button? I mean even Wiley has that and they’re the evil empire. They have a twitter button, and a mendeley button, and a del.ic.ous button, etc…
• Your personal scheduler for your meeting is the same one I used in 2007. No mobile version? I used my phone as scheduling device all meeting and it was a pain to scroll around an full page.
• No preprints? Still?

Look, I don’t expect you to be PloS, that’s too much to ask. Wiley, Elsevier, etc…That’s evil empire type shit, Darth Vader, Big Brother from 1984, but you’re my society. I want you to be modern, sleek, the place I go and see “Damn that’s some cutting edge funk!” Instead I see the same tired web site, the same difficult to navigate, difficult to share articles. I’m 33, there’s a whole crop of younger grad students than me, and if you’re losing me, you’re losing them. So what’s the deal? I mean every schmo with a wordpress blog can place a “tweet this” button on their article so why can’t you? Have you seen the slides from Jarrett Byrnes talk that he just gave at the annual meeting? I’m not down on you ESA just so I can hate for the sake of hatin’. It’s that I feel a sense of ownership. Like I said you’re my society, as in I give you money, and I want you to reflect my values of modern, socially connected, collaborative, open science. Right now you’re closed, with almost zero social presence. You want Ecosphere to be new and relevant right? That’s why you make it open access and rapid publication. But in the end it just looks like all your other journals. Now back to reading my RSS feeds that don’t include any ESA journals.

It’s official, I’ve joined the rOpenSci team. If for some reason you’ve found my blog but don’t know what rOpenSci is (I find that a bit hard to believe though), it’s a group of developers devoted to making open science tools for R. Our goal is to make data access and data gathering as easy as possible by coding up R-wrappers for API calls to open data sources. Basically we make it easier for you to get data into your working environment (R) without having to deal with lots of idiosyncratic data collection activities.

You can see my sweaty mug over at the dev team page. That’s a photo right after skinning up the highest mountain in Vermont for some early season tracks on a warm December day (32F!!!) I’m looking forward to some good development work and getting some projects going.