When learning R (or any other new task), it’s okay to start small: aim for improvement, not perfection

When I first thought about switching to R and doing reproducible data analysis, the idea was daunting. As a grad student, I couldn’t figure out how to even get my data into R. How would I figure out that plus mixed model analyses plus how to make figures in ggplot, with version control and a beautiful github rep for all of my work?! What I eventually accepted is: it’s okay to start small. Or, as a colleague of mine suggests: for any given project, aim to do one thing in R that you couldn’t before.

I’m not sure why I set the bar so high for initially learning R. When I was first learning how to knit (actually knit, with yarn and needles, not the R version of knit), I knit a square washcloth, not a sweater. So when learning R, why was I expecting I’d be able to start out with the coding version of knitting a sweater with multiple colors, a fancy pattern, and buttons?

File:Fair Isle knitwear geograph-3936603-by-Julian-Paren.jpg

Julian Paren / Fair Isle knitwear in the Shetland Museum / CC BY-SA 2.0 via wikimedia.org

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My goal as a reviewer: pass the Poulin test

As a graduate student, I attended my first infectious disease-themed meeting shortly after receiving the reviews on my first thesis chapter. I was excited about the work, and had sent it to Ecology Letters, which reviewed it but rejected it. I talked about the same study at that meeting. It was a small meeting, and one of the great things about the meeting was getting to interact with senior people in the field. This included Robert Poulin, someone whose work I really admired. I was really excited to get to talk to him! During our conversation, he asked about the status of the work I’d presented at the meeting. I said that it had just been rejected by Ecology Letters and then was about to launch into a vent about the reviewers. As soon as I said (in what I’m sure was an exasperated tone), “One of the reviewers”, he stopped me and said “I was one of the reviewers.” I will be eternally grateful for that.

That moment has stood with me throughout my career. In addition to preventing me from embarrassing myself (more!) in front of him, it taught me a really important lesson about peer review. We complain about Reviewer 2 and shake our fist at that mythical beast, but there’s a decent chance that Reviewer 2 is someone who carefully reviewed the manuscript and thought something was problematic. Or maybe it’s that, with a bit of distance from the work, Reviewer 2 thought the work wasn’t as novel as I did as an author, making rejection from a journal like Ecology Letters completely reasonable.

This interaction taught me an important lesson about how easy it is to think of an anonymous reviewer as an adversary, when there’s a good chance they’re a scientist whose work I admire and whose feedback I would value.

There’s an idea that anonymity leads to animosity. I think that’s more often discussed in terms of the person making the comments – for example, as a reason for the toxic nature of the comments on websites. But it also applies in the other direction – in an anonymous interaction, it can be easy to assume the person writing the comment is unreasonable (unless they think our work is brilliant – then clearly they are totally reasonable!) I think the way the scientific community discusses reviews (including on twitter) probably doesn’t help.

Personally, when I receive reviews, I have to work to put myself in the mindset that these reviews can help my paper, even if they’re negative. There are still occasions where my first reaction is something like “How is it possible for reviewers to be so clueless?!?!” but then, after coming back to the reviews a few weeks later, I realize that the reviewers were pointing out something that we didn’t explain very well or a part of the literature we really should have discussed more or an alternate explanation we hadn’t fully considered.

As I’ve blogged about before, I don’t sign most of my reviews. But I still write them with that interaction I had with Poulin in mind. My goal is to write reviews where, if I ended up in that same situation at a meeting, I would be okay with identifying myself as the reviewer, even in cases where my review was a critical one. In other words, I want to pass what I’ve come to think of as the Poulin test.

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Guest Post: What not to say to a pregnant colleague

Today, we have a bit of a hybrid post. It starts with a guest post from someone who wishes to remain anonymous about things colleagues have said to her during her pregnancy. Her post definitely resonated with me – I thought of writing a similar post when I was pregnant with my third child, because I was so annoyed by some of the comments I received at work. After the guest post, I’ve added some thoughts of mine, as well as some questions that I’d love reader opinions on. My hope is that this post will encourage people to think more carefully about what they say to pregnant colleagues and create a space where people can talk about their preferences.

The guest post:

I am a postdoc who also happens to be pregnant. Around the sixth month of my pregnancy something happened. I must have become large enough that it was obvious to everyone in the department that I was indeed, pregnant. Suddenly, I began receiving comments about my body, my impending delivery, and what my life would look like after having a baby. (This is my second child; I have no delusions as to what postpartum life is like).

Here are a few of the comments I received over the span of two weeks:

My body:

“Wow, you’ve really let yourself go”.

“If a baby weighs 8 lbs then where do the other 25 lbs come from?”

Misconceptions about maternity leave:

“It will be so nice for you to have a break while you’re on maternity leave”.

“Think of all the writing you’ll get done while the baby is sleeping!”

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Guest Post: iPads and digital data collection in the field

From Meghan: This is a guest blog post by ecologists Isla Myers-Smith and Gergana Daskalova from the University of Edinburgh. I loved their comment on my post on our new lab notebook backup system and asked them if they could turn it into a guest post. I was very happy that they agreed! Isla and Gergana are off to the Arctic this summer with the Team Shrub field crew for another year of hopefully successful digital data collection. To find out more about their research check out the Team Shrub website and blog (https://teamshrub.com/).

Guest post:

Two things have really changed my academic life over the past five years: the first is embracing GitHub for version control of code, data, manuscripts and my research group’s individual and combined science, and the other is switching over to digital data collection. For ecologists who haven’t made the switch from paper field books to iPads and digital data collection it is not as scary as you might think!!!

Caption: Collecting plant phenology data – the recorder sitting in the back with an iPad! (photo credit: Jeff Kerby)

The benefits of going digital

Digital data collection can be more rigorous with error checking as data are collected to prevent mistakes. Data can be better backed up. And finally, it forces us to put thought into the structure of data before we collect it (significant digits, continuous or categorical data, are the data unrestricted or constrained to a particular range or particular set of values, etc.), which helps down the road when it comes time for analysis. Digital data collection has saved days, if not months, of data entry each year for my team and has allowed us to go from ecological monitoring in the field to analysis of results within hours instead of days. Our work flows are streamlined and our iPads are waterproof, so data collection can occur under any conditions – and we work in the Arctic, so we experience it all from wet to dry, hot to cold, rain, snow, you name it.

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Social aspects of writing

Intro: this is the second of a series of posts exploring some common themes in three books: Anne Lamott’s Bird by Bird, Helen Sword’s Air & Light & Time & Space: How Successful Academics Write, and Tad Hills’ Rocket Writes a Story. The first post focused on getting started with a new writing project, rough drafts, and the pleasures of writing. This post focuses on social aspects of writing.

 

Writing is inherently social – at a minimum, your article is read by reviewers and, of course, we write hoping that colleagues will read and understand (and maybe even like!) our article once it comes out. But the process of actually doing the writing can sometimes feel very isolated. Certainly my general approach is to hole up in my office and try to crank out some text. I get feedback from coauthors, but that’s done at a distance and with little interaction outside Word.

So, I was interested to see that Helen Sword has social habits as one of the four components of a strong writing practice. She devotes a chapter specifically to writing among others, talking about writing groups, write-on-site boot camps and retreats, and online writing forums. Each chapter of Sword’s book ends with a “Things to Try” section; for the chapter on writing among others, it includes “start a writing group” and “retreat in the company of others” as two of the four suggestions.

Right after reading that section of Sword’s book, I read a Monday Motivator email from NCFDD (written by Kerry Ann Rockquemore) that also emphasized the social aspects of writing. That email also focused on social aspects of writing, including traditional writing groups, writing accountability groups, write-on-site groups, and boot camps.

Reading those back-to-back made me realize that I severely lacked social components in my writing. I have gotten very used to setting my own goals and not sharing them with anyone else, and to holing up in my office to write. But I also don’t feel like writing is generally a problem for me, so wasn’t sure if I really needed to address the lack of social habits. If there isn’t a problem, why try to fix it?

But then, on a solo morning run, I thought about how much further and faster and more enjoyably I can run on the days where I go with a friend. And I thought about how, when I first got into distance running, I would tell some friends and family members about my race plans, which made me more committed to sticking with my training runs. And I’m much less likely to skip a run if I am meeting a running buddy, which explains why I ended up running in a downpour recently. Could these same social habits help with writing?

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My lab’s new lab notebook backup system. Part 1: The backstory

Back when I was an undergrad, the fire alarm went off while I was working in the lab. As people gathered outside the building, it became clear that it wasn’t a drill – I don’t recall specifics, but I think it was actually an issue in a neighboring building that caused someone in our building to pull the fire alarm. In the end, it wasn’t a big deal (even for the neighboring building!) But while people were standing around outside, the conversation turned to how much data would be lost if there was a full-on fire. It was clear that lots of people did not have complete backups of their lab notebooks and other data files.

When I was telling about this experience to a friend, Brooks Kuykendall, he told me of his father Bill’s related horror story. In the fall of 1963, Bill had completed his PhD research at Johns Hopkins in Archaeology, and started teaching at Erskine College in rural South Carolina. In the summer and early fall of 1964, after his first year of teaching, he had managed to finish writing his dissertation. In early October, he had assembled the six copies (and these were the days of carbon copies) ready to be submitted to his committee. They were stacked on the floor of his office, needing only to be packed off to go in the mail.

And then that night Bill heard the sirens. Rushing to his office, he found that the building was on fire. The firemen had cordoned it off, but somehow two students—of whom he forever after spoke with gratitude—managed to get in through the window of his ground-floor office, recovering only 1) a single rough draft for the whole text, and 2) a box that had the originals for all of the illustrations. The copies on the floor—and virtually everything else in the office—were ruined by the water.

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There is Shit Going On but it’s not my story to tell

As I mentioned in my post last week, just before I headed to the airport, Terry McGlynn posted a list of topics that he wishes people would blog about. Given that I was already planning on doing some #airportblogging, this was really tempting! A couple of his ideas especially stood out to me. The first was about how graduate students can get experience that will prepare them for non-academic positions; I wrote about that last week. The second was this:

-Thoughts about parenting and doing science and academia. (I have written about being a parent and a spouse on the rare occasion, but at a very young age, my son asked for privacy about these matters, and I’ve respected this.) I realize I should be talking about being a parent-in-science more often, because this is a huge part of our lives, and keeping this sequestered just amplifies gender inequities.

I’ve written regularly about the juggling act of parenting and doing science and academia, so it wasn’t the first part that really caught my attention. It was the parenthetical bit. Something that I’ve been thinking about a lot lately is how quite a few people I know are juggling so many big things but, for the most part, only close friends or colleagues know about what they’re dealing with. A partial list of the issues includes personal health conditions; aging parents (or death of a parent); partners who have a chronic illness or major injury; non-trivial things with children; infertility; financial struggles; harassment and/or bullying; and major work upheaval.

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How my student has explored career interests outside academia

Last week, Terry McGlynn wrote a post with a list of things he wishes other people would write posts about. I read this minutes before heading to the airport, and this was like catnip given my #airportblogging habit. So, I sat in the airport thinking about this topic Terry suggested:

How PhD students and postdocs are getting professional development to do things other than become a tenure-track faculty member

This is something I’ve been discussing a lot on seminar trips, with prospective grad students, and with colleagues, but I hadn’t thought about writing a post on it before. So, with thanks to Terry for the prompt, here’s the story of how one of my students has explored career interests outside academia.

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#Readinghour: My plan to read more in 2018

A common theme that comes up when talking with other scientists and academics is that we wish we had more time to read. I’ve been trying to figure out how to do a better job of reading for years, and spent 2015 tracking my reading using #365papers. The goal of that was to read a paper every day – I wasn’t planning on reading work papers on weekends, but I thought there would be enough work days where I read more than one paper that it would offset it. I was wrong. I didn’t get anywhere near 365 (I got to 181), but it still motivated me to read more than I would have – at least, until teaching Intro Bio completely took over.

Having just completed another semester of teaching Intro Bio (and having it take over), I was thinking again about how to reprioritize reading. I decided that I would prefer to have a time goal (30 minutes per day) rather than a paper goal, since I felt like having a paper goal was distorting my reading habits in a way that wasn’t useful.

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Reflections on the one-year anniversary of my anxiety post, including thoughts on how to support students with anxiety

One year ago, I was sitting at my computer, working on a post in which I talked* about having an anxiety disorder. My hope was that, by being open about having an anxiety disorder, I could help reduce some of the stigma associated with mental health problems, be a more vocal advocate for mental health in academia, and could help other academics with mental health issues know that they are not alone and that help is available and worth seeking. I think the post succeeded in those goals.

Below, I talk more about how people responded, give my thoughts – as well as some crowdsourced from twitter – on how to be a good colleague or advisor to someone with anxiety, talk about ongoing bias against mental health issues in academia and how that might affect early career folks, and summarize some of the key messages that I think are most important related to mental health, anxiety, and academia.

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