Tricks of the Trade: LaTeX

Ok, guys. I’ve been studying as a baby statistician (scienctician? statscientist? ecologitician?)  for a little while now and I’m here to share some of their secrets. Before I started here at Penn State I had a couple ideas about what other grad students in my department would be like. First, everyone would be computer masters of any and all statistical programs: R, SAS, others that I hadn’t even heard of yet. Second, they’d all be completely on top of everything in all of our classes because they all would’ve completed undergraduate and master’s programs also in statistics. And thirdly, it’d be really hard to relate to other students because of my background in biology and my love for the outdoors (because clearly they’d all prefer sitting inside in front of their computers, right?). Thankfully, I was way off base and not only am I not left in the educational dust, but my cohort is full of awesome students with a wide variety of strengths and abilities. And I must collect them all. Yea, my new goal is to be like some sort of awesome Anna-Paquin-as-Rogue statistician and glean all of the amazing abilities and knowledge while I can. Except I think I’ll stick to taking the time to learn and practice things…instead of the whole touchy hurty thing she does. One of my absolute favorite new acquires is the ability to write code in LaTeX.


Another one of my pre-stats misconceptions was that whenever you saw an equation in a journal article it was created with Word’s super difficult equation editor.  Hopefully I’m not the only one who thought this, because now I feel really silly (Editor’s Note: I assumed mathematical witchcraft, so joke’s on me really.). LaTeX is a document preparation system for high-quality typesetting often used for technical or scientific documents. Long story short, you could be creating completely badass documents with lots of equations and badassery like these: [Homework with R Code, Homework with crazy stat stuff!]. I received my intro to LaTeX during one of the Cohort Workshops I have been arranging on Fridays for my department. Another grad student gave us a very brief introduction and showed us some of the basics. A few downloads, a bunch of googling, and several hours of practice later (not to mention an uninstall and redownload…) I was really starting to get the hang of it! Anyone who’s learning to program knows that you experience some of the most frustrating moments during that initial learning curve. WHY WON’T YOU JUST COMPILE AND SHOW ME A PDF OF MY NAME AND ‘HELLO WORLD’? I DID EXACTLY WHAT YOU TOLD ME…*deletes comma* Oh…well then. BEHOLD MY BRILLIANCE! FOR I HATH CREATED A MASTERPIECE!

I would like to encourage everyone to give it a go! I can answer basic questions, but I’ve found that the vast majority of my own beginner’s questions have been accomplished through a few key resources, including the Great Googily Moogily. Behold your starting point!

What to Download
  1. Tex – LaTeX is actually a sub-entity of Tex, sort of like Git and Github (which I also am just beginning to understand!) So you’ll actually need to download Tex in order to run LaTeX. Unfortunately, there are slightly different versions for Windows and Mac users but both deal with the same underlying program (if you run anything else, my apologies for being completely unaware of how to guide you).
  2. An Editor – The Tex download comes with everything you absolutely need, but I like using an editor for extra pretty colors and the option to code for other programming languages. I like working in Aquamacs, which is the Mac version of Emacs. (Update: I now use Sublime Text because Aquamacs kept giving me unhelpful error messages and I wasn’t having none of that.)
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Full disclosure: this took me a WHILE!
What to Try First
  1. Hello, World! – Your first task is to just compile and create a PDF file with the most basic of greetings. I used this website at Art of Problem Solving. Even still I spent way too long before I got my first code to compile and PDF produced. It’s a glorious achievement!
  2. Do a Homework in LaTeX – This is not applicable to everyone and for all classes. But if you have a math or stats course where the homework isn’t too intensive consider completing it in LaTeX! One of my professors even wrote lots of handy coding tips on one of my homeworks that helped me a lot the next time around. I love being able to feel accomplished at writing up a nice, clean looking final version even if the homework is crazy difficult. Helps me keep those imposter thoughts at bay!


Next Level Stuff
  1. Update your CV – This was one of my recommendations for our Motivation blog post last week. I used this one from Bradley P Carlin and you can check out my final form!
  2. Write and submit your next manuscript using LaTeX! – Now, I’m nowhere near this stage of my program but I’d wager that quite a few templates or style formatting guidelines available for submitting a paper using LaTeX! Go, go, go!
  3. Combine with RStudio to work with knitr and sweave to produce LaTeX documents with R code  and results spliced in!


Basically part of my grand PhD scheme is to master a lot of the computing and presentation side of statistics so that I will be a valuable asset and worthy of ALL the jobs. At least a few options after graduating will be worth the toiling away finding that stray comma or misspelled command. Now that you’ve heard my favorite new tool I’ve learned so far please share yours! Or even if your favorite is also LaTeX tell me all the little tricks  you’ve picked up! I want all the tricks!

Is there a Doctor in the House?

I’m over a month into my PhD program and I’m still oscillating between wild, ecstatic optimism and stone cold, stop you in your tracks fear of the route ahead.  Completing a Master’s degree was two and a half years of hard work and setbacks culminating in one of the proudest, happiest moments of my life – successful defending of my thesis. I’m back on track for five more years of the grad student life, but these will be harder, faster, stronger times ahead than before. Good thing I’ve got my Daft Punk pandora station ready to go. My Masters program didn’t entail any qualifying or comprehensive exams so they seem like lofty, impassable goals now. A sentiment shared by my cohort members, but we’ve found that the more information we have the more confidence we gain. We here at STS would like to share what we know about our own roads to knowledge with you the readers so that you guys can find the confidence to face this journey too.

Not freaking out. I am not freaking out. I’m not. 

First things first, what exactly is the difference between quals, comps, and a thesis defense? Well, if you’re in grad school you at least know enough to be shaking in your boots at the prospect of any one of them. As you progress through your PhD program the powers that be (general your advisors) will want to ensure that you’re advancing at the desired pace, thus a few intense, intimidating milestones are thrown at you. The first of these, the Qualifying exam, serves to assess whether the student is capable of conducting doctoral research/scholarship. Quals often also serves as the PhD candidacy examination. Qualification exams are taken early in your program and are often based on required coursework. Once you pass your quals (and sometimes it takes a few tries, don’t worry!) feel free to relax a tiny bit and allow yourself to celebrate! Throw a wild soiree with your cohort! The PhD Comprehensive exam is given by members of your committee once a student has completed the required coursework (generally year 2 or 3, but ultimately depends on your program) and serves to evaluate mastery of the major studied. Sometimes presenting your research proposal can be wrapped up within Comps, as a way so show you have mastered the content necessary to proceed. If you’ve passed your Comps go ahead and celebrate once more! Now all you have left is research, thesis writing, and a thesis defense! It’ll be tough, but you’re in the home stretch. A lot of students are terrified by the time they are fast approaching their thesis defense. A lot rides on that final presentation of research and oral examination by the committee, but honestly once your committee signs off on a date for you to present and defend you’re practically finished already! They don’t want to set you up to fail (it reflects poorly on them as well)! Smooth sailings on through to your doctorate! Congrats once more! You’re a doctor!!

Post Masters Celebrations!

If you picked up on how it sounds like your committee has a lot of power of your progress through your PhD project, then you’re not far from the truth! However, they will also be there to provide you with all of the guidance and insights that you could possibly need. After all, they’ve been in your shoes before and have helped others through your journey. The majority of your committee will be comprised of professors from your department, but if you’re one of those brave souls that goes for a more interdisciplinary approach you’ll likely find members from other departments or even other institutions.  You are in charge of approaching and inviting generally four professors to serve on your committee. Something to keep in mind while forming your own band of professors is that you’ll want to ensure that you choose members that will have the time and resources to help you with your thesis research, writing, and defending. You’ll need to have a close working relationship with these people so don’t be afraid to choose based on how well you foresee getting along with them. A highfalutin big wig in your field sounds great to have involved, but if they have no time for you then maybe it’s best to find someone else to serve instead. You want people who are passionate about being on your team and helping your grow and develop to ensure that upon completion of your PhD you’ll be ready to find a postdoc or a job in a variety of fields!

Workin’ hard with the cohort.

 If you are, like me, at the very beginning of your program with all of these hurdles strewn in your future it can be incredibly intimidating. A lot of doubts can creep into your mind about your ability to gain a mastery of the content, especially if you’ve changed fields! I’ve had quite a few chats with my cohort already about our looming quals at the end of this year. Our department recently changed it’s program for PhD students and we’re the first group to go through this new design! We feel a lot like guinea pigs – the kind that people eat rather than keep for pets! I have dealt with this nervousness by finding out as MUCH as I can about how I am expected to progress through each year. But what has really quelled my quals fears has been talking to my academic advisor and hearing his reassurance that no, the department really isn’t trying to scare anyone off or try and weed us out. They earnestly do want each and every one of us to pass and will provide us with all the resources to do so! Rather, instead of being a weed out process, the qualification exam more serves as a way to ensure that WE are absolutely sure that we want to put in the work necessary to earn a PhD. I’m so grateful that I am part of a large, wonderfully supportive cohort that is already working hard to make sure no one falls behind. If I can recommend just one thing to new graduate students feeling that fear creep in, it’s to talk to your cohort, the grad students that are ahead of you, and professor in your department. The reassurance I’ve gotten from admitting my fears and insecurities to others and in turn hearing theirs has been a tremendous confidence booster!

You can check out my (Meridith’s) Statistics PhD program expectations in the slide included! If you are interested in hearing about Rachel’s Ecology program (she’s in her 3rd year and has just schedule her comps!) you’ll want to keep an eye on our Sweet Tea, Science Tumblr this week! If you are also working on getting your PhD (or Masters!) we’d love to hear how these major exams work in your field/department! There’s so much variety that we can’t hope to cover how these things work for everyone, but go ahead and let your experiences be known down in the comments.

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Share a Science Documentary Day

Science documentaries. I’ve got a sneaking suspicion that you love them. You’ve watched both iterations of Cosmos; you’ve joined Stephan Hawkings on an exploration of the universe; you’ve learned about the rovers, landers, orbiters, and space stations exploring our solar system; you’ve experience Sr. David full-on gushing over a hedgehog. If I were to write a blog post trying to convince you to check out some of Sweet Tea Science’s favorite science documentaries, you would scoff because you are so on top of that. And that’s awesome! Seriously, let’s take a moment to appreciate our collective thirst for knowledge!

However, let’s not get so ahead of ourselves that we forget to share this excitement, enthusiasm, and thirst with others!

I have been inspired by a lovely evening out with my partner and his friend. We had been enjoying a few beers, and we got on the subject of education, intelligence, science, space and…well, you know how conversations can go. We eventually got on the subject of exploring our solar system and trying to understand the creation of the universe. Now, keep in mind that I love these kinds of conversations and could go on and on for a while. My comments are often prefaced with “I saw once in a documentary that…[insert science here]”. I was shocked to find that the friend had never heard of some of what we were discussing. It wasn’t that he didn’t have an interest in the topics, quite the opposite! He tried to write it off as us just being inherently smarter than him, but honestly, it was just a product of being an avid science documentary watcher. The knowledge is out there, I just Netflixed my way to it! I want others to know that they can too!

I am beginning to realize that there exists a set of people out there that are interested in exploring the sciences, but they don’t believe in themselves or don’t know what avenues to explore to help with their intellectual endeavors. This is where we come in. I’m going to assume that the majority of readers are here because they are totally into science. If we all independently hosts screenings of science documentaries and invite lots of our friends that might not normally choose such a film, then think of all of the science converts! I propose we
take this opportunity to organize. I nominate September 17th, 2014 as the first annual Share a Science Documentary Day!

This is a project that will require the help and support of the online scientific community. Science Side, I’m looking at you!

Your STS Homework:

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1. Share your favorite science documentary. You may do this in the comments here, on our Tumblr, or on your own social media outlet of choice! Be sure and tag us, @SweetTeaScience, so we can reblog/post/tweet you. Feel free to use the tag #SciDocuDay2014!

2. Host a Science Documentary Viewing on September 17th, 2014. Invite friends now and get people excited!

3. After your viewing don’t forget to try and start a dialogue. Talk about what you just learned and encourage others to share their impressions.  (Editor’s note: I think this would be a great time to talk about how to pick a documentary that isn’t bunk and how to be a skeptical consumer of information.  I mean, I love me some Netflix docus, but I’ve also quit some half way because…bunk.)

4. If you’d like, write up a little something about your event. What did you watch; did people enjoy it; would you host a similar movie night again, etc. We’d love to hear back and post your feedback on our blog or Tumblr!

Best of luck to everyone choosing a film to watch. Here might be a good place to start. We’ll keep you updated via tumblr about our own plans and movies that we choose to watch at our respective events! If you have any suggestions we’d love to hear them.