Plans for the Afterward

I’m studying for my qualifying exams right now, and I think I’m firmly in the “What if I FAIL?” phase.  I really don’t think I’ll fail.  But, WHAT IF?!!  In either case, I’ll know in about two weeks.  In the afterglow of my success or in the I-don’t-give-a-crap phase before deciding on my new career path, I plan to have two days of full on relaxation.  Hint, if you come to this blog to hear about actual science things, then now is the time to bow out of this post.  Otherwise, here are the things I plan to do when I can close my eyes and not visualize the carbon and nitrogen cycles.

Watch a lot of TV. Specifically, I’m hoping to catch up on Dr. Who and binge watch this potentially obnoxious anime about a high school swim team.  Don’t ask me why, it just seems like the right thing to do.

I have 55 new blog posts in my Blogger cue.  I will read all the blogs. In my PJs, with a latte, and my cat.

Listen to this song on repeat!  Alternatively, this one.

I’m going to clean my whole apartment.  Top to bottom, vacuum, dust, all the laundry, the works.  At the risk of exposing myself for the slob that I am, I’m out of clean forks.  That is all.

Sleep, sleep, sleep, sleep, sleep.

Right afterward, I will probably do a string of unhealthy things, like eating obscene quantities of Thai food.  After that, I plan to eat all the vegetables and things that you have to mince and chop and steam, because, really, I do not have time for that nonsense right now. 

I mentioned sleeping?  Yes, that.

There are other things on my mind (hiking, swimming, curating an amazing Facebook photo album, etc.), but I don’t want to overbook myself.

Making the Most of MCMC

Sometimes in grad school you need to write about topics that you yourself have little to no clue about. Part of this learning process is figuring out how to teach yourself some of these very difficult concepts. This blog post comes from a blog post I co-wrote with my cohort chum, Justin, 
By: Justin and Meridith

Markov Chains, and particularly Markov Chains Monte Carlo, are a difficult concept to explain. In fact, Dr. Hanks has stated that they are “Easier done than said.” At the very basis of everything, Markov Chains are a system that transitions from one state to another state. It is a random memorylessness process, that is,  the next state depends only on the current state and not on the sequence of events that preceded it. I have scoured the web and believe the following to be the simplest visual introduction to Markov Chains. (Spoiler Alert: It arose from someone – Andrey Markov –  being a sassmaster.)

From here, it’s easy to start to gain an appreciation for the wide breadth of applications available for Markov Chains. However, if we want to transition, as it were, from Markov Chains to Markov Chain Monte Carlo simulations, we must first explore Monte Carlo methods. These methods are a class of computational algorithms that utilize repeated random sampling (simulations) to obtain the distribution of an unknown probabilistic entity. The modern version of the Monte Carlo method was invented in the late 1940s by Stanislaw Ulam (coolest name ever), while he was working on nuclear weapons projects at the Los Alamos National Laboratory (think Manhattan Project). It was named by Nicholas Metropolis, after the Monte Carlo Casino, where Ulam’s uncle often gambled. Because reasons, apparently.  Peter Muller’s article gives a brief introduction of Markov Chain Monte Carlo simulation, a method that enables the simulation of Bayesian posterior distributions and thus facilitates the use of Bayesian inference.  According to Muller, the goal of MCMC is to set up a Markov Chain with an ergodic distribution and some initial state, where the term ergodic indicates that there is a non-zero probability of the process passing from one state to any other state at each step. Starting at the initial state, transitions (from one state to another) are simulated and the simulated states recorded. The ergodic sample average of simulated states will then converge to the value of the desired posterior integral. Muller notes that two conditions must be met in order to use the resulting integral estimates:

  1. As the number of simulated transitions, M approaches infinity, the chain must converge to the desired posterior distribution
  2. Some diagnostic must be found to determine when practical convergence occurs, i.e. when a sufficient number of simulations have been performed.

The first prerequisite, theoretical convergence, can be reduced to meeting the following three criteria: irreducibility, aperiodicity, and invariance. The second and more ambiguous of the two conditions—a criterion for practical convergence—has several proposed solutions in the literature. For example, Gelman and Rubin (1992) developed an “ANOVA type statistic [for considering] several independent parallel runs of the MCMC simulation,” and Geweke (1992) has suggested a comparison of an early-iterations ergodic average to an ergodic average of later iterations. However, Muller also suggests the simpler method of visual diagnosis via plotting the states for each iteration against the iteration number to judge convergence. 

Markov Chains and MCMC have many useful applications, ranging across a wide spectrum of fields. One such interesting application is in the game of baseball. When viewing a half-inning in a baseball game, there are 28 possible states based on number of outs–0, 1, 2, or 3–and runners on base–different combinations of having no runners, or having runners on first, second, and/or third base (see http://www.pankin.com/markov/theory.htm for a more detailed description of the transition matrix). This gives us a 28×28 transition matrix filled with the probabilities of being in each respective state. From here, we could calculate the expected value of runs scored from each state and analyze how this expectation changes from state to state. We could also extend this to analyzing the probability of scoring a single run by defining a slightly different transition matrix (again, see the link provided above for more detail). Due to its usefulness, MCMC has become a common tool for baseball analysts and sabermetricians (Editor’s Note: Totally had to Google sabermetrician.  I’m feeling I got short changed a little in the job naming category).

Another useful application is in the field of ecology. A useful paper, An Application of Markov Chain Monte Carlo to Community Ecology, serves as a wonderful walkthrough of MCMC with the easily conceptualized example of community assemblages (presence/absence) of birds among islands. As with our stated requirements for MCMC, the next state of bird species’ distribution among a set of islands only depends on their current state distribution. The article does a great jobs of connecting the dots from the ecological concept (birds disperse among islands, possibly due to competition) to an ecological question (given the starting state and some measures of competition among species, what is the probability that a random matrix will exhibit the same level of competition) to mathematical challenge (applying MCMC) and then loops the results back around to answer the ecological question (the distribution of finch species among the Galapagos shows evidence of competition!). If you’re feeling extra badass and want to make the jump from learning about MCMC to coding some examples in R be sure to check out the following blog posts!

Take the Bus! Good for the Environment, Your Wallet, and Your Wanderlust

And now for something a bit different!


We’ve been writing a lot in the past few weeks about life as a graduate student or some of the things we are learning while on our respective doctoral journeys.  However, if you will recall, we also love to go on journeys in general.  Meridith and I have always been avid travelers.  We have visited numerous other countries together (South Africa, Costa Rica, Panama, England, Aruba…) and separately (Kenya, Argentina, Ireland, Thailand…).  While traveling overseas is, literally, one of the best things ever, one of my favorite bar questions to ask people is, “What are the top 5 locations you want to visit in the United States?”  I think we spend a lot of time fantasizing about getting to far-off, exotic locations, and that can cause us to overlook the beauty in our own backyard (so to speak). (Editor’s Note: This is so true! One of my big epiphanies from my summer traveling Europe – by bus and train! – was that I had totally under appreciated all there is to see in the good ol’ U S of A.)  And while I might get to visit friends or make new friends when traveling overseas, getting a co-conspirator for your State side adventuring is a bit easier.


As Mer is one of my all time favorite partners in crime, she and I have always made a point to visit one another regularly.  Our college roommates (and often an all-star cast of their amazing boyfriends/girlfriends/partners/pals/siblings) make a point of gathering for New Years Eve.  That’s always a treat, and usually involves doing a multi-city flight out of California, to home, to the NYE destination (Boston 2015!), and then back to California.  While well worth it, that gets expensive.  If you add onto that a trip home during the summer and plane travel really starts to take a bite out of your budget.  So, what’s a budget-conscious, environmentally-minded person with a severe case of wanderlust to do?  Well, you can hop on the Greyhound and get to a regional destination with little money, hassle, and C02 wasted.  When I was living in Long Beach and Meridith was in Las Cruces, we were frequenting the Greyhound route between Long Beach and El Paso on a semesterly basis!
NYE 2014 Crew
“Whoa, whoa, whoa, Rachel.  Take the bus? I have a car!”  Yeah? Then find a bunch of friends and pile into the car.  Carpooling is great, and sometimes it is the most logical option.  But, maybe you have a more flexible schedule, you’re traveling solo, or you really want to cut your carbon emissions.  In that case, you should really be looking up the local Greyhound and Megabus schedules.  I’ve written about my internal conflict concerning the environmental impacts of travel here, and I’d suggest you check it out.  For those unwilling to read my previous ramblings, my conclusions are simply that bus travel is the most cost effective and environmentally friendly way to transit regionally.  Since writing that post over a year ago, I’ve had numerous conversations with people who just can’t seem to get over their bus hang-ups.  Maybe this isn’t the most glamorous way to move about the world, but if you are a reasonable traveler who keeps their wits about them, you have very little about which to worry.


Maybe you’re willing to give it a try?  I’ll give you a few tips from my numerous Greyhound adventures and misadventures to make your first bus trip a breeze.                     



Cat Bus.  The best kind of bus.
First, and foremost, put your patient pants on.  Unlike plane or train travel, hitting the open road on a Greyhound requires a little less coordination on the part of the company.  This might also be part of the “you get what you pay for” part of this equation.  I’ve been on some very punctual bus trips…I’ve also waited and waited for my connection.  Really though, I’ve slept in plenty of airport chairs waiting for my connecting flight when it was delayed.  So, meh, I’d call this a wash really.  I just tend to expect the bus to be a little behind its time. (Editor’s Note: For most people this goes without saying: double check your departure time AND date. I’m going to share my most shameful Greyhound experience because I love y’all. I’m not even sure if I ever told Rachel this, but last NYE my partner and I bussed to/from Chicago and I totally made us miss our bus because I was in charge of the tickets – we were still new and he didn’t know yet how horrible of an idea this was – and got the dates mixed up. So when we were leaving to catch our bus, I took our tickets out and realized that our tickets were for the day before. Cue full shame meltdown and us having to buy a whole ‘nother set of tickets day of, which meant paying full price.)


Once your bus arrives, where you sit matters a little bit more than where you sit on a plane.  Really, you don’t want to sit near the bathroom.  Obviously, right?  You should also choose your seat mate (if you have to have one) with at least a little care.  My brother has a theory that, when you’re on the bus, you’re much less focused on how you might die than when you’re 10,000 feet above the ground.  So, I have (unscientifically) concluded that people are generally less inhibited on the bus.  For this reason (or something), I’ve had a lot more interesting and friendly conversations on buses than I’ve ever had on planes.  If you want to chat, look for the person who looks like they want to converse.  Want to sleep?  Look for a fellow napper.  In my experience, there is generally at least one bus occupant who really needs to drop the mic; I would suggest not sitting with them.    


Mer took a 12 hour bus ride so we could surprise our friend
on his birthday!
Seat selection handled, now it’s time to occupy yourself.  If you’re doing a regional tip, you can try to choose an express bus that has wifi.  The wifi on buses is free, unlike on planes.  You probably won’t be able to stream Dr. Who, but you can check your email, access gDrive, and generally get some work done.  There are also, often, power outlets so you don’t have to worry about your computer or tablet crapping out on you.  This is my problem on, literally, every flight.  Why don’t I learn?  I’m not really sure if there is a cause and effect situation here, but I have found it much easier to get work done on the bus than the plane.  Again, maybe because I’m still on the ground?     


Normal travel tips apply on the greyhound as well.  Climate control can be something of an issue on the bus.  Consider your relative hot/cold scale when choosing an aisle or window seat.  Wear layers so you can add and subtract as needed.  Also, you really do want a blanket and a pillow.  There will be no smartly dressed attendant to hook you up with one if you forget.  Bonus points, you can bring liquids on the bus!  Beverages, peanut butter, hummus, and anything else delicious and spreadable is totally allowed.  This makes it way easier, for me at least, to avoid the pull of buying weird airport or plane food that is strange in my tummy and wrapped in a bunch of obnoxious, ultrathin plastic.


Night bus.  Also a good option.
How long will your bus adventure be?  The longest I’ve been on a Greyhound trip, to date, was 20 hours from El Paso to Long Beach.  It was a haul.  And as stifled and dehydrated as I usually feel getting off a plane, I felt downright stinky when I disembarked in Long Beach after a 20 hour coach trip.  You’ll feel way better if you can brush your teeth, change your shirt, and apply some deodorant during a layover.  Do yourself and the person receiving you at the end of the line a favor and stay fresh.    


Last tip?  Don’t be a douche-bag…or something like that.  The most common argument I hear from those reluctant to travel via bus is that it isn’t safe.  Not to sound harsh but, these may be the same people who want apps on their phones to keep them out of “bad” parts of town.  Get out of the bubble and give yourself a chance to not be afraid of others.  I’ve met some friendly, sad, unnerving, and genuinely hilarious people on Greyhounds.  And you know what?  I’ve met the same set of people in so many other places!  See my original statement above, be a wary traveler, but don’t be afraid of other humans who are just trying to get from point A to point B.  As Patty Griffith would say, “Grow kindness in our hearts for all the strangers among us, till there are no strangers anymore.”    
There you go, now take the plunge!  Your wallet, the environment, and your wandering soul will thank you!  (Editor’s Note: Benjamin and I are planning on taking a train from Boston to NYC then Megabusing back to State College! Yes, it’s more time-consuming and we’ll have to chill in the cold while waiting for the bus, but the money saved is going to be so worth it!)

Hiking after one of my bus trips to visit Meridith in New Mexico.