While I have been working full-time on my dissertation for the past 1.5 years (the bulk of it being fieldwork 2010-11 and more recently lab work), I’ve recently been diving headfirst into my behavioral data. My progress in this venture has inspired me to write this post—the first of a series—which I hope will be some sort of an unofficial guide to early Ph.D. students. Below, I list some of the computer programs primatology/behavioral ecology graduate students should master within their first few years of graduate school. This will help you avoid the “How do I do that again?” moment, when the post-field hangover makes you forget how to connect to the internet.
- A good reference management software program: There are many of these on the market. Some are free (Mendeley), some are ubiquitous (EndNote), while some are platform-specific (Sente-Mac). I use Sente, which has an embedded web-browser and pdf viewer (for mark-up and note taking) however it is a Mac-only and few people use it. Most of my friends swear by Mendeley, but I have yet to try it. The most important thing is to find one you like and stick with it. Accessing journal articles quickly and easily makes writing papers and “eventually” manuscripts with ease.
- Microsoft Excel (with VBA for writing macros). If you were like me, you arrived in graduate school with a passing knowledge of Excel. In other words basic knowledge of the most used functions (SUM, AVERAGE, STDEV, etc.) and a no real appreciation of the usefulness of this program. Moreover if you plan on collecting your data in the field electronically, chances are it will eventually make its way on to an Excel spreadsheet. Nearly everyone uses Excel (and other Microsoft Office applications) on a daily basis, but few use it to its full potential. Streamlining your data in Excel before importing it to other less “user-friendly” statistical analysis programs will save you lots of time. More importantly, if your data (behavioral data especially) end up as “strings” in your spreadsheets you will need to learn Visual Basic (VBA) macros to search strings and do basic data manipulation that Excel does not do well. Familiarize yourself with functions like (LEFT, RIGHT, MID, CONCATENATE, VLOOKUP, and HLOOKUP). Master “Pivot Table Reports” for quickly organizing data. Note: Office 2008 for Mac does not support VBA so Mac users make sure you get Office 2011.
- R and RStudio. R is an extremely powerful statistical computing language that is freely available. For someone with no experience with computer languages it can be intimidating. Seeing that blinking “>” and with no buttons to push for your “t-test” can make the best researchers quit and go back to SPSS. However, the R faithful have a strong online presence with plenty of help forums. Check out the Comprehensive R Network (CRAN) for all your R needs. RStudio is “integrated development environment” for R. In other words, it takes all the scariness out of that blinking “>” and turns R into to something more “user-friendly.” RStudio requires the full version of R to run, and makes importing data and packages much easier. Here is an excellent week-by-week introduction to R from a UPenn professor.
- NetLogo. Another freely available multi-agent modeling environment. This has its own package in R for extracting data from models and analyzing in R. I don’t use it, but my friends do.
- UCINET. Social network analysis is all the rage in behavioral biology and UCINET is the best of the social network analysis programs. While the learning curve can be steep (similar to R and MATLAB), do not fret! You can do just about all the SNA you need in this program and it comes with NetDraw visualization tool.
- MATLAB. If your institution has a license, MATLAB is one of the most widely used technical computing languages for research (both in academia and the private sector). MATLAB can be used for statistical analysis, data visualization, computational modeling, etc. I can’t speak much to using MATLAB as I just finished a seminar on it today (the real impetus for writing this post).
Readers of the blog: if you are a graduate student, soon-to-be graduate student, or professor in the natural or social sciences, feel free to add suggestions via the comments section.
Here are some other great resources for students and non-students alike:
DROPBOX: For backing up your files and accessing them across computers. This FREE software is amazing. Access it just like any other folder on your computer, and every time you change a file and have an internet connection, it uploads it to the cloud. It also saves previous versions of files and recently deleted files. Get this and save your dissertation in it. http://db.tt/2HEp09l
AMAZON: Do you have an amazon account? Did you know that you have free storage on Amazon’s servers, which means you can upload drafts of your dissertation there for safekeeping? You can! Google also does this, but since it saves your documents to Google Docs, be wary, all of your formatting will be broken if you ever have to download and use that file again.
GENERAL STORAGE ADVICE: Buy an external hard drive if you don’t have one. The biggest one you can afford – trust me, you’ll use it, and no matter what, in 3 years you’ll be kicking yourself for not getting the slightly larger one. Then use it to backup all the files on your computer as regularly as you can remember to do so.
MICROSOFT WORD: First, buy this because it’s the industry (of academia) standard. You can probably get Office at a student discount at your school, and it makes life so much easier to have the same software as 99% of the rest of the world. Then learn to use STYLES. These will keep your formatting from getting messed up, which isn’t a huge problem in short documents but is a real mess for dissertation-length documents. Then look into setting up a custom template (I called mine “Dissertation”) so that you can open a new doc with all your preset styles already set up (e.g., chapter titles need to have an inch of white space before them and be bold & centered; table captions need to be in italics and justified). And if you ever run into problems with formatting issues, use your resources. Chances are your school’s library has people who know how to get that figure to stay on pg 5 of chapter 3 instead of jumping to page 7.
LUCIDCHART: This is a website that lets you create flowchart diagrams and then save them as an image to insert into your document. It’s free, easy to use, and has professional-looking results (and is a lot better than Word’s chart-maker wizard). http://www.lucidchart.com/
MENDELEY: I am one who swears by Mendeley for pdf-organization and citation management. It’s free, you can edit (highlight, underline, add notes to) pdf’s in the program and it saves them separately from the pdf so you still have a blank pdf to send to friends. It syncs really well with Word. You can make folders of citations/pdfs or tag each one and search through them that way. You can back up your library online and access it from any computer even if the software isn’t installed. To add a pdf and it’s citation you just drag the pdf into the Mendeley window and it typically recognizes the metadata automatically. It’s amazing. And free!
DREAMSPARK: This site allows students to download some Microsoft software for free. Most of it is geared toward programmers or network specialists, but some of the programs might be useful for other grad students (e.g., Visual Studio for making super macros or Expressions Studio for making websites). Many of these are PC-only, sadly, but that’s what virtual boxes are for! https://www.dreamspark.com/
Great post Dave! On the analysis front, I spend most of my time in ArcGIS, Microsoft Access, and JMP for basic statistics. But, in may cases, Excel spreadsheets are the foundation of my analyses in each of these programs, so as you say, Excel literacy is vital.
Excel and SPSS are my mainstays… I used SAS in the past, but only reluctantly–the stupid code always trips me up! I just became acquainted with Mendeley, and so far I really like it!
Oh and I submitted abstracts for IPS on the last day to do so, of course