{"id":3330,"date":"2020-03-16T16:47:49","date_gmt":"2020-03-16T23:47:49","guid":{"rendered":"http:\/\/blogs.oregonstate.edu\/gemmlab\/?p=3330"},"modified":"2020-09-16T16:43:32","modified_gmt":"2020-09-16T23:43:32","slug":"coding-stories-tips-and-tricks","status":"publish","type":"post","link":"https:\/\/blogs.oregonstate.edu\/gemmlab\/2020\/03\/16\/coding-stories-tips-and-tricks\/","title":{"rendered":"Coding stories, tips, and tricks"},"content":{"rendered":"\n

Clara\nBird<\/a>1<\/sup> and Karen Lohman<\/a>2<\/sup><\/p>\n\n\n\n

1<\/sup>Masters Student in Wildlife Science, Geospatial\nEcology of Marine Megafauna Lab<\/p>\n\n\n\n

2<\/sup>Masters Student in Wildlife Science, Cetacean\nConservation and Genomics Laboratory <\/p>\n\n\n\n

In a departure from my typical science-focused blog, this week I thought I would share more about myself. This week I was inspired by International\u2019s Woman\u2019s Day and, with some reflection on the last eight months as a graduate student, I decided to look back on the role that coding has played in my life. We hear about how much coding can be empowering but I thought it might be cool to talk about my personal experience of feeling empowered by coding. I\u2019ve also invited a fellow grad student in the Marine Mammal Institute, Karen Lohman<\/a>, to co-author this post. We\u2019re going to briefly talk about our experience with coding and then finish with advice for getting started with coding and coding for data analysis.<\/p>\n\n\n\n

Our Stories<\/h2>\n\n\n\n

Clara<\/strong><\/h3>\n\n\n\n

I\u2019ve only been coding for a little over two and a half years. In summer 2017 I did an NSF REU (Research Experience for Undergraduates) at Bigelow Laboratory for Ocean Sciences and for my project I taught myself python (with the support of a post-doc) for a data analysis project. During those 10 weeks, I coded all day, every workday. From that experience, I not only acquired the hard skill of programming, but I gained a good amount of confidence in myself, and here\u2019s why: For the first three years of my undergraduate career coding was a daunting skill that I knew I would eventually need but did not know where to start. So, I essentially ended up learning by jumping off the deep end. I found the immersion experience to be the most effective learning method for me. With coding, you find out if you got something right (or wrong) almost instantaneously. I\u2019ve found that this is a double-edged sword. It means that you can easily have days where everything goes wrong. But, the feeling when it finally works is what I think of when I hear the term empowerment. I\u2019m not quite sure how to put it into words, but it’s a combination of independence, confidence, and success.\u00a0 <\/p>\n\n\n\n

Aside from learning the fundamentals, I finished that summer with confidence in my ability to teach myself not just new coding skills, but other skills as well. I think that feeling confident in my ability to learn something new has been the most helpful aspect to allow me to hit the ground running in grad school and also keeping the \u2018imposter syndrome\u2019 at bay (most of the time).<\/p>\n\n\n\n

Clara\u2019s Favorite Command: <\/strong>pd.groupby (python) \u2013 Say you have a column of measurements and a second column with the field site of each location. If you wanted the mean of the measurement per each location, you could use groupby to get this. It would look like this: dataframe.groupby(\u2018Location\u2019)[\u2018Measurement\u2019].mean().reset_index()<\/p>\n\n\n\n

Karen<\/strong><\/h3>\n\n\n\n

I\u2019m quite new to coding, but once I\nstarted learning I was completely enchanted! I was first introduced to coding\nwhile working as a field assistant for a PhD student (a true R wizard who has\nsince developed deep learning computer vision packages for automated camera\ntrap image analysis) in the cloud forest of the Ecuadorian Andes. This remote\njungle was where I first saw how useful coding can be for data management and\nanalysis. It was a strange juxtaposition between being fully immersed in nature\nfor remote field work and learning to think along the lines of coding syntax.\nIt wasn\u2019t the typical introduction to R most people have, but it was an\neffective hook. We were able to produce preliminary figures and analysis as we\ncollected data, which made a tough field season more rewarding. Coding gave us\ninstant results and motivation.<\/p>\n\n\n\n

I\ncommitted to fully learning how to code during my first year of graduate\nschool. I first learned linux\/command line and python, and then I started\nworking in R that following summer. My graduate research uses population\ngenetics\/genomics to better understand the migratory connections of humpback\nwhales. This research means I spend a great deal of time working to develop\nbioinformatics and big data skills, an essential skill for this area of\nresearch and a goal for my career. For me, coding is a skill that only returns\nwhat you put in; you can learn to code quite quickly, if you devote the time.\nAfter a year of intense learning and struggle, I am writing better code every\nday. <\/p>\n\n\n\n

In\ngrad school research progress can be nebulous, but for me coding has become a\nconcrete way to measure success. If my code ran, I have a win for the week. If\nnot, then I have a clear place to start working the next day. These \u201ctiny wins\u201d\nare adding up, and coding has become a huge confidence boost.<\/p>\n\n\n\n

Karen\u2019s Favorite Command: <\/strong>grep (linux) – Searches for a string pattern and prints all lines containing a match to the screen. Grep has a variety of flags making this a versatile command I use every time I\u2019m working in linux.<\/p>\n\n\n\n

Advice<\/h2>\n\n\n\n

Getting Started<\/h3>\n\n\n\n