R

Interactive effects of drought severity and simulated herbivory on tea (Camellia sinensis) volatile and non-volatile metabolites

Use of partial least squares regression (PLS) in ecology

PLS is a powerful multivariate regression method that has many applications for ecological data. When is it best used, what are its advantages, and how should you report your results?

Retrieve chemical retention indices from NIST with {webchem}!

My PhD has involved learning a lot more than I expected about analytical chemistry, and as I’ve been learning, I’ve been trying my best to make my life easier by writing R functions to help me out. Some of those functions have found a loving home in the webchem package, part of rOpenSci. Papers that use gas chromatography to separate and measure chemicals often include a table of the compounds they found along with experimental retention indices and literature retention indices.

Python is Weird (an unabashedly biased intro to Python for R users)

Last semester I took a class that used Python. It was my first time really seriously using any programing language other than R. The students were about half engineers and half biologists. The vast majority of the biologists knew R to varying degrees, but had no experience with Python, and the engineers seemed to generally have some experience with Python, or at least with languages more similar to it than R.

Cupcakes vs. Muffins

One thing I’ve learned from my PhD at Tufts is that I really enjoy working data wrangling, visualization, and statistics in R. I enjoy it so much, that lately I’ve been strongly considering a career in data science after graduation. As a way to showcase my data science skills, I’ve been working on a side project to use webscraping and multivariate statistics to answer the age old question: Are cupcakes really that different from muffins?

Importing data from a LI-COR photosynthesis meter into R

The LI-6400XT is a portable device used to measure photosynthesis in plant leaves. As you take measurements by pressing a button on the device, they are recorded into memory. In order to keep track of which measurments go with which plants (or experimental treatments), there is an “add remark” option where you can enter sample information before taking measurements. When the data are exported, you get a series of .

Quantifying leafhopper damage with automated supervised classification

As part of my fieldwork in China, I collected harvested tea leaves that were damaged by the tea green leafhopper. I want to quantify the amount of leafhopper damage for each harvest. I was able to find several solutions for quantifying holes in leaves or even damage to leaf margins, but typical leafhopper damage is just tiny brown spots on the undersides of leaves. I did find some tutorials on using ImageJ to analyze diseased area on leaves, but found that the leafhopper damage spots were too small and too similar in color to undamaged leaves for these tools to work reliably and be automated.

Making a website in RStudio

I’ve always thought I should eventually have a professional website for job hunting, but recently I’ve realized that it would be nice to have somewhere to collect my thoughts and contributions all in one place. Before having a website of my own, I generally shared updates and thoughts on Twitter and on other people’s blogs, which I will still continue to do, but having everything I do in one place seems like a good idea.

[poster] Generating and analyzing metabolomic data from tea plant volatiles