Blog

For older, tea-related blog posts, check out my page on teageek.net

Oh for {fs}, are you kidding me, base R?

r

This is a cautionary tale about the base R function list.files(). When you give it a vector of paths (which you totally can do), it re-orders the output alphabetically. This screwed me over in a project I’m working on where I took file…

New job: Scientific Programmer & Educator

at University of Arizona

alt-academic-careers

My postdoc with the Bruna lab coming to an end in June and I’m excited to announce my new position as a Scientific Programmer & Educator with University of Arizona! I thought I’d use this post to…

Assessing the reliability of an R package

r

In the most recent rOpenSci community call, Juliane Manitz presented on standards for statistical software in the pharmaceutical industry. One of her slides in particular was about how the pharmaceutical industry assesses the…

Fitting a DLNM is simple without the {dlnm} package

Wait, then what does {dlnm} do?

DLNMs

GAMs

r

This is part of series about distributed lag non-linear models. Please read the first post for an introduction and a disclaimer.

DLNMs: hypothesis tests and p-values

DLNMs

GAMs

r

This is part of series about distributed lag non-linear models. Please read the first post for an introduction and a disclaimer.

Speeding up DLNMs with bam()

DLNMs

GAMs

r

This is part of series about distributed lag non-linear models. Please read the first post for an introduction and a disclaimer.

DLNM marginal basis functions

DLNMs

GAMs

This is part of series about distributed lag non-linear models. Please read the first post for an introduction and a disclaimer.

Distributed lag non-linear models

DLNMs

GAMs

r

This is the beginning of a series of blog posts where I publicly stumble my way through figuring out some confusing, complicated, and, frankly, cutting-edge modeling and…

DLNMs: building and visualizing crossbasis functions

DLNMs

GAMs

r

This is part of series about distributed lag non-linear models. Please read the first post for an introduction and a disclaimer.

Working with matrix-columns in tibbles

r

The tibble package in R allows for the construction of “tibbles”—a sort of “enhanced” data frame. Most of these enhancements are fairly…

Treat your treatments as continuous

r

Taking a potentially continuous treatment, binning it into categories, and doing ANOVA results in reduced statistical power and complicated interpretation. Yet, as a…

Three ways to plot logistic regressions

r

data-visualization

If your data is just 1’s and 0’s, it can be difficult to visualize alongside a best-fit line from a logistic regression.

Looking under the hood with debug()

r

If you’ve ever tried to look “under the hood” of an R function, you know that sometimes it can be tricky to figure out what’s going on, especially…

COVID-19 pushed me to try something new in my classroom, and I loved it!

teaching

r

rmarkdown

Hacking GLMs to fit population growth models

r

I’m currently teaching Ecological Statistics and Data, a class I inherited from Lee Brown and Elizabeth Crone. In a lecture on population dynamics, they do some really cool things with generalized linear model—things that I don’t think are standard practice and as far as I can tell…

Tea Science Tuesday

tea

Tea Science Tuesdays are Instagram live streams where I’ll talk informally about…

My first R package is on CRAN!

r

multivariate-statistics

I woke up this morning to an email saying my first R package, holodeck, was on it’s way to CRAN! It’s a humble package, providing a framework for quickly slapping together test data with different degrees of…

Cupcakes vs Muffins: Round 2

data-science

multivariate-statistics

Have you ever pondered whether a muffin is really a…

RStudio::conf reflections

data-science

r

rmarkdown

This was my first time attending RStudio::conf, and I went primarily to explore my career options in data science. I…

Finding Cryptic Insect Eggs With Fluorescence

fieldwork

leafhoppers

tea

I recently gave a talk on some of my work as a PhD student on experiments manipulating densities of the tea green leafhopper (Empoasca onukii) on tea plants. What the audience liked most, I think, were my methods for finding leafhopper eggs in the field and rearing them in the lab (well, a guest room at a tea…

Last Fieldwork Season in China

tea

fieldwork

leafhoppers

I’m currently in Hangzhou, China at the Tea Research Institute(TRI) for my fourth and last time. It’s bitter sweet (like my favorite teas ;-) ) since I’m both glad to be nearing the…

Retrieve chemical retention indices from NIST with {webchem}!

data-science

data-wrangling

r

webscraping

GC/MS

My PhD has involved learning a lot more than I expected about analytical…

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

data-science

python

r

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…

PhDrinking Podcast

tea

I had the wonderful opportunity to be on Sadie Wit’s PhDrinking podcast. Check out the episode here and subscribe to PhDrinking wherever great podcasts are casted.

Cupcake Update

data-science

multivariate-statistics

I know you’re all waiting on the edge of your seats for an update on the cupcakes vs. muffins data science project, but…

Cupcakes vs. Muffins

data-science

regexp

r

multivariate-statistics

data-wrangling

webscraping

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…

Importing data from a LI-COR photosynthesis meter into R

data-science

r

data-wrangling

regexp

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…

Quantifying leafhopper damage with automated supervised classification

tea

r

leafhoppers

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…

Making a website in RStudio

r

rmarkdown

blogdown

I’ve always thought I should eventually have a professional website for job hunting, but recently I’ve realized…