Blog Archives

Cleaning Data and Graphing in R and Python

February 10, 2014
By
Cleaning Data and Graphing in R and Python

Python has some pretty awesome data-manipulation and graphing capabilities. If you’re a heavy R-user who dabbles in Python like me, you might wonder what the equivalent commands are in Python for dataframe manipulation. Additionally, I was curious to see how … Continue reading →

Read more »

ggplot2 in Python: A major barrier broken

January 20, 2014
By
ggplot2 in Python: A major barrier broken

I have been working with Python recently and I have to say, I love it. There’s a learning curve, of course, which has been frustrating. However, once I got comfortable with it (and continue to do so), I found that … Continue reading →

Read more »

Visualizing Dive Science (using R)

November 22, 2013
By
Visualizing Dive Science (using R)

My friends and co-workers got lucky enough to spend about two weeks living in the Aquarius habitat, NOAA’s undersea research lab in the Florida Keys. I, unfortunately, am stuck on dry land (or on a boat above the habitat, watching … Continue reading →

Read more »

R for Ecologists: RLQ analysis (semi) explained

September 3, 2013
By
R for Ecologists: RLQ analysis (semi) explained

I’ve been reading about RLQ analysis, also known as the fourth corner method, for analyzing relationships between environmental characteristics and species traits. I was interested because I thought I might be using RLQ analysis to answer a specific set of … Continue reading →

Read more »

R vs Python: Practical Data Analysis (Nonlinear Regression)

August 26, 2013
By
R vs Python: Practical Data Analysis (Nonlinear Regression)

I’ve written a few previous posts comparing R to Python in terms of symbolic math, optimization, and bootstrapping. All of these posts were pretty popular. The last one especially. Many of the commenters brought up the fact that R, while … Continue reading →

Read more »

R vs Python Speed Comparison for Bootstrapping

August 19, 2013
By
R vs Python Speed Comparison for Bootstrapping

I’m interested in Python a lot, mostly because it appears to be wickedly fast. The downside is that I don’t know it nearly as well as R, so any speed gain in computation time is more than offset by Google … Continue reading →

Read more »

Drawing a 95% confidence interval in R

August 5, 2013
By
Drawing a 95% confidence interval in R

I’m writing a post on how to draw a in 95% confidence interval in R by hand. I spent an hour or so trying to figure this out, and most message threads point someone to the ellipse() function. However, I wanted … Continue reading →

Read more »

Evaluating Optimization Algorithms in MATLAB, Python, and R

June 18, 2013
By
Evaluating Optimization Algorithms in MATLAB, Python, and R

As those of you who read my last post know, I’m at the NIMBioS-CAMBAM workshop on linking mathematical models to biological data here at UT Knoxville. Day 1 (today) was on parameter estimation and model identifiability. Specifically, we (quickly) covered … Continue reading →

Read more »

Eigen-analysis of Linear Model Behavior in R

May 7, 2013
By
Eigen-analysis of Linear Model Behavior in R

This post is actually about replicating the figures in Otto and Day: A Biologist’s Guide to Mathematical Modeling in Ecology and Evolution. The figures I’m interested in for this post are Figures 9.1 and 9.2 in the chapter ‘General Solutions … Continue reading →

Read more »

Citation Patterns in Ecology

April 29, 2013
By
Citation Patterns in Ecology

I’m always curious to see who is citing my one paper. Turns out I actually have two papers, and the most cited paper (with 19 citations, which sounds paltry but for me is quite exciting) is certainly not the one … Continue reading →

Read more »