Articles by Nathan Lemoine

Phylogenies in R and Python

June 2, 2014 | Nathan Lemoine

One of the reasons I switched to Python from R is because Python’s phylogenetic capabilities are very well developed, but R is catching up. I’m moving into phylogenetic community ecology, which requires a lot of tree manipulation and calculation of … Continue reading → [Read more...]

Cleaning Data and Graphing in R and Python

February 10, 2014 | Nathan Lemoine

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...]

Visualizing Dive Science (using R)

November 22, 2013 | Nathan Lemoine

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 | Nathan Lemoine

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...]

Eigen-analysis of Linear Model Behavior in R

May 7, 2013 | Nathan Lemoine

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 | Nathan Lemoine

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...]

Python Complements R’s Shortcomings

April 23, 2013 | Nathan Lemoine

I’m a big fan of open-source software for research. For example, R-statistics, Qgis, and Grass GIS are awesome programs. R can do any statistical tests and numerical modeling you can imagine; if there’s not a built-in function you can write … Continue reading → [Read more...]

Making Data Visually Appealing

December 16, 2012 | Nathan Lemoine

I’ve recently been considering the graphical presentation of data. I get the feeling that we, ecologists/scientsits, could be better at data presentation. Graphs must be informative, but they don’t have to be ugly. I think that making visually appealing charts … Continue reading → [Read more...]

R for Ecologists: Permutation Analysis – t-tests

October 24, 2012 | Nathan Lemoine

You’ve carefully designed your experiment, you’ve meticulously collected your data, and you have a hypothesis to test. Unfortunately, your data is typical of ecology data: small sample sizes, messy, and non-normal. Your ideal test, the t-test, won’t work because of the … Continue reading → [Read more...]

R for Ecologists: Putting Together a Piecewise Regression

August 19, 2012 | Nathan Lemoine

Piecewise regression comes about when you have ‘breakpoints’, where there are clearly two different linear relationships in the data with a sudden, sharp change in directionality. This crops up occasionally in ecology when dealing with, for example, species richness of understory plants … Continue reading → [Read more...]

R for Ecologists: Phylogenies in R

July 22, 2012 | Nathan Lemoine

I’ve only recently begun working from an evolutionary perspective, and I can’t imagine why I haven’t thought about it much before. After all, it comes up in just about everything that we do in ecology. For example, I’m currently feeding … Continue reading → [Read more...]
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