Ecology

The USDA maintains a database of plant information, some of it trait data, some of it life history. Check it out at https://plants.usda.gov/java/ They’ve been talking about releasing an API for a long time, but have not done so. Thus, since at least some version of their data is in the public web, I’ve created a RESTful API for the data: source code: https://github.com/sckott/usdaplantsapi/ base URL: https://plantsdb.xyz Check out the API, and open issues for bugs/feature requests in the github repo....

scrubr is an R library for cleaning species occurrence records. It’s general purpose, and has the following approach: We think using a piping workflow (%>%) makes code easier to build up, and easier to understand. However, you don’t have to use pipes in this package. All inputs and outputs are data.frame’s - which makes the above point easier Records trimmed off due to various filters are retained as attributes, so can still be accessed for later inspection, but don’t get in the way of the data....

After my presentation yesterday to a group of grad students on R resources, I did a presentation today on intro to R data manipulation, visualizations, and analyses/visualizations of biparite networks and community level analyses (diversity, rarefaction, ordination, etc.). As I said yesterday I’ve been playing with two ways to make reproducible presentations in R: RStudio’s presentations built in to RStudio IDE, and Slidify. Yesterday I went with RStudio’s product - today I used Slidify....

As ecologists, we often start graduate school worshiping the ivory tower of academia with its freedom to pursue important ecological questions. However, studies have shown that most of us do not end up in academia. Greater numbers of ecology graduates are leaving the ivory tower for non-academic career paths. But for many graduates, moving from an academic environment to a non-academic job may be difficult. In graduate school we are trained to work in a particular way, often with loose deadlines and unlimited intellectual freedom (within reason of course)....

Have you ever wanted to easily visualize your ecology data in Google Earth? R2G2 is a new package for R, available via R CRAN and formally described in this Molecular Ecology Resources article, which provides a user-friendly bridge between R and the Google Earth interface. Here, we will provide a brief introduction to the package, including a short tutorial, and then encourage you to try it out with your own data!...

So I want to mine some #altmetrics data for some research I’m thinking about doing. The steps would be: Get journal titles for ecology and evolution journals. Get DOI’s for all papers in all the above journal titles. Get altmetrics data on each DOI. Do some fancy analyses. Make som pretty figs. Write up results. It’s early days, so jus working on the first step. However, getting a list of journals in ecology and evolution is frustratingly hard....

So I heard many people say after or during the recent ESA conference in Portland that they really enjoyed the converstations more than listening to talks or looking at posters. There was some chatter about doing an unconference associated with next year’s ESA conference in Minneapolis. And Sandra Chung (@sandramchung) got on it and started a wiki that we can all conribute ideas to. The wiki is here What is an unconference?...

Many R packages/tools have come out recently for doing ecology and evolution. All of the below were described in Methods in Ecology and Evolution, except for spider, which came out in Molecular Ecology Resources. Here are some highlights. mvabund paper - get R pkg Model-based analysis of multivariate abundance data. Visualising data, fitting predictive models, checking assumptions, hypothesis testing. popdemo paper - get R pkg Population demography using projection matrix analysis....

Many ecologists are R users, but we vary in our understanding of the math and statistical theory behind models we use. There is no clear consensus on what should be the basic mathematical training of ecologists. To learn what the community thinks, we invite you to fill out a short and anonymous questionnaire on this topic here. The questionnaire was designed by Frédéric Barraquand, a graduate student at Université Pierre et Marie Curie, in collaboration with the International Network of Next-Generation Ecologists (INNGE)....

This blog has lasted a whole year already. Thanks for reading and commenting. There are a couple of announcements: Less blogging: I hope to put in many more years blogging here, but in full disclosure I am blogging for Journal of Ecology now, so I am going to be (and already have been) blogging less here. More blogging: If anyone wants to write guest posts at Recology on the topics of using R for ecology and evolution, or open science, please contact me....