dyerlab

Fixing Imports to Hugo

The solution to this, is to recognize that a lot of the content I make (in fact most of it) will be presented as output from R Markdown. The tutorials I create, the analyses I do, etc. As such, why not start with an R Markdown file in the first place and go from there? Enter blogdown devtools::install_github("rstudio/blogdown") I then had to install python3 and pip to get the academic Hugo theme going.

get_map() Problems w/o Google API

There is a persistent problem with the get_map() function now that the google api is required. Even if you ask for source=”stamen” you still get an error asking for the google api. A fix is to do the following: library(gstudio) data(arapat) coords <- strata_coordinates(arapat) b1 <- c( left = -114.2935, bottom = 23.0757, right = -109.1263, top= 29.32541) map <- get_stamenmap( bbox = b1, zoom=7 ) ggmap(map)

Landscape Genetics Workshop 2019

This week I’m in the wonderful town of Glasgow giving a workshop on Applied Landscape Genetics to a wide and interesting population of researchers. Here is the link to the content. If you are not taking it, you can follow along at your own pace, it is all available under the following CC-SA 4.0 license.

RStudio Server on Ubuntu

Ubuntu server is a nice platform for server-related activities. Here is a short tutorial of how I updated my most current version to the latest available by rstudio.org. Here is how I got it going. If this is your first install, you need to grab the gdebi stuff sudo apt-get install gdebi-core Next download the latest deb from rstudio. I typically like to try out the preview release, often stable enough to get what you want done while at the same time highlighting the latest features.

UVa Center for Public Health Genomics

Today, I’ve been invited to give a talk at the University of Virginia Center for Public Health Genomics. I’ll be introducing the Population Graph framework we’ve been developing over the last decade with highlights on how we are applying it to SNP-level genomic data analysis in non-model systems.

Jane Remfert, Doctoral Candidate

Jane Remfert has successfully completed the necessary steps to proceed to Doctoral Candidate by completing her written and oral defense and submitting her research proposal. Thank you to Drs. Eckert, Gough, Johnson, and Keyghobadi for their insightful comments and expertise in helping to shape a dynamic and exciting research project. Now, you just have to do it!

Setting up Atom for Pweave. Or: What the what?

So as a way to expand some of the analytical tools we offer the students at my work, I’m developing a version of my Data Literacy course that will use Python as well as R. There is a lot of overlap in these two languages and both are of interest to our students as they develop their toolkits. This document walks through how to set up Pweave on your machine so you can engage in a little Literate Programming (trust me, it will make your life suck a lot less.

Using Google Drive as an R Data Repository

This is such a common thing to do these days, it is easier to just post this here rather than search through my class notes each time someone asks me how to do this. Here is the issue. Say you have some data associated with your research project and are adding to it and doing analyses. Chances are, you have it shoved into an Excel spreadsheet that is on your laptop, your home computer, the computer in the lab, a backup disk (you are keeping backups, right?

Poisonous Plants in the Commonwealth

This past summer has seen some rather spectacular cases of where people have run afoul of dangerous flora, the most recent of which was a college student after a runin with Giant Hogweed–the results were not good. Information The Virginia Tech Cooperative Extension group publishes a nice overview of toxic plants in the Commonwealth. It has some useful information in that all of us should be aware of.

The Atom Editor

Being new to the Windows platform, I'm on the look for a good text editor that can do the myriad of tasks that we do each day. Notepad is not an option, let's be real. I'm looking for something that can be extended and has been designed from the bottom up for wrangling text and writing code. Ultimately, I would like something that is amenable to teaching both R and Python using a single interface.