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intersecting landscape ecology, open science, and R

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Things I Forget: Push/Pull Greyed out in RStudio?!?

So, on more than one occasion I have set up a repository locally, then on GitHub and pushed to that repo from the shell. This works great, but this would always result in the Push and Pull buttons in RStudio getting greyed out. I could push just fine from the shell, but not from the GUI. Not a big problem, but always kind of annoyed me. Today I took...

A great idea: R Markdown for Undergrads

A recently published paper by Baumer et al (2014) caught my eye today (HT to Bruce Caron).  I wanted to share it here because I thought it was cool and also had a few comments to make about some of the issues the authors raised. First, a bit about the paper.  Partly in response to all the media attention to the crisis in reproducibility in science (e.g....

Rstudio and makefiles: Mind your options!

I have written this post mostly for myself. I don’t want to waste 2 hours on this problem again at some point in the future.  Hopefully others might stumble on it too and save some aggravation. So, the issue I had this morning was writing up a a makefile in RStudio.  I am new to make and makefiles, but have been able to get them running successfully...

SPARROW + Lake Volume + Field Data = PLOS ONE Paper

So this one goes in the category of shameless self-promotion (or shameless promoting of my co-authors).  We have a new paper out in PLOS ONE about how we combined the USGS SPARROW model, modeled lake depth and volume, and field data from the National Lakes Assessment to improve predicitons of TN and TP. There is no need for me to re-hash this here,...

RStudio, and Presentations, and Git! Oh my!

I have been using R for many years now and it has served me quite well.  I have used it for all manners of data prep work, analysis, developing figures, and more recently GIS and creating reproducible reports with knitr.  During this time my typical workflow included creating new folders for projects, throwing in an R shortcut that opens in the project...

Post-Doc Position: Landscape Scale Cyanobacteria Modelling

So, I normally try to keep work stuff and blog stuff separated, but I figured the four of you who read this might be or know of someone who might be interested in a one year (with possible extension) contract position with my research group at US EPA in Narragansett, RI. And besides, its my blog. I can do what I want. Our group works on various aspects...

An R function to download shapefiles

This post is a follow up from my latest Things I Forget post on reading in shapefiles.  That post assumed that you already had access to all the relevant files (e.g. .shp, .shx, .prj, .dbf, etc.).  A task that I routinely need to do is locate shapefiles on a website, grab those files, and read them in.  Instead of having to do this manually I wrote...

Things I Forget: Reading a Shapefile in R with readOGR

One of the more common ways that I read vector data into R is via shapefiles.  I tend to use these partly becuase of my own sordid past with Arc/INFO, ArcView and ArcGIS and partly due to their ubiquity.  In any event I have found the R package, rgdal, indespensible for this.  One of the workhorse functions for pulling in vector data is readOGR().  It...

Open Access and Landscape Ecology

I’ve got a dilemma.  I recently received a request to review a manuscript for the journal, Landscape Ecology.  It is the primary journal for the field.  If I am to be a good landscape ecology citizen I really should do the review.  The problem is that Landscape Ecology is not an Open Access journal.  If I am to be a good science citizen then, I believe,...

Things I Forget: Installing new python packages on Windows

I can never remember how to do simple things, be it in Python, R, or Java (hope I don’t have to do too much more work in Java…).   Given that, I plan to post these kind of things, when I remember of course, under the title of “Things I Forget”.  My primary aim for this is to help myself, but I do hope others with a similar memory affliction will also...

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