I think I’m capturing molting of an eastern chipmunk in some of these photos: in late spring, male chipmunks molt into their summer coat. Apparently, the molt sequence is the same as that of red squirrel, so I tracked down the old paper describing red squirrel molt to compare notes with the chipmunk photos (Yerger 1955). “The first […]

Happy May Day! Go bird-watching! During this week in Wisconsin’s history, these species have been found in past years… black-throated sparrow Baird’s sparrow

It was great to end the month with a lifer: a ruff that stopped over at Horicon National Wildlife Refuge! I saw the post on Wisconsin Rare Bird Alert and immediately hopped in the car with my optics. The clouds parted and the rain stopped long enough to make it out to the boardwalk, though […]

I had a new species captured recently now that the feeder cam is on the ground! Seeing the bird puffed up below a window at first made me wary, but I don’t think it was a window casualty. The window it’s below is buffered by an outer screen on the lower half, and is usually […]

Fitting Bayesian models has gotten even better with the R package INLA. The fact that it’s integrated into R has led to more simplistic scripting, and the approach means much reduced computational time. There is a lot of literature out there about “why and how” the integrated nested Laplace approximation, which is why my treatment of it in this blog […]

First, get to the right webpage, click the button that says “Retrieve Raw Data” and then “Proceed to FTP site.” There, you’ll find lots of files, including README’s with data descriptions. Look at README.txt to see what each of the listed files includes. Grab useful information: I recommend you download… routes.zip: I use the CSV in […]

I like to start with a clean slate. Set your working directory to wherever you store your BBS, etc. files that will go into the script. rm(list = ls()) setwd(“”) Here, you need to put the full path to the BBS files. library(data.table) BBS <- rbindlist(lapply(list.files(“”,full.names=TRUE),read.csv)) This following line creates a unique identifier for each […]

If you want to use the finer-scale BBS data, here’s a tweak to the R code I presented. In this case, you won’t want the SpeciesTotal, country number (perhaps, otherwise add it it to the ID variables) or StopTotal (again, I assume). BBS$countrynum <- NULL BBS$SpeciesTotal <- NULL BBS$StopTotal <- NULL Then, you’re going to […]

There’s a great data set of worldwide bird ranges that you have to request. They have breeding, wintering, and resident ranges of every species for which they have data in shape files. Once you get it, though, you can work with it using GIS. As usual, I like to script things. I downloaded all the […]

Let’s start with simple listing (i.e. all of your rasters are in one folder). Start the script with the basics. import os import arcpy from arcpy import env env.workspace = “wherever your stuff is” Make sure you’re in the right place and Arc is “seeing” your files by just running arcpy.ListRasters() after you set the […]