GIS for Fun: My Digitized BBS Route

The North American Breeding Bird Survey (BBS) was meant to be a stratified random sample of the continent’s terrestrial bird populations, so we could monitor the pulse of populations and trends. When I went to the American Ornithologists’ U/COS conference (back when it was still called that) in 2015, I presented in a symposium dedicated to BBS. The opening talk was about the history of BBS, which helped give me some historical context about the data set. It added a dimension to my understanding of the time periods of ecological research. The data set was developed before landscape ecology really took hold in the U.S., and along with it an explicit awareness of spatial analysis.

The spatial data we have for the BBS is what I believe to be digitized route paths from old highlighted paper route maps. As such, it’s rife with errors: I’ve found routes in the layer of many variable lengths, but some egregiously too long. Being that it’s a volunteer effort, it’s at times hard to get clarification on what’s going on here. I’ve done and continue to do analyses based on these route paths, so their accuracy matters to me. Side note: if the United States Geological Survey – Patuxent would have me, I’d be happy to travel the country in something like the “Google street view car” and help digitize these routes during BBS season! Just putting that out there.

I decided to pull up my route in GIS to see what calculated stops would look like, by first placing stops every 0.5 mi. (probably the more correct method) and then placing 50 equally spaced stops along the route. Since the route is a little long, the 50 stops end up probably being more spread out than they should be. Also, as route runners know, it’s not an exact science, in that you might need to move a stop up to 0.1 mi. for safety concerns.

Anyway, when I synced this up to road data, I found that the routes were significantly off from the latest road path data, probably because the latest version is > 4 years old now. The road data I’m using is quite intensive, and I’m trying to figure out what to do next. How will I line up the paths, and will this little experiment even matter in the long run?

Proposed Tiers of Birding Involvement

My post critiquing the latest federal report trying to quantify birders suggested that perhaps we try to break birding into additional categories, to somehow scale between the active birding community and the federal report’s estimated number of birders. I’m open to name changes, commentary, new definitions, etc. but here’s where I’m at. These should be thought of as concentric circles, where each group is hypothetically included in the next category in the list.

  1. “Hardcore birders” – This is how the birding community would largely self-identify, which is essential to this definition: I believe the attempts of those of us to define birders in this sense are trying to define our community. Thus, many of us know each other by means of our membership in this group. These are the people who are constantly driven to “new heights” in birding, seeking novel experiences with birds in some fashion. Birding is a life priority and a passion. Whether they aim to up their ID game, add a lifer, or add to some other list they keep, these are your true hobbyist birders. My educated guess, along with those of other birders on social media, is around 250,000 in the U.S.
  2. “Non-hardcore birders” – I think this is the group where I found myself describing perceived members as “he/she likes birds” but not necessarily as a birder. These are people who know about, are interested in, and seek out opportunities to go birding, but are often not known to local birding communities. They may care enough to participate in local citizen science efforts, or support local bird-related organizations/events, but do not necessarily keep lists or put in effort to see new birds, or learn about birds purely for curiosity’s sake. This is where I’d go with the upper limit of my original guess, which is 300,000 people in the U.S.
  3. People with special knowledge of birds – I was shocked when my undergrad ornithology professor told me she wasn’t a birder; I thought the profession necessitated that hobby! I’ve come to learn, though, that it doesn’t, and she inspired this category: these are often (though not necessarily exclusively) people who have some professional association with wildlife. They may be very knowledgeable about ornithology, and support birds in some fashion, but are not necessarily birders (it actually makes me wonder if this category should thus be taken out, but this is a draft without a specific goal of categorization specified, yet). This could perhaps be estimated by how many people have worked with birds in any capacity, be it seasonal field work or otherwise.
  4. Backyard/Local Area Birders – These are people who do own a field guide and are willing to at least make guesses at what they see in the backyard, or adopt local knowledge about what’s around them. They may stay in their backyard, but they look beyond their feeder to try to learn what’s going on around them. I’m not sure how to estimate this, as different from the next categories up: I think the number of “active birders” from the U.S. Fish & Wildlife Service (USFWS) is inflated by waterfowl hunters who go to scout their spots, and necessarily own binoculars and other gear for hunting. Thus, they’re not birding purely to watch wildlife watching, but instead it’s intertwined in the goal of another hobby.
  5. Birder-curious – These are people who are intrigued by e.g. a local bird walk at a nearby natural area, and who may participate when they can, but do not necessarily take their hobby personally. In other words, they’re happy to look at birds when someone else is pointing them out, but it doesn’t necessarily translate to pursuing their hobby independently. It also may just be a part of general interest in wildlife, but not a special interest in birds. (This hypothetically includes what USFWS would loosely call “active birders.” Though the same problem mentioned above applies, the associated number from the report is 18 million).
  6. Feeder watching – These are people who feed birds and try (at least vaguely) to identify them. This likely includes anyone who owns a bird feeder, and/or buys bird food. This is meant to be the end scale of the USFWS definition, < 47 million.

Misadventures in Open Source GIS

When most ecologists conceptualize “GIS” we often think of a desktop GIS program, most likely ArcGIS. When we want to not use ArcGIS (or can’t), we most likely say “is there an R package for that?” In many cases, there is, and the repository keeps growing! The ever-growing number of R spatial packages reflects the general trend in GIS right now: it’s booming in lateral growth. Everywhere you turn, there’s something new, and actually my motivation for writing this post is just to try to keep up.

Going back “old school,” perhaps the most famous and long-running (i.e. older than I am) open source program is GRASS GIS. Here’s where the open source movement GIS movement fails, though: the point-and-click functionality and friendliness of interfacing with the program stops before you even get to the gate. If I go to the Ubuntu software center, it points me to an outdated version of the program that won’t even launch, so I had to remove it before installing the newer version (where the version number is in the command name). Luckily, though, it points me to a broader repository whereby I can access the “Ubuntu GIS” suite.

# Add Ubuntu Unstable PPA when running LTS Ubuntu release
sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable

The real problem I’ve had with GRASS from the beginning, though, is the beginning: you can’t just open the program and try to open some spatial data like you can in ArcGIS. You have to start by selecting a home folder, defining a “location” which must have uniform spatial reference, and then making a map set with spatial reference info. It’s where I admittedly gave up trying with GRASS long ago, in favor of the ease of just launching ArcGIS and adding a shape file.

QGIS solves more of this problem, but there are again some hangups on the install: it’s not in the Ubuntu software center, and installing it “the old fashioned way” seems to get an older version of the program (and the terminal errors will tell you so if you launch it from the terminal).

I’m thinking about finally trying to learn PostgreSQL in conjunction with PostGIS. I’m trying to retrace my thoughts on that to last year, and I think it was because I found out that SQL was a solid way to build my own GIS tools. I remember settling on that PostGIS was probably my best bet to learn open source GIS, and ironically I just saw a post-doc advertisement that specifically requested PostGIS knowledge.

Want to keep up? I compiled a certainly-not-exhaustive-but-pretty-comprehensive list of people I could find tweeting about open source GIS

Let me know if you should be on that list!

True Life as a Continual “Student”

It’s a sign of a good attitude when you hear people say they’re perpetually a student of life. Academia is, unsurprisingly, one of the career tracks where you’re seemingly always learning something new for your job, and I think all of us are here because we love to learn. I’d venture a guess that science fields in particular garner a disproportionate number of INTJ (my Myers & Briggs type), and we like to get things as right as possible, even if that means deconstructing the current system and starting over. That’s certainly, for better of worse, who I am. It’s not good enough until it’s the best it can possibly be (and now you can see why I’m prone to perfectionism), and I relentlessly pursue the best solution to any problem. I generally see it as a strength (I guess that’s obvious because I do it), though others might see it as a hindrance, or at least a waste of time to “do something better” that works just fine as is. It has led me to learn a lot that I wouldn’t have otherwise learned. Plenty of what I’ve learned on my career track, though, is just necessity and not striving for the perfect solution. Thinking back to especially grad school and my current job, I wanted to look back at what I’ve learned when, and chronicle it here. It’s a mix of programming languages, operating systems, software/libraries, platforms and even fields of study with associated tools.

  • Before college: DOS, HTML, QBASIC, Visual Basic
  •  Undergrad
    • 2004: MATLAB, Java
    • 2006: Linux, bash scripting, using servers
  • MS
    • 2009: SAS, ArcGIS
    • 2010: Patch analyst, FRAGSTATS
    • 2011: Sigma Plot, PC-Ord, R
  • PhD
    • 2012: remote sensing (ENVI), various landscape ecology tools (introduced to Conefor, etc. through class labs)
    • 2013: Python
    • 2014: GME
    • 2015: GDAL, CSS
  • postdoc
    • 2016: STELLA
    • 2017: NetCDF, Google Earth Engine, Github

Critique of the Federal Birding Report

In 2011, the US Fish and Wildlife Service (USFWS) published “Birding in the United States: A Demographic and Economic Analysis.” It was created as an addendum to the National Survey of Fishing, Hunting, and Wildlife-Associated Recreation. They claim it’s the most extensive survey of wildlife recreation in the U.S. to date.

“Overall, about 9,300 detailed wildlife-watching interviews were completed with a response rate of 67 percent. The Survey focused on 2011 participation and expenditures by U.S. residents 16 years of age and older.” – USFWS

The stated mission was ambitious.

“The following report provides up-to-date information so birders and policy makers can make informed decisions regarding the management of birds and their habitats. This report identifies who birders are…how avid they are…In addition to demographic information, this report also provides an economic measure of birding. It estimates how much birders spend on their hobby and the economic impact of these expenditures.

By understanding who birders are, they can be more easily reached and informed about pressures facing birds and bird habitats. Conversely, by knowing who is likely not a birder, or who is potentially a birder, information can be more effectively tailored. The economic values presented here can be used by resource managers and policy makers to demonstrate the economic might of birders, the value of birding – and by extension, the value of birds.” – Report 2011-1

When birders actually read the report, the first statistic they were confronted with was what seemed to be a gross overestimation of their community size: they estimated bird watchers to number 47 million in the U.S., which would be 20% of the national population! Here, I actually think the semantic difference is important: it has come up that “birdwatcher” and “birder” likely have, at least, different connotations if not different definitions. Birdwatcher is a dated term, and I think thus has the connotation at the very least that it indicates a less rigorous activity than the hobby of birding. Indeed, that’s what the survey seems to measure, though they use the terms interchangeably.

“The National Survey uses a conservative definition. To be counted as a birder, an individual must have either taken a trip one mile or more from home for the primary purpose of observing birds and/or closely observed or tried to identify birds around the home…Backyard birding or watching birds around the home is the most common form of bird-watching. Eighty-eight percent (41 million) of birders are backyard birders. The more active form of birding, taking trips away from home, is less common with 38 percent (18 million) of birders partaking.” – Erin Carver

In other words, people who watch their feeders with a bird guide make the cut, and this is strongly reflected in the original report (to which the addendum was made). They count almost 1/3rd of the U.S. population as wildlife watchers, the overwhelming majority being those that feed birds and/or other types of wildlife. Most people who call themselves birders would disagree that this definition is conservative; by contrast, this definition is the most liberal end possible. While it is indeed heartening that that many people care about birds, my communication with other birders has led us to an estimate closer to between 250,000-300,000 birders in the US.

The study used this data to extrapolate demographic information about what they call birding. Part of that was location, where they seem to favor raw numbers over participation: they say the average birder is southern, though the 1st southern state in participation ranking is 17th. They also made an attempt to measure what we’re traveling to see:

“Seventy-five percent of away-from-home birders reported observing waterfowl (ducks, geese, etc.), making those the most watched type of bird. Birds of prey (hawks, eagles, etc.) were also popular with 72 percent of birders watching them, followed in popularity by songbirds such as cardinals and robins (68 percent) and other water birds such as herons and shorebirds (60 percent).”

Going back to the original survey, and the suspected bias in targeting sportsmen, I found that 57% of hunters and 51% of anglers also put themselves in the wildlife watching category, making 29% of the wildlife watchers surveyed either hunters or fishers (or both). This helps explain the overwhelming representation of waterfowl-watching as the main target of birding. The accuracy of these representations ultimately bear on the conclusions at the end, namely the economic impact of birders.

I think this calls for a more specific survey effort to better quantify and define birders, and thus assess their impact, both current and potential. It may thus be best to take a tiered approach, from what birders would consider their community up to the levels addressed by the federal report. In other words, it would mean a “scaling up” from populating what birders would call birders, to everyone that feeds birds in their backyard and watches said feeders. I think identifying subgroups within this number would elucidate special interests, needs, concerns and ultimately economic potential.

Extracting NetCDF Values to a Shape File

Here’s a script that loops over climate NetCDF bricks in a folder and extracts the values for each layer in the brick of each file, in this case averaged over polygons in a shape file.

rm(list = ls())
library(raster)
library(rgdal)
library(ncdf4)
library(reshape2)
library(stringr)
library(data.table)
setwd("where your climate files are")
your_shapefile <- readOGR("path to your shapefile","the layer name for your shapefile")

climate <- rbindlist(lapply(list.files(pattern="nc"), function(climate_file)
{
#in my case, the weather variable is in the filename
climate_var = ifelse(grepl("pr",climate_file),"pr",ifelse(grepl("tmax",climate_file),"tmax","tmin"))
print(climate_var)
climate_variable <- brick(climate_file,varname=climate_var,stopIfNotEqualSpaced=FALSE)
#I needed to shift the x-axis to be on a -180 to 180 scale
extent(climate_variable)=c(xmin(climate_variable)-360, xmax(climate_variable)-360, ymin(climate_variable), ymax(climate_variable))
blocks <- spTransform(blocks,projection(climate_variable))
r.vals <- extract(climate_variable, blocks, fun=mean,na.rm=TRUE,df=TRUE,layer=1,nl=1680)
r.vals <- melt(r.vals, id.vars = c("ID"),variable.name = "date")
r.vals$climate <- climate_var
#depending on the filename convention of your files, get a variable for your climate model and name it "modelname"
r.vals$model <- modelname
climate_variables[[length(climate_variables)+1]] <- r.vals
}))

climate <- rbindlist(climate_variables)

At this point, you have a data frame called “climate” that has all your data long-form. You can cast this as you see appropriate depending on your needs!

Why Define What it is to Be a Birder?

I think the crux our pursuit in defining what it is to be a birder is that we’re looking to define criteria for membership of our tribe, which would be the group of people that “speaks the same language as us.” We recognize each other by our habits and field gear, and location. We can assume similar interests and motivations. There are many factors that may vary among birders, but the general idea remains, or at least insofar as I (and others) have taken a stab at defining it.

There are probably narrower definitions and thus “tribal affiliations” within this umbrella of birders. I think this is harder to define, because it varies among many factors, and is even perhaps evidenced in the small group birding friendships that are formed in a general area. For instance, how about the people I can find at a good birding spot, and they immediately know what I’m there for? Those are people with whom I feel the strongest birding connections, because it indicates a lot about how much we’re on the same page and interested in the same things. In that case, to me, it’s birder-specific, so then I find others who feel the same way to hang out with!

This isn’t meant to be an exclusionary statement or attitude, nor do I think I’m by any means limited to interacting with people that are like me in the birding world. I’m just trying to get at that shared sense of purpose and kinship, or “fellow traveler” feeling, that we get when we encounter others on the same path we’re on. I think that’s what many are trying to get at when we define what it is to be a birder, in part by looking in a mirror.