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I thought I'd write a bit about bat houses, and I'll start with my own. As you can see below, it's showing some wear and tear from the weather. It's been up over seven years now, and stood through several hurricanes.

Of course, it looks better at night. (And as a photographer, grainy black and white is my true medium.)


Before I built it, I searched around a lot on the 'Net, incorporated some best practices I found there, and threw in a few twists of my own. Since I've put it up some of the advice about bat houses has improved, and I've come to realize that some of the design decisions I made might be wrong. But the good news is that it doesn't seem to bother the bats, so that means if you're even close on the design of your bat house, you are likely still to get residents.

Things I did right:

I built it strong and weathertight. I've since had to re-caulk a few seams, but in general, I used solid pine for the exterior, and thin plywood for the interior petitions. I sealed all the seams between the boards and I think that my domed aluminum roof sheds water pretty well. Bats don't like leaky abodes, and if you look at some of the big box store, pre-made houses, they're made of loose fitting boards, sometimes with openings for rain and daylight to come through. My house isn't pretty, but it doesn't leak and it is really dark inside.

I spaced the interior petitions the recommended 3/4 inch apart. From what I continue to read, this is a crucial feature. The size of the openings is a big part of making a structure attractive to a bat population. Since the most likely denizens of your house are Brazilian Free-Tailed bats, it's a good idea to follow the dimensions they seem to prefer. Wider openings might attract a different species of bat, but unless you're building a house that is large enough for you to experiment with different spacings, 3/4 inch is you best bet.

I covered the inside of the box and the partitions with a material that give little bat claws some traction -- nylon window screen, and I added a landing area at the bottom of the opening, using plastic gutter guard. You can see how bats have actually worn the screen in places going in and out.

I built the largest box I thought I could support without excessive weight and visibility. Most garden-store variety bat houses are smaller than recommended. Bats like dwelling in groups, and I've had up to seventy bats in my house from time to time. Larger houses hold more bats.

I mounted the bat house on predator-resistant poles, as high and as clear of obstructions as practical. Folks want to put their bat houses on tree trunks, but from what I read the experience with getting tree-mounted houses populated is mixed, at best. This may be because trees shade the bat house and reduce the internal temperature below what the bats prefer. My theory is that trees don't appear to bats as sufficiently predator resistant -- perhaps this is excessively anthropomorphic, but I think bats somehow sense that trees provide a viable climbing stand for snakes, opossums, and other threats. Slick metal poles pose much more of a barrier to potential enemies.

I was patient. It took a couple of years for bats to inhabit my house. I'm not really sure how long because I had grown accustomed to just ignoring the bat house on the assumption that it was empty. My daughter discovered that its inhabitants quite by accident one afternoon when she heard noises from the bats while hanging up laundry.

Things I could have done better:

I probably should have painted the house a dark color. I just couldn't believe that bats wouldn't find a dark colored, enclosed wooden box too hot in the Florida summer sun. Now, as I read more recent material on the 'Net, it seems like folks are learning that bats like their house really, really warm. Still, it works even at its current dirty white color. But paint or stain yours brown anyway.

I used insulation inside the house. This was definitely my own idea, or at least I don't recall anyone suggesting it. I placed the thin, aluminum coated mylar insulation (like that used for automotive window shades) around some of the partitions in the bat house. You can see it in this interior shot of the bats inside. I thought that this might help stabilize the temperature, keeping it a bit cooler in the daytime and a bit warmer at night. For the next house I build, I think I will make one chamber insulated still, but leave the others uninsulated. I don't know exactly how bats move in the bat house during the day, but I have read that they seek out a variety of temperature zones, depending on the weather and the time of day. Insulating some of the house, but leaving the others more subject to temperature fluctuations might actually prove attractive to the bats. In smaller houses, I'd just dispense with the insulation entirely.

Although I added some instrumentation to the house, I did not exercise enough care so that the instrumentation would still be working when the bats actually moved in. I put a camera in the roof of the house (one reason the roof is domed), but since the window covering it eventually fogged to such an extent that the focus is shot. For the next house, I'm going to make the camera, along with any other instruments, replaceable from outside without disturbing the bats.

I added a temperature sensor and while this was a good idea, it failed not too long after installation. Temperature is known as an important correlate of bat activity, so if you only placed a single instrument in a bat house, a temperature gauge of some sort is probably the best choice. I used solid-state, analog temperature sensor. Now I would use a digital temperature sensor, and I'd make it replaceable from the outside of the box.

I probably should have mounted the house higher. Mine's at about fifteen feet as measured from the point where the poles leave the ground to the top of the house. I arrived at this altitude by mounting two ten-foot chain link fence poles, each standing on a four-foot section of 2x4. This is a convenient height from a construction standpoint and it has the (to me) desirable side-effect of leaving the house just below my rooftop, rendering it invisible from the front of the house.

Looking from my rooftop, my bat house looks like this, about even with my roofline.


But this shot of the bat house at Lake Lotus park in Altamonte Springs shows how high you really might want to mount your house:

Over the years, more obstructions have grown up around my bat house. Tree limbs now approach from one side, and the neighbor's bushes are crowding in. Still, the bats deftly avoid these and other man-made obstacles, such as camera stands and the like. But to start out, you should probably place your bat house in as clear a spot as possible.

So I think the bottom line is this -- follow the best practices for bat house construction contained in the links below, but don't despair if you can't get everything perfect. Given time, bats likely will come to live in your yard, even if their house is too light, too short and too crowded.

Why Bat Houses Fail -- mistakes to avoid
Criteria for buying and building bat houses
List of bat house plans and guides

Visitor

Ducking in and out of the back door the other night, I was surprised to see something small and dark moving by the outside door frame. Probably a frog, I thought. We get lots of them on the glass sliding door during rainy summers like this one.

Then I shined the flashlight and looked more closely - yikes a bat! Now in all the years I've had the bat house in my backyard, I've never come face-to-face with a live bat. Never. And yet here was a quiet, but very much live, bat clinging to the rough wood of the door frame. What to do -- my own usual advice flashed through my head -- never handle a sick or injured animal. But this one didn't look sick or injured, in fact he or she was industriously climbing up the outside door frame to get away from the light.

Another possibility that dawned on me was this; the back door is covered with an overgrown trellis, a knot of vines that extends from the eves, out over the picnic table and down to the ground. Maybe this little guy had flown up under the trellis and just gotten trapped. Bats can't take flight from the ground, after all. They rely on dropping down a bit from a height to gain airspeed before flapping off. But there was no way that this individual could do that from where he or she was clinging. Even if the bat made it to the top of the door frame, the vines and the trellis blocked any reasonable launch trajectory.

So I ran around to the front door, and got my son, something of a animal wrangler himself, and my daughter to hold the flashlight. Together, and wearing my heaviest neoprene-impregnated work gloves, I managed to trap the bat (who remained superficially calm) under a plastic flower pot. Sliding a plastic plate underneath between the pot and the door frame, we succeeded in removing the bat from the door, hopefully with little trauma. Spotlighted by the flashlight, I climbed a ladder to the roof and gently placed the bat on near the edge. When I checked five minutes later he or she was gone, so I'm hoping the outcome was positive.

From the picture, it's pretty clear our friend is a free-tailed bat, probably a Brazilian Free-Tailed bat. Another clue was the distinctive musky odor emanating from the bat. I often get a whiff of the same scent near the bat house. Not obnoxious really, and definitely not fecal, just "pungent" for lack of a better term. The cats smelled it too, I'm sure since they were actively prowling just inside the glass door.

So what should you do if you encounter a bat? Well, if the individual is in a dwelling, then you may have to intervene. The flower pot (or bowl) and plate technique will work well indoors. Insectivore bats, like almost all bats in Florida, have very small teeth (bugs are crunchy, no incisors needed) so a pair of heavy gloves provides pretty good protection in the unlikely event that the bat actually takes a nip. Bat Conservation International has a great video showing how to humanely and safely capture and remove a bat from your dwelling.

Outdoors, I'd recommend leaving found bats alone. Most sick or injured bats aren't rabid, but there is little point in taking chances. (This advice applies to foxes, racoons, skunks and loose pets as well). For more information about bats and rabies, please see this (pdf)

Activity in the bat house seems to be picking up again, and I'm hoping that I avoid anymore close encounters.

They're Back -- or they never left?

One reason I haven't posted as often as I would like here is that I was feeling a bit depressed since it seemed that all or almost all the bats had rather suddenly left the bat house in July. The number of bat transitions -- bats passing in or out of the bat house opening -- had plummeted.

In June, I logged an average of 64 transitions per night, with at least a few detected every night. But in July, the number dropped to 38, and there were long runs of zero or very few ins and outs. Strange. By early this month, things were very quiet around the backyard.

The amount of bat guano collecting on a board positioned below the bat house also dropped, and I no longer heard lots of shrieks and screeches every time I walked under the house. I began to consider why the bat house might become unattractive to bats. True, it is getting old, having been up some seven years and several hurricanes. I hypothesized that perhaps leaks had formed in between the boards, aggravated by the especially rainy summer we're having. I had caulked the seams last summer, but maybe the house needed another going over. I was smelling the distinctive odor of free-tailed bats less as well. Something seemed to have changed.

I actually stopped logging nightly bat transitions for a while, since nothing seemed to happen on the counter.

But tonight I turned on the audio feed from the bat detector, and just at dark, I was surprised to hear a burst of bat echolocation calls. I sprinted out of my workshop and sat down in a lawn chair near the bat house to watch. Over the next twenty minutes, I counted 17 bats emerging. Now it may just be my excitement from seeing that not all the bats had left, but it seemed to me that these bats were a bit larger than the ones I usually saw emerging. Maybe another species had moved in?

Maybe I'll poke the video camera back inside the bat house soon and just take a look around. Meanwhile, welcome back.

Graphs and Automation

Software

Making graphs is a lot of work, even if the subject is bats (and their songs). And while automated systems, like the bat logger, are a great boon in the unattended collection of information, they can pump out data at an alarming rate.

Here's some quick arithmetic:

Hours (8:00 PM – 6:00 AM) - 10

Samples per hour (6 samples every 10 seconds) - 360

Total - 3600

So I can draw a graph like this every day:

But how? Excel can make really pretty graphs, but that's a lot of work. Here's what always happens to me – 2 minutes to make the graph, 15 minutes to make it pretty. In other words, it takes longer to remove lines, edit the legend, choose colors, fix the axes, and so on, by far, than it does to whip out a basic graph in the first place. Fifteen minutes per day, every day is not all that attractive.

The solution to an automated data deluge is automatic graphing, or at least scripted graphing. And Excel doesn't lend itself to easy scripting. But gnuplot does. Here's a link with some examples:

http://nucl.sci.hokudai.ac.jp/~ohnishi/Lib/gnuplot.html

As you can see from the link above, gnuplot will draw a wide variety of graphs from text files, all neatly scriptable with program code. I had to add a bit of external awk scripting to filter the data logger output stream, but the bulk of the work is done by gnuplot. Yes, it took a while to set up and debug, but it saves a ton of time over trying to generate the same graph every day with Excel.

Here's how it works: The bat logger writes the data it collects in ASCII text, comma-delimited files. These land on a USB stick plugged into the logger and I just unplug it one day during the week (when the logger like the bats, is sleeping) and transfer the data to my laptop.

Here's a sample:

2,02/25/2009 - 18:32:00,2
2,02/25/2009 - 18:32:02,2
1,02/25/2009 - 18:32:04,5
2,02/25/2009 - 18:32:04,2
3,02/25/2009 - 18:32:06,7465
4,02/25/2009 - 18:32:06,9221
5,02/25/2009 - 18:32:06,7007
6,02/25/2009 - 18:32:06,0
2,02/25/2009 - 18:32:06,2
1,02/25/2009 - 18:32:08,10
2,02/25/2009 - 18:32:08,2
1,02/25/2009 - 18:32:10,40
2,02/25/2009 - 18:32:10,2
1,02/25/2009 - 18:32:12,15

The first column, that is the number before the first comma, is the channel number. I've numbered the channels like this:

#define BAT_ECHO_COUNT_CHANNEL 1
#define WIND_COUNT_CHANNEL 2
#define TEMP_CHANNEL1 3
#define LIGHT_CHANNEL 4
#define BATTERY_CHANNEL 5
#define RAIN_SENSOR_CHANNEL 6

So the very first two rows shown are from channel 2, and represents the a count of anemometer cup rotations, which in turn is a measure of wind speed. (The idea is to collect some data to see if high winds really do deter bat activity, as some have quite logically suggested.)

The next row starts with a 1, so it's a count of bat echolocation clicks from the bat detector. Basically each pulse that makes up a bat echolocation call gets counted this way. Given that each bat call is composed of tens of clicks, this count mounts up rapidly.

Channel 3 (the fifth row) shows a raw temperature value. I keep meaning to calibrate the sensor, but right now all I'm collecting is a count from the logger's Analog to Digital Converter (ADC). It could range from 0 to 4096.

Channel 4 is a measure of daylight from a photoresistor. The bat logger software uses this to decide when to sleep, and when to wake up and collect data.

Channel 5 shows the battery voltage, again uncalibrated.

Finally, Channel 6 is a rain sensor from an irrigation system. It is ON, (greater than zero) when it gets wet, and OFF otherwise. The data above show that it was a dry night on Febrary 25th, at least around 6:30 PM.

The first task for my script is to split the raw data file into separate files, one per channel. Using a bash shell either on Linux or on Windows under Cygwin (http://www.cygwin.com), this is really just a grep. (Non-Unix weenies can tune out now).

egrep "^1," $1.DAT >$1_1.tmp
awk -f ./bin/filter_bad_dates2.awk $1_1.tmp >$1_1.DAT
egrep "^2," $1.DAT >$1_2.tmp
awk -f ./bin/filter_bad_dates2.awk $1_2.tmp >$1_2.DAT
egrep "^3," $1.DAT >$1_3.tmp
awk -f ./bin/filter_bad_dates2.awk $1_3.tmp >$1_3.DAT
…
awk -f ./bin/filter_bad_dates2.awk $1_6.tmp >$1_6.DAT
#awk -f combine_echos.awk $1_1.DAT >$1_1a.DAT

The egrep command (http://unixhelp.ed.ac.uk/CGI/man-cgi?grep) looks for lines starting with the digit 1, and siphons them off into a file named ending in .tmp. So when this script is run on the data from February 25th, 2009 the input file name is 20090225.DAT and the samples for channel 1 will end up in 20090225_1.tmp. Samples from channel 2 will end up 20090225_2.tmp and so on.

The awk command (http://www.hcs.harvard.edu/~dholland/computers/awk.html) that follows performs a bit of data cleanup on the dates. More on that in a latter post about the bat logger. For now, just know that I sometimes get some zero dates that need removal to avoid messing up the time scale for the graphs.

To graph a single channel of data, each file is complete. Just script gnuplot, point it to the .tmp file and run. But to graph multiple channels on the same graph, so as to show, say temperature and wind versus echolocation calls, I need to put the relevant files back together again. Gnuplot expects each data series to be grouped together in a single input file, so concatenating the individual channel files back together provides the needed input. Each data series is separated in gnuplot's input file by two blank lines. Hence this odd-looking code:

echo >>$1_1.DAT
echo >>$1_1.DAT
echo >>$1_2.DAT
echo >>$1_2.DAT
…
echo >>$1_5.DAT
echo >>$1_5.DAT

This just appends two newline characters to each channel file.

cat $1_1.DAT $1_2.DAT $1_3.DAT $1_4.DAT $1_5.DAT $1_6.DAT >$1_all.DAT

The result of this command is a single output file that consists of 20090225_1.tmp with 20090225_2.tmp, 20090225_3.tmp and so forth appended. This is the data file for gnuplot.

gnuplot -background black gnuplot_20090225.plt

At long last we're ready to run the gnuplot script. Here it is:

# Draw bat graphs
set terminal png x000000 xFFFFFF x404040 xffa500 x66cdaa x9500d3
set output './plot/20090225_plot.png'
set datafile separator ","
set xdata time
# Use this format for the data as spat out by the logger, with the hyphen
# between the date and the time.
set timefmt "%m/%d/%Y - %H:%M:%S"
set title "Bat echolocation calls, Temperature and Wind Gusts, beginning 20090225"
#set xtics 1000000
#set ytics 0, 100
#set y2tics 0, 100
set ylabel "Calls"
set y2label "Temp"
unset key
set format x "%H"
set yrange [0:1000]
set y2range [2000:4000]
plot '20090225_all.DAT' index 0 using 2:3 smooth frequency axis x1y1, \
'20090225_all.DAT' index 2 using 2:( 10240 - $3 ) smooth frequency axis x1y2, \
'20090225_all.DAT' index 1 using 2:($3 * 100 ) axis x1y1 ;

Now it took me quite a while, and a lot of peeks at the web to set this up, but the beauty of the system is that I can produce today's graph with a single bash command. Notice that the output terminal is set to “png” in the second line, so gnuplot draws the graph in 20090225_plot.png.

The result is a graph like this:


The main things I learned from this whole exercise were:

1.Script everything or drown in data from your automation.

2.Clean the data, and remove errors and outliers, before they mess up your graphs and analysis.

3.The simplest tools are the best. It's amazing what you can do in a shell script and with awk.

4.Create output files in ascii and use simple delimited formats. Yes it takes up a bit more space than some obtuse binary format, but it facilitates using simple tools and makes the observations easy to view, sanity-check and edit.


I'll post more information about the bat logger in the future.

Open-Source Bats

Bat calls, "songs" to keep to the theme of this blog, are hardly inarticulate shrieks. In fact, bat echolocation calls are finely honed sonar pulses and have a complex and time-varying structure. The audio and rather low-resolution spectrograms in my earlier postings should hint at that.

There's a fair amount of interesting scientific research out focusing on bat echolocation, in a much more systematic and detailed way. I was delighted to find not only the article below, but an entire on-line journal whose content is completely free, readily accessible, and freely redistributable.

For example, the graphic at the top of this post, which shows the frequency composition of several individual bat calls, comes from The Voice of Bats: How Greater Mouse-eared Bats Recognize Individuals Based on Their Echolocation Calls.

The authors here show that in addition to all the sonar ranging information encoded in bat calls, there are also individual differences and these differences are recognizable to other bats. They say:

Animals must recognize each other in order to engage in social behaviour. Vocal communication signals could be helpful for recognizing individuals, especially in nocturnal organisms such as bats. Echolocating bats continuously emit special vocalizations, known as echolocation calls, and perceive their surroundings by analyzing the returning echoes. In this work we show that bats can use these vocalizations for the recognition of individuals, despite the fact that their main function is not communication.

Yovel Y, Melcon ML, Franz MO, Denzinger A, Schnitzler H-U, 2009 The Voice of Bats: How Greater Mouse-eared Bats Recognize Individuals Based on Their Echolocation Calls. PLoS Comput Biol 5(6): e1000400. doi:10.1371/journal.pcbi.1000400

Now the abilities of at least some bats to recognize one another's songs is an interesting finding in itself, but what I really like about this article is the philosophy of open research enabled by the journal in which it appears. The articles in the Public Library of Science Journal Computational Biology are freely available under a Creative Commons License. You can download them, read them, comment on them, and upload them to your own site, as long as you accurately attribute them.

I don't know if you've ever had the misfortune to try to download an article from some of the more Intellectual Property-obsessed scientific publishers, but it can be a real hassle. I recall one attempt to buy an article on Organizational Psychology from a well-known publishing house. My wife was in a red-hot hurry for this article in preparation for a job interview the next day.

Not only was the e-commerce part of the web site needlessly complex and cryptic, but when the article for which I paid $35 never arrived as promised by e-mail, we began a saga of phone calls and e-mails that spanned two continents. Turns out that the reason they didn't answer the number provided for technical problems during what seemed normal business hours here in EST was that the number rang in the UK.

Someone from the UK eventually returned the call a few days later, and ultimately my card was credited for the purchase price. It seems that once again, one publishing house had acquired another, and the integration wasn't going smoothly (surprise, surprise). By the time all this was complete, we could easily have gone to the college library and photocopied the article, and for about $33 less, too.

We never got the article. Congratulations old-line publishing house, your intellectual property is safe -- so safe that even those folks who might, out of desperation, pay your inflated prices can't get it.

PLoS is a pleasant change of pace. I think folks like this, along with the legions of scientists who understand that science benefits when information is shared, and not when it is hoarded, will gradually drag the old-line publishers into the post-copyright age, but if my experience is any guide, it may be painful and slow.

In the meantime, let's celebrate the availability of open-source research to complement our open-source software.

Now which bat was that I just heard -- I could almost make out little Vlad's call...

Mortality

Looks as if my explanation the other day for the high level of daytime excitement by the bats was both too pat and too optimistic.

It turns out that the individual whom I could see so clearly on the landing area of the bat house was not so much protective as in need of protection -- this bat was injured and subsequently died.

Looking up the next morning, I saw this:
Not good. I carefully removed the poor thing's body from the landing area (with a stick and gloves) and took a couple of pictures before burial.

Here's one closeup (color-enhanced):

We're looking at the deceased bat's back. The folded wings end at the top with a claw (a vestigial thumb?) used for climbing around in the bat house, and you can clearly see a foot with tiny claws at the bottom of the picture. This unfortunate individual is about four inches long.

I'm sure that there is substantial mortality among bats, like any wild species, but in the three years or so that I've been paying attention to the bats in my bat house, I had never actually seen a sick or injured bat. And since White Nose Syndrome is killing many bats in the Northeast, I was really concerned about what might have caused this bat to die.

Fortunately, the expert folks at the Florida Bat Conservancy were kind enough to look at my pictures and answer my concerned e-mail. Assistant Director Jennifer Smith writes, in part:

As of now you shouldn't be concerned. From the picture it looked like the bat had a broken wing and couldn't fly out each night to forage for insects. The bat's wing bones are very fragile and can break easily. Due to the bat's high metabolism, it doesn't take long for a bat to starve to death. The wound site might have been infected as well. ...

White Nose Syndrome hasn't spread this far south. It started off in New England and has spread farther down through Pennsylvania and West Virginia. So far it's affecting the cave dwelling bats and scientists are still trying to figure what is actually causing it. They are starting to link it to pesticide use on agricultural lands. We hope that it never reaches us!

I was relieved. Jennifer's observation about the broken wing fit with what I had observed the day before the bat perished, when he or she was carrying on in daylight outside the bat house. The bat I saw that day was flexing one wing while vocalizing, and now it seems that may have been because the other wing was injured. Sad, but not as sad as if we had a virulent bat disease like White Nose Syndrome to worry about -- yet.

So far, all the remaining bats (about 25 as of my last visual count) seem fine.