Lichen adventure

A fallen jack pine cone and twig in some neat lichen which might be Cladonia.  20 March 2016, east of Winnipeg, west of Elma, Manitoba.

Latitude

Sweet, sweet warmth and growing plants.  03 March 2016, Stillwater, Oklahoma.

Admittedly there IS a live plant in there, but it's not really doing much yet as the winter snow attempts to melt off.  08 March 2016, Winnipeg, Manitoba.

Worms or cigarette butts: all the same to a bird

Google translate tells me that the text reads "I refrain from smoking because cigarette butt or worms, it's all the same for a bird".  An excellent point with an excellent illustration.  Maison de la nature (nature center?), Lattes, near Montpellier, France, 05 August 2015. 

Back to the past

Both from last summer and waaaay back.  Here are a few more pictures from France this summer, at the Temple de Diane, which seems to have no actual relation to the goddess Diana.

Le Temple de Diane, Les Jardins de la Fontaine, Nîmes, southern France, 29 July 2015. 

There seems to be a problem with people climbing the monument.  Temple de Diane, Les Jardins de la Fontaine, Nîmes, southern France, 29 July 2015. 

Entering the temple!  Temple de Diane, Les Jardins de la Fontaine, Nîmes, southern France, 29 July 2015.

This rat graffiti from 1738 might have been my favorite thing about the temple.  Temple de Diane, Les Jardins de la Fontaine, Nîmes, southern France, 29 July 2015.

Pigeons everywhere in their native lands!  Temple de Diane, Les Jardins de la Fontaine, Nîmes, southern France, 29 July 2015.

Nesting pigeons in the high arches.  Temple de Diane, Les Jardins de la Fontaine, Nîmes, southern France, 29 July 2015.

Looking out at ground level. That shading thing is for tables at an adjacent cafe where we ate lunch afterwards.  Temple de Diane, Les Jardins de la Fontaine, Nîmes, southern France, 29 July 2015.

In the gardens around the temple I found some critters.  This appears to be some sort of hairstreak (Lycaenidae), but I haven't actually looked up what species it might be yet.  Temple de Diane, Les Jardins de la Fontaine, Nîmes, southern France, 29 July 2015.

A shy new lizard friend.  Temple de Diane, Les Jardins de la Fontaine, Nîmes, southern France, 29 July 2015.

You can walk around the side gardens (where I found the lizard and butterfly) and see neat views of the top of the temple.  Temple de Diane, Les Jardins de la Fontaine, Nîmes, southern France, 29 July 2015.

Adventures in compiling bgc for Bayesian estimation of genomic clines

Now that I have Ubuntu, installed the required libraries, and downloaded the program source code, I can install bgc.  It took me a lot of following error messages and looking for files, so please go to the end to see my final commands to get it compiled.  Even then, do not use my commands exactly.  This post is more to show you how the compilation process went and where things went wrong.  (Everywhere, that's where; mainly due to my inexperience.)

After reading the instruction manual for bgc, I ran this in the terminal:

/usr/local/src/bgcdist$ h5c++ -Wall -O2 -L/usr/include/gsl/lib -I/usr/local/gsl-1.15/include -o bgc

I got an error message:
The program 'h5c++' is currently not installed. You can install it by typing:
sudo apt-get install hdf5-helpers

So I did.

Note that I changed the directory for where to find GSL (highlighted) because I couldn't find it in usr/local.   Eventually I gave up looking for it and uninstalled GSL, then downloaded it to install from source where I specified the directory using ./configure --prefix=/usr/local .  (Spoiler alert: I mistyped this as "user/local" when I downloaded from source and this caused most of my problems later on.  I believe I should have used the Ubuntu software center to resintall it and make sure I had all the GSL libraries I needed because when I reinstalled GSL at the very end, it worked fine from the software center.)

**********************************************************************

 Done. The new package has been installed and saved to

 /usr/local/src/gsl-1.16/gsl_1.16-1_amd64.deb

 You can remove it from your system anytime using:

      dpkg -r gsl

**********************************************************************

It still went into src.  Hmm.

h5c++ -Wall -O2 -o bgc bgc_main.C bgc_func_readdata.C bgc_func_initialize.C bgc_func_mcmc.C bgc_func_write.C bgc_func_linkage.C bgc_func_ngs.C bgc_func_hdf5.C mvrandist.c -lgsl -lgslcblas

Be careful pasting from the manual, as in my terminal the underscores disappeared and then it couldn't find the files.

This gave me different errors, where it couldn't find GSL and compilation terminated.

h5c++ -Wall -O2 -L/usr/local/src/gsl-1.16 -I/usr/local/src/gsl-1.16 -o bgc bgc_main.C bgc_func_readdata.C bgc_func_initialize.C bgc_func_mcmc.C bgc_func_write.C bgc_func_linkage.C bgc_func_ngs.C bgc_func_hdf5.C mvrandist.c -lgsl -lgslcbla

This changed the missing files from those from gsl to one called hdf5.h.

h5c++ -Wall -O2 -L/usr/local/src/gsl-1.16 -I/usr/local/src/gsl-1.16 -prefix=/usr/local/src/hdf5-1.8.15-patch1/hdf5 -o bgc bgc_main.C bgc_func_readdata.C bgc_func_initialize.C bgc_func_mcmc.C bgc_func_write.C bgc_func_linkage.C bgc_func_ngs.C bgc_func_hdf5.C mvrandist.c -lgsl -lgslcbla

Nope.

Uninstalled hdf5.  Then I found a recommendation to install an hdf5 cpp.  Nope, still didn't work.  (The observant or more experienced reader may note that I keep changing that last green-highlighted portion of the commands to have an s at the end or not.  You will see below that this was of course a problem too.)

**********************************************************************
Finally, I was told that I had the prefixes wrongly specified (prefix just means it should be L or I, not actually saying prefix) and I had accidentally installed GSL into "user" instead of "usr" (the standard folder name).  So this code below works because I needed to replace prefix with -I/, installed hdf5-dev and hdf5-serial-dev to get some of the files when they weren't found, and pointed the compiler to the wayward GSL files in the weird directory.  I also sometimes forgot the s at the end of the green-highlighted command in previous attempts.
h5c++ -Wall -O2 -L/user/local/lib -L/usr/local/src/hdf5-1.8.15-patch1/hdf5/lib/ -I/usr/local/src/gsl-1.16 -I/usr/local/src/hdf5-1.8.15-patch1/hdf5/include/ -o bgc bgc_main.C bgc_func_readdata.C bgc_func_initialize.C bgc_func_mcmc.C bgc_func_write.C bgc_func_linkage.C bgc_func_ngs.C bgc_func_hdf5.C mvrandist.c -lgsl -lgslcblas

As with most things, essentially the installation process is following the error messages.  If the compiler can't find a file, make sure the compile commands point to the correct directories (search for where the file is located), or go install the package/library or a related thing (like the -dev versions of hdf5) if it can't find it because it doesn't exist yet.  Finally, when I went to run the compiled bgc, it turned out that the bgc program still couldn't find GSL in the misnamed "user" folder anyway.  I uninstalled GSL (using the Ubuntu software center), reinstalled it, and bgc started then.

UPDATE 2016/07/14: This is much easier if you don't fill your commands with typos and install the required packages in the correct places.  I upgraded to Ubuntu 16.04 LTS and it apparently removed GSL, so bgc no longer ran.  I reinstalled gsl and the gsl development versions from the command line this time using 'sudo apt-get install gsl-bin libgsl-dev'.  That presumably put them in the right place this time.  I then navigated to the bgcdist folder where the files were stored, and ran the exact compiling command from the user manual/documentation.  I was dreading a multi-hour fiasco again and it just worked.  I think the moral of the story here is that this is a lot easier if you have installed packages a few times in Ubuntu by the time you attempt this, but it is doable even if you are brand new.

Recent snow-birding

Milkweed pods in the snow along a snowmobile trail just off Hwy 15 between Elma and Vivian, Manitoba.   We saw lots of birds: Northern Hawk-Owl, Spruce Grouse, Pine Grosbeak, Gray Jay, and Common Redpoll!  31 January 2016.

New paper: anthropogenic noise affects detectability in grassland bird surveys mainly via errors in distance estimates

My post-doc mentor, Dr. Nicola Koper, has recently published a new (open access) paper on the effects of ambient noise on detectability in grassland birds in Ecology and Evolution (I am a co-author on this paper) on whether bird survey results might be affected by anthropogenic noise.  The main message is that species are still detectable, but noise can affect observers' ability to estimate distances to unseen vocalizing birds.