New paper out: Cattle grazing intensity and duration have varied effects on songbird nest survival in mixed-grass prairies

I'm a co-author on a new paper out in Rangeland Ecology and Management.  It's currently up online though it hasn't been assigned a volume/issue yet.  We looked at effects of different grazing regimes (differing duration stocking rates) in Grasslands National Park (Saskatchewan, Canada) and nearby areas on nest survival, and found few effects overall.  A few species had lowered nest survival in some years at low to moderate grazing intensities, such as Sprague's Pipit, Chestnut-collared Longspur, and Vesper Sparrow. Check it out!

Nestling Chestnut-collared Longspurs, near Brooks, Alberta, Canada.  14 June 2016.

Basic version control with Git and GitHub in RStudio in both Windows and Ubuntu

I don't remember why, but a few months ago I decided I finally had to try out this "version control" thing.  I love it SO MUCH.  Github and git can be a bit confusing initially, especially as I had the added layers of making it work with RStudio and on two different operating systems, but now that I've got it going it's great.

I started and installed git with this tutorial for starting with RStudio and git/github on Windows.  To understand how push and pull work (as this confused me), I read through several pages.  I started with this graphic of the workflow.  That one ignores RStudio and is just about git and github.  This essay has great illustrations and more details (code to use in the shell/terminal in RStudio).  Finally this one is github/git only (no RStudio) but I still found it helpful to read about push/pull/branching in yet another way.

Next problem was that when I opened up my project on Ubuntu, git said all lines in files were modified when I had not actually changed all lines.  This turned out to be an issue between line endings in Windows and linux type systems, and this would hide any actual changes if I had just made a few, so just committing every time was not a good option.  I decided to go with adding a gitattributes file in each repository (so all users will get the same line endings regardless of who I share with).  I added a gitattributes file (I combined general settings and the R settings available here) into the main project directory.  For a directory that I had already used a lot (so lots of files with the wrong line endings) I followed these steps for the per-repository settings, including opening a shell in RStudio to input their code for refreshing my repository.  (I backed up on a separate hard drive first in case I totally messed something up.)  At first this didn't work, because I have a dual-boot situation, not using the files in two separate computers, according to this top answer.  I ran the two lines of code in the top answer's update and that fixed it.
$ git config core.eol lf
$ git config core.autocrlf input

I now copy the custom attributes file into any new R repository I have, run those two lines, and haven't had any problems going between operating systems now.  Keep in mind this is where I have two different operating systems accessing the SAME FILES on the SAME drive/partition.  If I understand correctly the gitattributes file should work fine without the extra lines if you have different computers, but I have not yet tested this.

Finally, when I tried pushing in RStudio to github, I kept getting two errors:
error: unable to read askpass response from 'rpostback-askpass'
fatal: could not read Username for 'https://github.com': No such device or address

As I had already done the git config steps to add my github username and github email address, I looked up the error and found that I needed to create a private/public key pair because RStudio has issues authenticating apparently.  I followed the top answer's links, which resulted in my changing the url in the .config file and then generating and linking an SSH key.  I did this on both Ubuntu and Windows following the same instructions, resulting in two new key pairs (one for Ubuntu, one for Windows).

2016/11/04 edit: I got the askpass response error again in a new repository, but on the same computer that already had the SSH keys.  In this case I only changed the url in the .config file and then it worked swimmingly.  I've also had consistent success with line endings using the custom .gitattributes file followed by the two git config commands above.

Dual-boot Ubuntu 16.04 with Windows 7, then upgrading to Windows 10

I have a small Lenovo (ThinkPad X100e) running 32-bit Windows 7 Home edition.  I wantd to add dual-boot, then upgrade to Windows 10 to test that it won't erase my Ubuntu partition.

I first tried just running a bootable Ubuntu 16.04 LTS (long term stable) USB, and it got me into Ubuntu install, but when I got to the partitioning step the computer said okay, then shut down, and it never seemed to install.  I suspected I might need to partition first.  I pre-emptively went ahead on shrinking the Windows partition before repartitioning, following these steps as in my previous post just adjusting steps by looking in Windows 7 places for the settings.   System protection was already off and I skipped CHKDSK because Windows ran it on its own after my failed original Ubuntu automatic repartitioning attempts.  My computer also insisted on rebooting between steps 4 and 5.  Disk cleanup (step 5) took less than 20 minutes. Disk shrinking was maybe less than an hour.

I also realized during the Windows shrinking that I was trying to install 64-bit Ubuntu (the main file that downloads) onto a 32-bit computer.  I downloaded 32-bit from a mirror (there didn't seem to be an easy link on the main Ubuntu site, had to look around for it in their site) and made a new bootable USB.  I tried again.  At the partitioning step, I got a scary looking message about whether I wanted to continue with automatic partitioning (it said it will change and format some things).  I answered continue, and then I went on with set up.  That worked and I now have Ubuntu 16.04 LTS dual booting with Windows 7.

This went a lot faster than with my last dual-boot setup.  I think this was because I had Windows 7, an older laptop, and a bit more experience, and probably mostly because I cared less about whether I ruined my Windows set up. This older computer also didn't have weird boot settings that the newer one did (secure boot), nor did it have Windows 8 hibernation and fast shutdown/startup to worry about.  I also did not want to set up a shared data partition on this laptop so that did not take up any time.  So I did less prep, and it still turned out okay.  Your results may vary.

Now, the Windows 10 upgrade over the dual-boot system.  I ended up not having enough space on my Windows partition because I had some duplicate users and all their data.  I uninstalled a few large programs that I didn't use any more and then removed the two duplicate users and their data (be careful with this!  I was very sure I did not need those user profiles).  After following the various on-screen prompts, I eventually got a message that I had to log into my administrator account.  I did so, waited for the download again, and then the Windows 10 upgrade just... failed, every time, even though I was booting back into Windows 7 and not Ubuntu.  With the error code, I found that I should be rebooting into the system recovery partition.  I did that and sure enough, it worked!  The install crashed once because my laptop overheated, but that's my laptop's problem.  I set it on an air vent in the house and the AC kept it cool enough to restore Windows 7 (Windows did this on its own).  I then started the Windows 10 upgrade again and it finished the install.  I missed a few reboots and it booted into Ubuntu, but in those instances I just rebooted and watched to select the Windows system recovery partition and it resumed where it had left off.  Windows 10 did not erase my programs or apps, so I am pleased with how this went and might even try it on my main working computer now.

New paper out: "Shadow of a doubt"

I am very pleased to announce that my behavioral work on reproductive isolation in hybridizing titmice has been accepted in Behavioral Ecology and Sociobiology and is now out as an online early!  It was the main experimental work from my Ph.D. dissertation and is co-authored with my Ph.D. advisor Michael Patten.

Using R to work through Sokal and Rohlf's Biometry: Chapter 4 (Descriptive Statistics), exercises

Previously in this series: Chapter 4 (sections 4.6-4.9 in Sokal and Rohlf's Biometry).

I sure fell off the Sokal and Rohlf horse.  Time to get back on track!  Let's finish up Chapter 4.  From this point onwards, I will do only the exercises that add to the code base I've written for the rest of the chapter.  In this case there is just one.

Exercises 4 (selected)

#Exercise 4.3
#Use the data to get mean, standard deviation, and coefficient of variation,
#then repeat using groupings.
e2.7<-c(4.32, 4.25, 4.82, 4.17, 4.24, 4.28, 3.91, 3.97, 4.29, 4.03, 4.71, 4.20,
        4.00, 4.42, 3.96, 4.51, 3.96, 4.09, 3.66, 3.86, 4.48, 4.15, 4.10, 4.36,
        3.89, 4.29, 4.38, 4.18, 4.02, 4.27, 4.16, 4.24, 3.74, 4.38, 3.77, 4.05,
        4.42, 4.49, 4.40, 4.05, 4.20, 4.05, 4.06, 3.56, 3.87, 3.97, 4.08, 3.94,
        4.10, 4.32, 3.66, 3.89, 4.00, 4.67, 4.70, 4.58, 4.33, 4.11, 3.97, 3.99,
        3.81, 4.24, 3.97, 4.17, 4.33, 5.00, 4.20, 3.82, 4.16, 4.60, 4.41, 3.70,
        3.88, 4.38, 4.31, 4.33, 4.81, 3.72, 3.70, 4.06, 4.23, 3.99, 3.83, 3.89,
        4.67, 4.00, 4.24, 4.07, 3.74, 4.46, 4.30, 3.58, 3.93, 4.88, 4.20, 4.28,
        3.89, 3.98, 4.60, 3.86, 4.38, 4.58, 4.14, 4.66, 3.97, 4.22, 3.47, 3.92,
        4.91, 3.95, 4.38, 4.12, 4.52, 4.35, 3.91, 4.10, 4.09, 4.09, 4.34, 4.09)

#a. without groupings
(e2.7.mean<-mean(e2.7))
(e2.7.sd<-sd(e2.7))
(cv.e2.7<-(e2.7.sd*100/e2.7.mean))

#b. with groupings.
#To create groupings, we use hist() but with plot=FALSE, which we did not use before.
(e2.7.hist<-hist(e2.7,
                 breaks=seq(min(e2.7),
                            max(e2.7),
                            length.out=11), #use 11 to get 10 groups (number of groups you want + 1)
                            #R will chose binning automatically if you do not use the breaks argument.
                 plot=FALSE))
#It comes out as a list so we need the midpoints (or "class marks" in the books' terminology)
#and the counts as a data frame.
#We also multiply the two to get class sums as in section 4.1 (and box 4.2)
(e2.7.grouped<-data.frame("frequencies"=e2.7.hist[[2]],
                         "classmark"=e2.7.hist[[4]],
                          "classsums"=e2.7.hist[[2]]*e2.7.hist[[4]]))

(e2.7.samplesize<-sum(e2.7.grouped$frequencies))
(e.2.7.summing<-sum(e2.7.grouped$classmark*e2.7.grouped$frequencies))
(mean.moo<-e.2.7.summing/e2.7.samplesize)

#These numbers are the same as before because I didn't code the class marks.
#You can see how to do that in the previous post.
#In the modern computing age we are unlikely to group the data to get averages,
#but you can see where it would be useful if you are given data in that format,
#or want to calculate by hand.

Winter: the sequel

The snow keeps melting and then coming back.  Seven Sisters Falls, Manitoba.  20 March 2016.

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.