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.

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.