Friday Links (1/27/2017)

This Friday, it’s mainly book suggestions. It’s like Oprah’s Book Club- except I’m running it. It’s Treat Yo Self 2017 and you deserve some great science books.

Disease related news

Macroecology, the study of statistical relationships explaining species, abundance, and trait distributions at a broad scale, can be crucial in understanding the drivers of infectious disease ecology. Authored by some of the most influential academics in the infectious disease world (The macroecology of infectious diseases: a new perspective on global-scale drivers of pathogen distributions and impacts by Stephens et al. 2016)

Barbara Han is a visiting speaker next week, so here is a paper by her (side note: she was a coauthor on an article above). So one of her well known paper is about analyzing existing data on mammalian host species to discuss their zoonotic potential. She provides great insight into the future of disease surveillance (Global Patterns of Zoonotic Disease in Mammals by Hans et al. 2016)
C.difficile infection is a serious issue in hospitals, and a new study indicates that restricting antibiotic usage and not hospital infection control lead to the decline of C.difficile in England. (Effects of control interventions on Clostridium difficile infection in England: an observational study by Dingle et al. 2017)

Rstats/Data Visualization

The Genetic Map Comparator, a user friendly bioinformatics application (Shiny) to display and compare genetic maps. (Useful for: Bioinformatics students)

R for beginners: basic graphics code to produce informative graphs, everyone can code in R. Here is a tutorial for creating a 3D scatterplot. I suggest following the blog as it has a lot of tutorials (Useful for: Just starting out R)

The Annual Rstudio Conference happened last week and here are some tips and tricks written by some of the attendees.(Useful for: Anyone interested in seeing what new things are happening in the R world)

Visual Resume {VisualResume}, a new R package (and Shiny App) for creating a really great looking resume. From meth-making chemistry teachers to new PhD holders, this might be great for a personal website.

Science Arts/Science Communication

Jen Burgess is a science illustrator that I have been following on Twitter. She collaborates with researchers all over the world to draw some very beautiful artworks. I can’t praise her work enough so I’ll let her art do the talking. Follow her on Twitter as well!

What can the anti-vaccination movement teach us about improving the public’s understanding of science? An interesting opinion piece by Jeanne Garbarino (PhD, Director of Science Outreach at Rockfeller University) on why anti-vax groups have such a hold of our nation.

Such sites [anti-vaccination sites] skillfully cultivate feelings of trust and credibility by aiming their message to hit the more human side of things. These sites get human behavior, while pro-objective evidence sites often do not.

The sound of climate change from the Amazon to Arctic, a string quartet with each instrument representing different latitudes of the world. They play together to demonstrate how rapidly temperatures have been fluctuating.

We often think of the sciences and the arts as completely separate — almost like opposites, but using music to share these data is just as scientifically valid as plotting lines on a graph,” he says. “Listening to the violin climb almost the entire range of the instrument is incredibly effective at illustrating the magnitude of change — particularly in the Arctic which has warmed more than any other part of the planet.

Book suggestions

It’s the best day of the year!

Calculus in Context, a free introductory calculus book for anyone looking to brush up on their calculus. Highly, highly recommend for life-science people because it focuses more on the context rather than pure theory or pure application. Also Spencer highly approved of it (and he does a lot of mathematics!)

Data Analysis with R, there was a free giveaway and I nabbed one. Looks like it has great reviews (I skimmed through it and it seems very substantial!). So if anyone wants to add this to their Ebook collection, go ahead and download from my Google Drive. I would recommend for any beginner/intermediate users of R.

Weapon of Math Destruction: How Big Data Increases Inequality and Threatens Democracy, “Models are opinions embedded in mathematics,”author Cathy O’Neil declares as she pinpoints the dangers of mathematical models that run our lives. From the lack of transparency to the significant problems that arise with fitting models from past data, O’Neil takes a stand for ethics in our data-driven world.

Theory-Based Ecology: A Darwinian Approach, I think this should be the standard textbook for all ecology students. All ecological concepts are explained with an Darwinian insight and combines genetics, ecology, evolution, and mathematics into this amazing textbook. Celebrates both theoretical frameworks and empirical works equally. If you’re also interested in learning mathematical concepts used in ecology, this is quite a wonderful resource!

The general principles behind formalized ecological theories correspond to principles regularly recurring in Darwin’s texts (the rule of geometric increase, the doctrine of Malthus, and the inevitable connection of similarity and the strength of competition that lead to the principle of natural selection, and the principle of character divergence)

Mathematical explanation example

Dear Data: Two information designers send each other postcards… but of the data they collected each week. A really fascinating project because they redefine what “data” is to them. They say data was not only a dataset during this project, but a “souvenir, a love letter, and a self-portrait.”

Each week, and for a year, we collected and measured a particular type of data about our lives, used this data to make a drawing on a postcard-sized sheet of paper, and then dropped the postcard in an English “postbox” (Stefanie) or an American “mailbox” (Giorgia)!