How to make a baller CV in R!

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Do you ever find yourself in front of your R console pondering to yourself how much time consuming side-projects can I do on here?

The answer, quite simply, is that the limit does not exist.

People throughout the R community have created a wealth of insane things to do with our beautiful coding language, from art (which I really appreciate and would like to learn some day) to horoscope-generating bots!

If your current code is causing you mental anguish, why not treat yourself to a lil’ bit of FUN coding and converting your CV into a Latex-R-Code wonder! Besides looking slick, it’s just a nice exercise.

First of all, shout out to Julie Jung who did this way before me. If my explanations here are insufficient, then click on any of the links below to learn more from smarter people.

Okay, let’s get this party started.

1: MAKE SURE YOU CAN KNIT YOUR DOCUMENTS TO PDF. If you have never done this before, this can be a bit of a nightmare. You’re gonna have to venture into this (La)TeX business, which is scary at first, but will be okay, I promise. You can download a baby version (smaller and faster download, Basic TeX), here. A full-blown step-by-step for those who are truly lost (. . . no comment on how I have this link. . . ) can be found here.

2: Now you need to download a template! This is the most fun part! Imagine, you can use any template in the whole wide world. In the future, if you want to change what your CV looks like, all you need to do is change the template. This dude, SV Miller, has a bunch of ’em. The one for CVs specifically is here. He seems pretty funny and nice– as is most of the R community, so you know, if nice people can do this, so can we.

To get all of this sweet, sweet code, you can just download it (green button that says “Code”).

Once downloaded, add the template (called svm-latex-cv.tex) into your working directory. Now, I don’t know about you, but I made my own CV project so that way I could just drag this thingy to my RProject and move on with my life. Bam!

3: Okay. You have everything you need. NOW WHAT. Design that YAML (the top part and also the “rule book” (re: font, font size) for the rest of the document).

You can do a bunch of stuff. Check out Julie’s and SV Miller’s Websites for further inspiration.

What I wanted to get into here are little things that aren’t well covered in the tutorials and RMarkdown language reference guide (which is still pretty awesome though).

Chloe’s Tips N’ Tricks for a super cute CV because she spent way too much time googling it and now she has to do something with the information.

Indent! All you gotta do is start your line with “>”

   > Ph.D Student in Biology \hfill 2019- In progress  

Getting a part of your line to the other side of the page. (\hfill)

   > Ph.D Student in Biology \hfill 2019- In progress  

Cool symbols! Like ‡ and †

$\ddag$  ##This is a double dagger
$\dag$  ## This is a dagger

Websites and links! Okay, so here “+ Media Coverage” is just normal text. In the square brakets is what will become that “clickable” text that takes you to the website in parentheses.

+Media Coverage [Hespress Online](https://www.examples.com)

Tables! Yo, you like columns? WELL HERE YOU GO!

The input within the R chunk is a little bit of a mess, but here she is:

(More on this whole ordeal here)


```{r table2, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'}
tabl <- "
| Source      |Amount          | Year  |
|:---------------|-------------:|------:|
| EXAMPLE 1    | XXX | 2020 |
|  |     |    |
| EXAMPLE 2   | XXX    |   2019 |
|  |     |    |
| EXAMPLE 3 | XXX    |    2015-2018 |
|  |     |    |
"
cat(tabl) # output the table in a format good for HTML/PDF/docx conversion
```

Where you place your colon (:) indicates if the line is left, right, or centered within the column.

Little Brother for Breakfast

science

Aaaand, we’re back! This time around I was able to play around with manipulating physical (size) and genetic (relatedness) variables between aggressive cannibal tadpoles (the infamous Dendrobates tinctorius) in collaboration with Lutz Fromhage, Janne Valkonen, and Bibiana Rojas.

The D R A M A is for real. . . it turns out that both size and relatedness play a role in driving aggression between tadpoles, where individuals are more aggressive towards a counterpart with increased size asymmetries and decreased genetic relatedness. In other words, large non-siblings are significantly more aggressive than large siblings (exhibiting almost twice the amount of aggressive behaviors).

But it doesn’t stop there.

The most fascinating thing (IMO) is the shift in latency to aggression depending on relatedness. We find that there is inversion in biting behavior as size differences increases, where sibling pairs with large size differences attack significantly faster than non-siblings. Thus, although large siblings were less aggressive overall, they had a shorter latency to aggression in dyads with large size differences.

Is that not simply fascinating? Why are siblings who are quite disproportionate in size demonstrating aggressive behavior so quickly? Perhaps that biting is not simply an aggressive behavior, but a means for identification and the assessment of relatedness? Or perhaps it is a behavioral response to establish dominance within a pair?

No matter how you slice it, there is something going on in their little tadpole brains where individual behavior is different when faced with non-related or related individuals. From this clear kin discrimination and really cool cognition work headed by Fischer (2020), we believe that there is kin recognition in Dendrobates tinctorius. To read more about the details of our study and learn about aggression in cannibals, check out our pre-print!

If reading is too troublesome and you would like a 10-minute synopsis by your-truly, click the video I made explaining the paper (presented at ASAB Winter Conference 2020).

Shine bright like a tadpole

science

Visible implant elastomer success in early larval stages of a tropical amphibian species

Access the peer-reviewed article here: https://peerj.com/articles/9630/

When we observe animals, be it in the jungle, under water, or even in your own back yard, we learn to recognize individuals over time. Maybe you know your neighbourhood squirrel because it has a ripped ear, or you notice a butterfly because it has a unique pattern. This process, the act of distinguishing individuals, is fundamental in behavioral research.

But what do you do when all of your individuals within a population look similar?


In this study, I attempted (along with one of my best friends, Guillermo Garcia-Costoya and my advisor Bibiana Rojas) to tag young poison frog tadpoles with fluorescent elastomer tags. This is especially interesting because, to date, tropical larval amphibians had never been tagged; further, we marked the smallest and youngest amphibious animal ever recorded.

.

Now you see me, now you don’t:

When tracking tags across development we find that the probability of retention and observation differ across time. This means that just because someone didn’t observe the tag doesn’t mean that the tag is actually lost. This is important to take into account when working with mark-recapture studies.


What’s so cool about elastomers is that they’re small and durable. We now have work showing that we can tag tiny little tadpoles (before they have cool back patterns or are transported by their fathers!) and find out where they are carried or even how tadpole communities change over time in small water holdings. This methodology will hopefully be of use to future biologists who working in conservation or on behavior in the tropics.

Hungry to learn more about cool science?

The Sweet Escape

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Work funded by Karen M. Warkentin and done in collabortion with KMW, Julie Jung, Ana M. Ospina, and Rachel Snyder.

Also find the poster, presented by me at the 2019 ESEB conference in Turku Finland here

It’s not only Gwen Stephani that sings about a Sweet Escape. . . turns out that the natural world is full of pretty ferocious predators that have evolved a myriad of adaptations to rip, tear, dismember, and sneak up on their unsuspecting prey. But predation isn’t a one way street– prey have developed some evasion tactics of their own. . .

But you already knew that. Crabs have shells, gazelles use evasive darting tactics, and stick-bugs use morphological camouflage to look like. . . well. . . sticks! But did you know that there are embryos, meaning individuals that haven’t even hatched from their egg capsules yet, use information from the outside world to that trigger escape hatching responses?

That’s right, and we see this in red-eyed treefrogs– imagine a snake sneaking up a tree branch where an unsuspecting clutch (which has no parent to protect it, as there is no parental care in the species) hangs over a nearby pool. Well, instead of just laying around and becoming fresh snake food, embryos cue on both tactile and motion modalities to inform premature escape hatching. Read more about our findings in our abstract and conference poster below! (with hopeful full-length paper coming out in 2020 🙂 )

ABSTRACT— When defense is more costly, prey should differentiate more strongly between predator cues and benign stimuli and may therefore use more sources of information. Red-eyed treefrog (Agalychnis callidryas) embryos hatch prematurely to escape from egg-eating snakes and wasps, cued by physical disturbance in attacks. Missing predator cues is always costly, but false alarm costs decrease with development. We assessed developmental changes in how embryos use and combine information from two sensory modalities, using a playback system to present motion (shaking), tactile contact (rubbing), or both cue types to eggs in custom-made trays at two ages. Younger embryos showed a stronger hatching response to bimodal over unimodal cues. This synergistic effect disappeared in older embryos, which responded equally strongly to unimodal and bimodal cues and had a shorter latency to hatch. This indicates younger embryos – facing higher predation risk as tadpoles – use more information for their hatching decisions. We also investigated changes in response to tactile cues (simulated wasp attack) manually applied directly to embryos through the capsule (higher threat) or on the capsule away from embryo (lower threat). Younger embryos hatched faster in response to direct tactile contact than capsule-only contact, whereas older embryos responded equally to both. Both within and across sensory modalities, developmental changes in embryos’ cue use are consistent with ontogenetic adaptation, based on improved survival chances outside the egg. Embryo hatching timing can be crucial for survival, and the cognitive processes underlying their behavioral responses have likely been shaped by developmentally changing selection pressures.

A Quick Guide to Cannibalism

science

Review written by Chloe Fouilloux, Eva Ringler, and Bibiana Rojas

Animals can sometimes be downright bizarre. We, as biologists, still don’t quite understand why animals behave the way they do, but every day we get a little bit closer to a more complete reality of the natural world that we observe. One of the most fascinating behaviors I have ever watched is that of cannibalism, where an individual kills and then consumes part or whole of another individual of the same species. And although it’s weird, it’s not rare at all; in fact, it’s present in every animal clade alive on Earth today! Mothers eat their babies, fathers feed their babies to other babies, babies eat each other. . . the carnage is truly ubiquitous.

Feel free to download our quick guide to cannibalism– but watch out! It’s a slippery slope to becoming fascinated with this deliciously intriguing behavior 😉

Les Secrets de la Septième

Photography

There are no forces of good or evil in the jungle.

There is only that which blooms and that which decays,

all returning to an earth that experiences the same breath.

Nothing is removed from this great living circle—

even the igneous traces an inception

some circles are much larger than others:

from up close, peering into a decade’s exhale,

the horizon may lose some curvature

a second’s worth flatness

heaved into an entire history

there are no consequences where lines are concerned.

Yet, just as gravity renders all things spherical,

essence renders all life cyclical

the rivers that were will be again

and the fallen tree will rise

there is only a balance between the miraculous and the mundane.

Circles (Jungle’s Law)

The Nomad, Setti Fadma

Photography

Rabiaa

In the rebirth of the valley

between the green fruit

and the rushing snow melt

between black pelts

and the baritones of new fathers—

 

In all of this new life

is the reminder that not all survive.

not all buds bloom,

or fruit ripen

or newborns leave the blood clotted fur of their mother’s coat.

 

not so kind is the flooding of pastures for the foxhole,

or hungry vipers awakening from hibernation

or the sharp bite of the mongoose.

she, too, has mouths to feed.

None of it is evil.

a manifestation of

will, innateness, and luck,

 

And a reminder that I survived the floods

and the sharp teeth;

that my probability turned to actuality

and I am here breathing

all these beginnings and ends

in the mountain spring

in a far-off land

that I call home.

April 2019

There are times that a troop will cast off an individual or that an individual will isolate themselves from the bulk of the group. There are a slew of reasons: disease, deformities, an approach to the end of life. . .either forced by the alphas or a behavior that is completely self-imposed, you’ll find these individuals hanging around the periphery of activity, usually perched many meters above the center of activity. 

I’ve come to call this ancient male, “The Nomad”. I’m not sure where he’s from or how long he’s been away. But he’s back now.

Toubkal, Morocco

Photography

I wondered for a moment, if their souls were there with us–

gasping for air, murdered as they were.

Toubkal 2019

In response to the 2018 murders of two young women in the mountain region where I lived, I embarked on an expedition with my Moroccan friends both as a pilgrimage and way to deal with grief.

Toubkal is the highest peak in North Africa; with Yassine, Daoudi, and Ouba, we were the first people to summit the mountain in 2019.