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@appliedepi.bsky.social

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Improving Applied Epidemiology worldwide. Increasing the knowledge and resources of Epidemiologists no matter who or where they are. Creator of the EpiRHandbook: https://epirhandbook.com/

epirhandbook.com

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appliedepi.bsky.social @appliedepi.bsky.social · Dec 5

Hello Bluesky! We’re Applied Epi! What do we want? To improve Applied Epidemiology worldwide! When do we want it? Well probably in an achievable timeframe that doesn’t completely destroy a much needed and already existing infrastructure that is overburdened!

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appliedepi.bsky.social @appliedepi.bsky.social · Jul 14

We're hiring!

Applied Epi is looking for a capable epidemiologist for a full-time 1-year remote contractor position.

Take a look at our website for more details on the role and how to apply: appliedepi.org/about/join.h...

Application deadline: July 31, 2025.

join – Applied Epi

lnkd.in

appliedepi.bsky.social @appliedepi.bsky.social · Jun 10

🚨 Rare opportunity! Our advanced R courses start end of July:

📈 Time series & outbreak detection in R
📊 Intro to Stats in R
🗺️ Intro to GIS in R
🖥️ Shiny in R
📝 Advanced R Markdown

Plus: Lots of Intro to R courses running all summer! 🌞

Taught live by experienced epidemiologists. 🌍

🔗 appliedepi.org

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appliedepi.bsky.social @appliedepi.bsky.social · Mar 13

“I’ve taken several R trainings - this is the BEST!”
📢 New courses posted! Intro to R for public health
🗓️ 40 hours part-time, synchronous, with unlimited 1-on-1 coaching and options for ALL time zones.
✏️ Register: appliedepi.org/training/pub...

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appliedepi.bsky.social @appliedepi.bsky.social · Feb 3

📢 Last week to apply for the Applied Epi scholarships!

Transition your team to R with free or discounted courses and services.

Why apply?
✔️ Full or partial scholarships
✔️ Focused on strengthening public health capacity

🗓️ Apply by Feb 10, 2025! 🌐 appliedepi.org/training/scholarships-ae

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appliedepi.bsky.social @appliedepi.bsky.social · Jan 27

📢 Ready to move your team to R? Applied Epi’s scholarships are OPEN!

✅ Funding available for teams in LMICs
✅ Even teams of 1 can apply with leadership support
✅ Deadline: Feb 10, 2025

Why team applications? Collaboration ensures a smooth transition to R! Apply today: 🌐 appliedepi.org

Applied Epi

appliedepi.org

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appliedepi.bsky.social @appliedepi.bsky.social · Jan 21

🚨 Applications are NOW OPEN for Applied Epi’s 2025 scholarships! 🚨

💡 For teams in low- & middle-income countries working in epidemiology, this is your chance to access funding for courses and support services that help transition to R.

🗓️ Deadline: Feb 10, 2025
🌐 Apply here: appliedepi.org

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appliedepi.bsky.social @appliedepi.bsky.social · Jan 17

🎉 R scholarship applications open on January 20!

If your team (government or nonprofit) works in applied epidemiology in a low- or middle-income country, you could get access to our Intro to R course and Support Desk! Details: appliedepi.org/training/sch...
#Rstats #epitwitter

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appliedepi.bsky.social @appliedepi.bsky.social · Dec 24

The main takeaways are:

1) Ggplot customization possibilities are pretty endless.
2) Merry Christmas and happy holidays to you all!

🎄🎄🎄

appliedepi.bsky.social @appliedepi.bsky.social · Dec 24

That code shows other cool things too, like how we added in a new font ("Grand Hotel") for the ggplot title.

We used the {showtext} package for this: font_add_google() loads the font from Google Fonts, and showtext_auto() ensures R applies the font to the plot.

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appliedepi.bsky.social @appliedepi.bsky.social · Dec 24

Repeatedly rerunning the code is quite fun

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appliedepi.bsky.social @appliedepi.bsky.social · Dec 24

And how did we get Santa's coordinates?

Since he didn't share his location, we created a function (get_random_night_coords()) to randomly generate coordinates of a location with a current local time between 11pm and 3am, assuming those are his working hours!

Close enough!

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appliedepi.bsky.social @appliedepi.bsky.social · Dec 24

Both of these figures are created with ggplot2, and use a saved PNG file of Santa.

geom_image() from {ggimage} places the image at specified coordinates, reading from the file path.

Here's the ggplot code for the second figure:

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appliedepi.bsky.social @appliedepi.bsky.social · Dec 24

And if you want his current location:

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appliedepi.bsky.social @appliedepi.bsky.social · Dec 24

🎄 Merry Christmas Eve, everyone! 🎄

To wrap up this advent calendar, here’s our final tip:

Did you know you can use your own images in ggplot?

Check out this festive example with a cartoon of Santa —on his (surprisingly inefficient?) route tonight! 🎅✨

#DataViz #RStats

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appliedepi.bsky.social @appliedepi.bsky.social · Dec 23

coalesce() is from the {dplyr} package. It returns the first non-missing value from a set of columns, based on the order you specify.

It’s not just for dates, but for any use-case where you need to pick one value from across columns!

appliedepi.bsky.social @appliedepi.bsky.social · Dec 23

Today's post is for anyone with bdays this time of the year. We see you!

This includes our Exec Director, an expert in "combo Xmas/bday" presents! Happy birthday Neale! 🎂

On that note, ever work with multiple date columns but need to pick one? Use coalesce() to easily prioritize a value!

#Rstats

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appliedepi.bsky.social @appliedepi.bsky.social · Dec 22

Can you recommend any other holiday or Christmas-related R packages? We'd love to know!

appliedepi.bsky.social @appliedepi.bsky.social · Dec 22

Here's the code if you like the "minimalist" aesthetic.

That said, it does show the versality of ggplot!

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appliedepi.bsky.social @appliedepi.bsky.social · Dec 22

P.s. Before finding the {christmas} package I was ready to make this the main event for this post:

appliedepi.bsky.social @appliedepi.bsky.social · Dec 22

🎄Day 22: An R Christmas Tree 🎄

There's still time to write your Christmas cards!

And what better captures the yuletide spirit than...R...

Seriously though, check out the {christmas} package by Jose Barrera-Gomez.. Stunning!

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appliedepi.bsky.social @appliedepi.bsky.social · Dec 22

And finally, if you want the function code pasted above, you can get it from the Applied Epi Community: community.appliedepi.org/t/custom-ggp...

Enjoy!

#RStats #Dataviz

Custom ggplot functions!

Hi all! I’m pasting in some example code to create a custom ggplot function. This example creates different epicurves using the Ebola linelist from Applied Epi’s introcourse. It allows you to defin...

community.appliedepi.org

appliedepi.bsky.social @appliedepi.bsky.social · Dec 22

You can make the function more complex, but don't overdo it - too many arguments could become hard to understand and edit!

It's all about balance and the best solution for your problem🤓

Learn more here:
epirhandbook.com/en/new_pages...
ggplot2.tidyverse.org/reference/ti...

Tidy eval helpers — tidyeval

This page lists the tidy eval tools reexported in this package from rlang. To learn about using tidy eval in scripts and packages at a high level, see the dplyr programming vignette and the ggplot2 in...

ggplot2.tidyverse.org

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appliedepi.bsky.social @appliedepi.bsky.social · Dec 22

Want to further customize colours? 🎨

The example above uses the same colour palette for each plot, with scale_fill_brewer().

For custom colours, you can also define a palette inside scale_fill_manual() - or as a separate object that you refer to (as discussed yesterday).

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appliedepi.bsky.social @appliedepi.bsky.social · Dec 22

Why the squiggly brackets {{x}}? 🤔 They're for tidy evaluation!

{{ }} allows ggplot() to recognize the inputs for "xvalue" and "fillvalue" as column names from your data.

Without them, your function won’t know how to evaluate these column names properly!

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appliedepi.bsky.social @appliedepi.bsky.social · Dec 22

The code defines a function for an epicurve with geom_histogram(), taking three inputs:

1️⃣dataset object name ("data"),
2️⃣column name for the x axis ("xvalue"),
3️⃣column name for the fill colour ("fillvalue").

So you can easily make epicurves with different breakdowns or date types!