Discover and read the best of Twitter Threads about #rmarkdown

Most recents (10)

New version of {grateful}, the package that makes it very easy to cite #Rstats packages, so that #software authors get their deserved credit.

pakillo.github.io/grateful/

Major changes: 1/6
2/ To get a document with formatted citations for all the #rstats packages used in your analysis, just run

library(grateful)
cite_packages()

Now includes pkg versions and all their citations, ready to paste into your manuscript or report Image
3/ {grateful} can now be used within #Rmarkdown!

Just include a chunk with

cite_packages(output = 'paragraph')

and you'll get a paragraph with in-text citations for all pkgs and a formatted reference list ImageImage
Read 6 tweets
1/10 Very happy to share my first PhD paper in @naturesustainab on the relationship between modern energy access and fertility transition in 44 countries over 26 years. 💡👨‍👩‍👧‍👦🪵

Team work with @RmnHoffmann, @pppichler and Helga Weisz (@PIK_Climate @IIASAVienna @WICVienna @OeAW)
2/10 Today ~ 2.6 billion people lack access to modern energy, and a large share of women worldwide do not have complete control over their reproductive choices. What empowers women to make reproductive choices?
3/10 Access to modern energy improves women’s well-being as it saves time on household chores, improves health and enables access to education and information.
These foster women’s ability to make reproductive choices, which tends to reduce birth rates.
Read 10 tweets
Hi all 👋 today I would like to talk about #CV tips. Did you know you can create your CV in #rstats? There are so many cool 📦 out there!
I personally use {vitae} with a good range of eye-catching templates to choose from, I highly recommend it!
What I like the most about building my CV in R is that I can organize everything in an R-project, I push to GitHub which gives me track changes and I can use the great advantages of #rmarkdown and #latex. Here is the repo of my #vitae CV github.com/loreabad6/R-CV
I had to modify a bit the .csl file to adapt certain details to my taste, and I included a 🗺️ of my journey which has had some nice feedback, as it serves as a visual presentation card 💃 A preview of my CV made with the vitae R package
Read 6 tweets
Morning! Let's continue with the polling results, today and get some #learningtips. Here is what people voted for regarding learnings strategies! Not surprisingly, the big majority likes some hands-on exercises, although a mix between theory and practice is also welcome 😎 Results to poll about learn...
📚 Very few people voted for learning from books about coding, but have you already seen all the resources out there? #rstats has a big pile, and the best way to browse them all is with the Big Book of R #rmarkdown #bookdown
bigbookofr.com/index.html
Most of the people like blogs and written content. Well this is the perfect opportunity to point you to the #RLadies blogs collected by @PipingHotData & @DrMowinckels
Read 4 tweets
Latest paper is up! We fed mice high protein diets for 24 weeks and measured the #microbiome 🦠, #kidney function and #gut leakiness. Here's what we found: onlinelibrary.wiley.com/doi/abs/10.100… @sihmin_tan @MelindaCoughlan @MonashDiabetes
1) high protein diets alter the microbiome...but what's interesting is when we looked at the predicted metagenomes (using picrust2) we saw⬇️BCAA synthesis and⬆️urea cycle pathway.
2) the high protein diet caused inflammation and intestinal permeability:
⬆️ plasma endotoxin
⬆️ plasma MCP1
⬆️ TNFα expression in jejunum and ileum
⬇️ occludin expression in jejunum
Read 5 tweets
Fall is here and a lot of students are starting their journey as #rstats users. This can be tough, especially with all the barriers to learning that 2020 is throwing at us. Here are some tips (almost all from @JennyBryan!) I wish I’d followed from the start of my #rstats career
Beginning #rstats users sometimes focus on the mechanics of R and don’t get around to establishing some best practices that will set you up for writing more efficient and reproducible code. These all will make your life easier in the long run, I promise! #openscience
1. Develop a project-oriented workflow. Decide on a common file structure and stick with it for every project. Here’s what I use, based on this great paper journals.plos.org/ploscompbiol/a…. That way, you always know where to find files in any project Image
Read 10 tweets
THREAD/RANT: Just watched a great #rstats webinar. Presenter is an author of many📦s. At the end, the host suggested that the (100s of) attendees go file issues on the 📦s Github repos & comment on the presenter's blog posts to ask Qs they didn't get answered in the webinar. 1/?
This is absolutely NOT how you get answers to #rstats questions. Not only will you waste the package author's time, you will waste your own time. So, here are some tips on how to get help in #rstats. TL;DR: filing Github issues, tweeting/emailing pkg author are LAST RESORTS. 2/?
(These tips are ordered based on my experience to get you an answer as fast as possible.)

#1: Read the relevant documentation. #rstats Many packages have websites & vignettes. Consult those, too.
Read 18 tweets
I need to teach get ~40 new #rstats students up and running with #RStudio and using #rmarkdown. Here's some resources I'm looking checking out for use in my class
1/n
"Introduction to R Markdown" by Michael Clark has good overview information on #rmarkdown
m-clark.github.io/Introduction-t…
2/n #rstats
"Getting used to R, RStudio, and R Markdown" by the prolific @old_man_chester looks like it has some very practical material for #rmarkdown and #rstudio, including GIFs
bookdown.org/chesterismay/r…
2/n #rstats
Read 9 tweets
1. New (first) paper now available: Exploring the effects of BCG #vaccination in patients diagnosed with #tuberculosis: Observational study using the Enhanced Tuberculosis Surveillance system

Paper: doi.org/10.1016/j.vacc…
Preprint: doi.org/10.1101/366476

#phdchat #rstats
2. Highlights

Evidence of an association between BCG vaccination and reduced all-cause mortality in TB cases.

Weaker evidence of an association between BCG vaccination and reduced repeat TB episodes in TB cases.

Little evidence of an association with other TB outcomes.
3. Background: Bacillus Calmette–Guérin (BCG) is one of the most widely-used vaccines worldwide. BCG primarily reduces the progression from infection to disease, however, there is evidence that BCG may provide additional benefits.
Read 7 tweets
At #SDSS2019, I am chairing a session on workflows with @TiffanyTimbers @mikelove @stephaniehicks at 3:45 in Regency C - it is tucked away a bit in the corridor between AB and D
Read 55 tweets

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