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# Welcome to the CEEDS use-r Github repo!

This repo stores the R demos and tutorials from our R community. Feel free to use and re-use - head to **[demos](demos)** for all materials.

**We meet in LEC 3 Boardroom and on Teams every Thursday at 10am** to chat, demo useful R tricks, and debug our coding problems.

*Message James Robinson (james.robinson AT lancaster.ac.uk) if you'd like to join the slack channel or get the Teams link.*

Download these materials by clicking the green **Code** button above. Or stay up to date with git by using  ```git clone``` and pulling updates.

# Past Demos

**Style & Workflow**

* Workflow | [Resources](demos/workflow) | [Video](https://livelancsac.sharepoint.com/:v:/r/sites/Grp-LECCodingandStatsSupport/Shared%20Documents/General/Recordings/View%20Only/20231123%20-%20Workflow%20-%20Lisa.mp4?csf=1&web=1&e=2T5Ql9)
* Staying organized in R | [Video](https://web.microsoftstream.com/video/b00b07fc-7895-4624-a02c-0437beda1849)
* Intro to GitHub | [Video](https://livelancsac.sharepoint.com/:v:/r/sites/Grp-LECCodingandStatsSupport/Shared%20Documents/General/Recordings/View%20Only/20231130%20-%20GitHub%20-%20James.mp4?csf=1&web=1&e=KZLtEa)

**Tidyverse**

* Intro to tidyverse 1 | [Resources](demos/tidyverse) | [Video](https://livelancsac.sharepoint.com/:v:/r/sites/Grp-LECCodingandStatsSupport/Shared%20Documents/General/Recordings/View%20Only/20231109%20-%20Intro%20to%20TidyVerse%20-%20James.mp4?csf=1&web=1&e=o8ibYx)
* Intro to tidyverse 2 | [Resources](demos/tidyverse) | [Video](https://web.microsoftstream.com/video/caab2def-9c6c-425e-aadf-a4b0cb51fe8e)
* Data to figure using tidyverse & Strava |  [Resources](demos/rStrava) | [Video](https://web.microsoftstream.com/video/efb019bc-eb20-4017-b4b1-7a6480e4495b)
* Tidyverse tricks |  [Resources](demos/tidyverse/tidyverse_tricks.Rmd) | [Video](https://web.microsoftstream.com/video/db32b9cf-e4b7-402b-8a79-8b2a530f2792)

**Data visualization**

* Intro to maps | [Resources](demos/mapping/) | [Video](https://web.microsoftstream.com/video/38ae2633-3ea9-4450-9c1b-0d81f7249a16)
* World maps | [Resources](demos/mapping) | [Video](https://web.microsoftstream.com/video/ff061266-b657-4391-92d7-f37db352c2bd)
* Intro to ggplot2 | [Resources](demos/ggplot) | [Video](https://livelancsac.sharepoint.com/:v:/r/sites/Grp-LECCodingandStatsSupport/Shared%20Documents/General/Recordings/View%20Only/20231116%20-%20Intro%20to%20GGplot%20-%20Lisa.mp4?csf=1&web=1&e=D4RVBf)
* Extending ggplot | [Resources](demos/ggplot_extensions/) | [Video](https://web.microsoftstream.com/video/7057bdea-f4b4-41a6-8f73-cb8500519044)
* Themes | [Resources](demos/ggplot_extensions) | [Video](https://web.microsoftstream.com/video/9215e127-42f5-4fa9-8171-0c6a8ef8ab63)
* Publication quality in base R | [Resources](https://github.com/smuel-tylor/Fast-Deactivation-of-Rubisco/blob/main/2_scripts_sun_shade_sun/Figure1_Multipanel_S_Vcmax_Vi_Vt.R)

**Statistics**

* Intro to linear models (lm) |  [Resources](demos/linear-models) | [Video](https://web.microsoftstream.com/video/f224466c-7214-4830-925d-5791440dad8d)
* Intro to mixed effects models (lme4) |  [Resources](demos/linear-models) | [Video](https://web.microsoftstream.com/video/d99d3ddf-9350-4591-9a97-9a62f2284be8)
* Intro to Bayesian (brms) | [Resources](demos/brms) | [Video](https://web.microsoftstream.com/video/c7ca7ed2-3a6b-420c-ba93-87c30994e7b0)
* Intro to non-linear models | [Resources](demos/non-linear-models) | [Video](https://web.microsoftstream.com/video/84aa500c-9a36-4f1c-8a0c-e08513c15267)

**R-markdown, Shiny & scraping**

* Intro to R-markdown | [Resources](demos/rmarkdown-html)
* R-markdown in an R script | [Resources](demos/render-rscripts-rmd/) | [Video](https://web.microsoftstream.com/video/9c767fc9-1935-4d93-ad2b-9449da9fae39)
* Web scraping | [Resources](demos/web-scraping)
* Web scraping with Selenium & Python | [Resources](demos/scraping-py) | [Video]()
* R-markdown for supplementary materials | [Resources](demos/rmarkdown-for-figures)
* Intro to Shiny | [Resources](demos/shiny) | [Video](https://web.microsoftstream.com/video/16f4a128-73c3-4114-9443-072773d1aba4)

**Base R**

* Intro to functions | [Resources](demos/intro-to-functions/) | [Video](https://web.microsoftstream.com/video/b5086b5b-c10d-42ec-9e99-f45a15e9b4a9) 
* Intro to loops | [Resources](demos/intro-to-loops/) | [Video](https://web.microsoftstream.com/video/30c83fa7-b74b-45ad-a79b-4cb31a63a6f1) 
* Control structure: loops + logic |  [Resources](demos/loops) | [Video](https://web.microsoftstream.com/video/87cf1743-33a2-4953-8021-4f9478384366)

**Tips & Tricks**

* Keeping R & R Studio up-to-date | [Resources](demos/updatingR) | [Video](https://web.microsoftstream.com/video/41a084d1-2c02-449c-8b33-bf94197ed30f)
* Bioconductor for bioinformatics | [Video](https://web.microsoftstream.com/video/5b485f83-55b0-426f-a4b4-70907fb3178b)
* Show-and-tell (May 2021) | [Video](https://web.microsoftstream.com/video/f11fd5ba-fefc-4e52-bfd6-d79a471e133a)
* Extracting text from images | [Resources](demos/TextExtract) | [Video](https://web.microsoftstream.com/video/c49a8776-5eeb-4f2a-aa94-4d199606c7a3)

## Useful R stuff

**Show-and-tell / handy packages**

* [Beepr](https://www.r-project.org/nosvn/pandoc/beepr.html) - makes your R script goes bing when it finishes (or [rap adlibs](https://github.com/brooke-watson/BRRR))
* [Janitor package](https://garthtarr.github.io/meatR/janitor.html) for finding duplicates and cleaning column names
* [Rainbow brackets](https://blog.rstudio.com/2020/11/04/rstudio-1-4-preview-rainbow-parentheses/) in R Studio
* [litsearchr](https://elizagrames.github.io/litsearchr/) -automated searches for systematic review

**Everything Tidyverse**

* [R for Data Science](https://r4ds.had.co.nz/index.html) (book - Hadley Wickham)

**Data visualization**

* [Fundamentals of Data Visualization](https://clauswilke.com/dataviz/) (book - Claus Wilke)
* [ggplot2 extensions](https://exts.ggplot2.tidyverse.org/gallery/)
* [Data Visualization course](https://wilkelab.org/SDS375/) (slides - Claus Wilke)

**Models**

* [Best practice & R packages for mixed models](https://bbolker.github.io/mixedmodels-misc/glmmFAQ.html) (Ben Bolker)
* [Bayesian visualization](https://arxiv.org/abs/1709.01449)
* [Bayesian workflow](https://arxiv.org/abs/2011.01808)
* [Statistical Rethinking (intro to Bayesian)](https://xcelab.net/rm/statistical-rethinking/) (Richard McElreath)

**Maps**

* [Simple Features for map analysis](https://r-spatial.github.io/sf/) (sf package)
* [Geocomputation in R](https://geocompr.robinlovelace.net/) (book - Lovelace et al.)
* [Geocoding and Google Maps in R](https://evamaire.com/2020/04/16/geocoding-with-ggmap-in-r/) (LEC's Eva Maire)

**R-markdown**

* [R Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/) (book - Xie et al.)
* Section 19 of [Happy Git with R](https://happygitwithr.com/) explains using Markdown in an R script, and is a good primer on Markdown in general 
* Section 27 of the [R for Data Science](https://r4ds.had.co.nz/r-markdown.html) site explains modifying .R files 
* The [RStudio Markdown Cheat Sheet](https://www.rstudio.com/wp-content/uploads/2016/03/rmarkdown-cheatsheet-2.0.pdf)

**Github and version control**

* [Software Carpentry lessons](http://swcarpentry.github.io/git-novice/)
* [Learn Git in R Studio](https://afredston.github.io/learn-git/learn-git.html)
* [Happy Git and Github with R](https://happygitwithr.com/index.html) (book - Jenny Bryan)

**Shiny**

* [R Studio Shiny gallery](https://shiny.rstudio.com/gallery/)
* [R Studio Shiny build tips](https://shiny.rstudio.com/articles/build.html)
* [Mastering Shiny](https://mastering-shiny.org/index.html) (book - Hadley Wickham)
* [Shiny package page](https://rstudio.github.io/shiny/)

**R workflow**

* [here() package](https://github.com/r-lib/here)

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