nhs-r-community / intro_r

Workshop materials for revised NHS-R Community "Introduction to R and R Studio" course.

Welcome to the NHS-R Community Introduction to R and R Studio!

Attending the course?

If you are attending the course check all of our course materials and preparation instructions.

Are you wanting to update or use the slide code?

This repository is split into 3 areas:

• RMarkdown files and dependency files - slides have been built in {xaringan} which requires the css, img and libs folder to render
• html pages - are automatically rendered using GitHub actions (no need to knit every file!) and are kept on a separate branch. The html files are published through GitHub and being {xaringan} they are interactive and accessible
• data files are in a separate repository to help learners access the data files separate to the code for the slides

Set-up

You will need to have R, R tools (on Windows), RStudio, and git installed in order to use this project locally.

Clone the repository, then run the following code chunk to initialise the project.

# the data directory is a git submodule, which needs to be downloaded
if (length(dir("data", ".csv")) == 0) {
  system("git submodule init")
  system("git submodule update")
}
# install all of the required packages
renv::restore()
# download fontawesome icons used in slides
icons::download_fontawesome()

Once you have run these steps, in RStudio you can open the individual Rmarkdown documents and render each file. Alternatively, you can render all of the slides at once using the “Build All” button on the “Build” tab in RStudio.

Spotted a mistake?

Please let us know if there are mistakes or improvements by creating an issue.

intro_r's Issues

New features in R Studio

I've made references to some of the new features in RStudio (like Rainbow parenthesis) but these need new slides. Also, missing some existing functionality like Session refresh. I add that in often but it would be good to be explicitly covered.

{nhsrtheme} needs more detail on installation for all presentations

The package {nhsrtheme} is not on CRAN so needs more information in the slide code itself. https://github.com/nhs-r-community/nhsrtheme

devtools::install_github('nhs-r-community/nhsrtheme')

01 Slides error

• Slides 01 line 387 has a bug needs. Explain GitHub and ROpenSci without icons.
• Line 358 duplication of tidyverse package call needs to be explained
• Remove <br> by using two spaces at the end of the previous line
• Remove italics and use .blue[] for colour definition (italics is not accessible for everyone)
• Update README with how to install packages that are not on CRAN and fontawesome icons

Slides haven't rendered code

The html for ggplot2 hasn't rendered the code: https://nhs-r-community.github.io/intro_r/04-workshop_ggplot2.html#41 (this slide should have code as the answer).

Packages location slide needs updating

• Slide https://nhs-r-community.github.io/intro_r/01-workshop_intro.html#32 has the date 20201. The count of CRAN packages could be updated now too.
• Reference should be made to ROpenSci as well as GitHub for repositories, particularly as packages like https://github.com/ropensci/fingertipsR are on it now (no longer CRAN). Perhaps something about convention being how the install code is written out on the repository's README.

Many dependencies

Hi,

There are a lot of dependencies. Could you check that they are all needed?

Add negative operators to slide

I've realised there is a lot of positive operators (==) but negatives are not included (!=) and these should be included in the same slide, perhaps with reference elsewhere to other operators like > and <?

Link to blog has changed

Slide https://nhs-r-community.github.io/intro_r/05-workshop_functions.html#10 is a link to https://ijeamaka-anyene.netlify.app/ but the blog site has changed position.

Replace with the

• YouTube of the R Ladies talk https://www.youtube.com/watch?v=h0i6KAahLY8
• source code https://github.com/Ijeamakaanyene/aRt_ggplot
• slides https://ijeamakaanyene.github.io/aRt_ggplot/index.html#1

Remove some of the repetitive text

As a feature of the slides some of the text is repeated as this looks visually good but will not be good for screen reader users who will have this repeated when it isn't necessary. Some slides require changing around, perhaps using just -- breaks to introduce new information and remove this repetitive text.

Emails appear as clickable links but they are not.

We can remove the underlining on these

GitHub action failed on slide build - icons package

Error:

Run library(icons)
── Installed icons ─────────────────────────────────────────────── icon 0.2.0 ──
✖ ionicons             ✖ google_material 
✖ academicons          ✖ feather_icons   
✖ simple_icons         ✖ octicons        
✖ bioicons             ✖ fontawesome     
! No icons are currently available, start by downloading icons with the download_*() functions.
Error in open.connection(con, "rb") : 
  cannot open the connection to 'https://api.github.com/repos/FortAwesome/Font-Awesome/releases/latest'
Calls: download_fontawesome ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
In addition: Warning message:
In open.connection(con, "rb") :
  cannot open URL 'https://api.github.com/repos/FortAwesome/Font-Awesome/releases/latest': HTTP status was '403 Forbidden'
Execution halted
Error: Process completed with exit code 1.

Typos and corrections

Few corrections required in the slides.

Link to NHS-R Community Slack errors

The slide https://intro-r-slides.netlify.app/05-workshop_functions.html#4 has a link to NHS-R Slack but this errors - it might be better now to direct this to the main website because this has a direct link to the Slack group.

repackaging the NHS template

Hi there, thank you for the package.
it is really useful and given I do many slides with the branding guidlines for the company I work at. suppose I successfully edited the css file how would I package the whole thing so that I can follow the same steps and generate a slide deck with the same formatting i need

i am a new R coder and would appreciate your guidance

GitHub cannot be viewed by all organisations

A suggestion from a Midlands Analyst Network is to publish through NHS Futures which is a reasonable solution to get around this - particularly for people who are very new to R and want access to the slides.

Broken link

Hi,

There is a broken link where you get sent to 'https://nhs-r-community.github.io/intro_r/www.moderndive.com' rather than 'www.moderndive.com'. not sure why because the code looks fine to me.

intro_r/01-workshop_intro.Rmd

Line 242 in 2294de3

[www.moderndive.com](www.moderndive.com)

Add more to the index.rmd and README

Currently the page: https://nhs-r-community.github.io/intro_r/ just has the code to automatically generate the links from the GitHub Action https://github.com/nhs-r-community/intro_r/blob/main/index.Rmd but more information can be added here including details on how to book onto the NHS-R Community course https://nhsrcommunity.com/events/, perhaps the YouTube link too for related workshops:

Part 1 https://www.youtube.com/watch?v=Wmc0GS6gayI
Part 2 https://www.youtube.com/watch?v=N3pIxcCB9K8&t=1s
Part 3 https://www.youtube.com/watch?v=PX316WC0oiU&t=1s

dplyr https://www.youtube.com/watch?v=y5ispDcKfHw&t=1s
RMarkdown https://www.youtube.com/watch?v=UrZsKfNw1wc
ggplot2 https://www.youtube.com/watch?v=jiuDr4aYgkY

Correction - ggsave gives error in ggplot slides

The use of + between the ggplot and ggsave https://nhs-r-community.github.io/intro_r/04-workshop_ggplot2.html#62 causes an error although it also saves and is because it should be a pipe.

It can be run separately where you can ggsave() the last run chart http://www.sthda.com/english/wiki/ggsave-save-a-ggplot-r-software-and-data-visualization but @ChrisBeeley cautioned this practice as it wouldn't work interactively within something like Shiny.

Odd that this error hadn't occurred previously but I've just updated all the packages on the cloud and my own computer.

there is no package called ‘httpuv’

i keep getting the below whenever i need to activate the moon reader feature

could you please help out

Output created: NHS.html
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘httpuv’

Accessibility - change "here" to more descriptive link

Following the thread https://twitter.com/Em1lySm/status/1516741011422199810 it's advisable to not just use "here" as a link for accessibility.

https://github.com/nhs-r-community/intro_r/blob/9038f31fbfb570d49c5e50641d4c7f6928d88ee4/README.md
https://github.com/nhs-r-community/intro_r_data/blob/c401dc2313e223e38d4a222ec5b292c07b31251f/README.md
https://github.com/nhs-r-community/intro_r/blob/3f6e336f75cc87ca1d1d1dc73c1a6ca2e678f6c6/05-workshop_functions.Rmd

No specific database section

I suggest that many of the analyst users, and managers, may leave the course thinking they can only get data in as flat files. Database connections are necessary and common in R use. I think a brief intro to DBI and how it works with dplyr would be good here, and I'm happy to adapt it from my NHS-R seminar.

Slide with link to original pdf slides is a repeat to this repository

https://nhs-r-community.github.io/intro_r/01-workshop_intro.html#15

The slide probably needs to just refer to this GitHub repository and not the original slides/repository.

Remove 'Remotes' section from DESCRIPTION

I think we should remove the remotes section from the description file, because it blocks users in Posit Cloud from downloading any packages. They don't have permissions to install from github in that session (no credentials I assume), and it just errors out. This derails you if any packages are missing in their project. E.g. when using readr to import data, a couple of people were missing it but couldn't install until I showed them to delete the remote section.

@Lextuga007 @tomjemmett , what do you think?

Rmd's have different default options

The reports 1-3, 10 & 11 have echo = FALSE, whereas 4-9 have echo = TRUE. This could be confusing for development, so we should look to standardise this across all files.

transfer ownership to NHS-R community

1. merge changes from NHS-R-Community/Intro-R
2. rename NHS-R-Community/Intro-R to intro-R-archive
3. transfer ownership of this repository to NHS-R-Community
4. archive the intro-R-archive repository

Accessibility of text

-[X] Check that colour is used appropriately in text
-[X] Capitals are read out often as acronyms so ensure these are not in the text

Reference: https://presentable-user2021.netlify.app/materials/act-02/05-accessible-design/

code chunk not appearing in 01-workshop-intro.Rmd

https://github.com/nhs-r-community/intro_r/blob/main/01-workshop_intro.Rmd#L444

This code chunk does not get displayed in the slides as it does not include echo=TRUE

Update to base R pipe |> from magrittr %>%?

Following the update that's being written for R4DS the move to the base R pipe is recommended which will require updates to the introduction course and materials.

Tagged this as a question as it's open for discussion on which pipe to use/teach.

Space between bullet points

When using NHS-R CSS here, bullet points are very close and overlap because they have paragraph line height. Suggesting increasing them for the li element so bullets are clearly visible.

Indentation error on slide

In the ggplot2 section/Code script the indentation for the first example should have the colour = "red" aligned with the aes() function. Copying and pasting it into an R script should automatically realign or highlighting then using Ctrl+i to indent.

Data file link

The data file link https://github.com/nhs-r-community/intro_r_data/tree/26a2e39bd49d4aa95a8efc5b45c398386e6e4ed4 (which is not directly accessible through the intro_r_data repository https://github.com/nhs-r-community/intro_r_data) only links to a branch where the csv files are. Is that correct or should it be updated with the additional RMarkdown files too? If these modules/branches have two different functions then I suggest an update to the README to explain what the purposes are.

README link to preparation instructions is a 404 page

The text:

If you are attending the course all the course materials and preparation instructions are here.

Needs to go to https://philosopher-analyst.netlify.app/intro-r/nhsr-intro/prework/.

Blank slide

I think https://nhs-r-community.github.io/intro_r/05-workshop_functions.html#10 has code that has eval=FALSE so isn't rendering.

Remove author from the slides

Author is currently me but these should be removed to make it more generic for people to use.

DB exercise download move to data repository?

@chrismainey Should the database exercise and solutions be moved to the data repository where people download the data files? I missed this with the pull request but would be handy, I think, to have everything all together in one download.

Alt text on images

Alt text needs to be added into the pictures and charts. This is probably with ```{r fig.alt=""` for the images but charts may need https://ggplot2.tidyverse.org/reference/get_alt_text.html

Incorrect code on slide

The link on https://intro-r-slides.netlify.app/06-workshop_dplyr.html#57 says na.rm = NA but should say na.rm = TRUE.

Remove <br> code from slides

Many of the slides have
to create line breaks and this can be done in RMarkdown using two spaces at the end of the line to break it up.

Removed:

• Slide deck 01

Links don't open correctly (https://intro-r-rstudio.nhsrcommunity.com/session-intro.html#/reasons-to-use-r)

Hello,

RE: https://intro-r-rstudio.nhsrcommunity.com/session-intro.html#/reasons-to-use-r

The four links open if you right-click and say "open link in new tab" but don't open if you simply left-click

Community
Collaboration
Open coding
Reproducible Analytical Pipelines

Not a big issue but might put some ppl off