01-workshop_intro.Rmd

---
title: "Introduction to R and Rstudio"
subtitle: "Session 1"
institute: "NHS-R Community"
output:
  xaringan::moon_reader:
    css: 
      - default
      - css/nhsr.css
      - css/nhsr-fonts.css
    lib_dir: libs
    seal: false
    self_contained: true
    nature:
      highlightStyle: googlecode
      highlightLines: true
      highlightLanguage: ["r"]
      countIncrementalSlides: false
      ratio: "16:9"
    includes:
      after_body: [css/insert-logo.html]
---

```{r libs, include=FALSE}
library(knitr)
library(tidyverse)
library(xaringan)
library(magick)
library(icons)
library(xaringanExtra)

xaringanExtra::use_share_again() # need to get the slide button on html view

opts_chunk$set(
  echo = FALSE,
  eval = FALSE,
  message = FALSE,
  warning = FALSE,
  fig.width = 7.252,
  fig.height = 4,
  dpi = 300,
  dev.args = list(type = "cairo")
)

```

class: title-slide, left, bottom

# `r rmarkdown::metadata$title`
----
## **`r rmarkdown::metadata$subtitle`**
### `r rmarkdown::metadata$author`
### `r rmarkdown::metadata$date`

---

class: center, middle


# Agenda
Using R Studio  

Importing data  

--------- Break ---------  

Introduction to ggplot2  

What does this function do?  

--------- Lunch -----------  

Data wrangling with dplyr  

Naming objects | Relational data  

--------- Break ---------  

R Markdown  

Ongoing learning  

.green[Finish about 4 - 430pm]  

---

class: center, middle

# Course Aims  

####1. To show you some of the possibilities:  
####2. To give you a feel for how R works.  
####3. To show you enough for you to begin teaching yourself  

.blue[(Excellent free resources available)]


---

class: inverse, middle, center


.left-col[.center[
### elegant
# Graphics
]]

---

[<img class="center" src="img/session01/heatmap_colin_angus.PNG"/>](https://github.com/VictimOfMaths/COVID-19)

---
The original blog is no longer available that featured this

<img class="center" src="img/session01/london_cycle_routes.PNG" width="90%"/>

---

class: center, middle

# Collaboration  

`r icons::fontawesome("arrow-down")`

## Reproducibility

`r icons::fontawesome("arrow-down")`

### R Markdown

---

<img class="center" src="img/session01/automated_reports.PNG"/>

---

# (Interactive) Dashboards

[Mental Health Surge Modelling](https://strategyunit.shinyapps.io/MH_Surge_Modelling/)

<img src="img/session01/mental_health_modelling.PNG"/>

---

[Trafford Data Lab](https://trafforddatalab.shinyapps.io/trafford-tweet-dash/) and the main [site](https://www.trafforddatalab.io/)

<img src="img/session01/twitter_dash.PNG"/>

---

# R to SQL connection


[NHS-R Community Webinar](https://nhsrcommunity.com/learn-r/workshops/database-connections-in-r-webinar)

<img src="img/session01/webinar_nhsr.PNG"/>

---

class: center, middle

# Inclusivity

```{r inclusive, eval=TRUE}

rladies <- magick::image_read('img/session01/r_ladies_twitter.PNG')
mir <- magick::image_read('img/session01/mir_twitter.PNG')
nhsr <- magick::image_read('img/session01/nhsr_twitter.PNG')

img <- c(rladies, mir, nhsr)

magick::image_animate(image_scale(img, "600x600"), fps = 1, dispose = "previous", loop = 6)

```

---

class: inverse, middle, center

.left-col[.center[

## Course Philosophy
]]

---

[Minimum Viable Product](https://blog.crisp.se/2016/01/25/henrikkniberg/making-sense-of-mvp)

.left-col[.center[
<img src="img/session01/mvp.PNG" width="75%"/>
]]

---

class: center, middle

# Course philosophy

Relaxed and informal  

Slides and code are available on [`r icons::fontawesome("github")`   GitHub](https://github.com/nhs-r-community/intro_r)    

The truth; but it can’t be the whole truth…  
too much to cover in a day

---

class: inverse, middle, center

# Let's begin

---

class: center, middle

## R vs. RStudio
R is a programming language  

RStudio is a software application with tools to  

improve your programming experience

---

<img class="center" src="img/session01/race_car.PNG"/>

---

<img class="center" src="img/session01/roberto-nickson-unsplash.PNG"/>

---

# RStudio  

Many excellent features to help you with your analyses.  

Never again have to think about R and RStudio as separate:

Opening R Studio opens an R session.  

Analogy from the book Modern Dive:
[www.moderndive.com](https://moderndive.com/)

---

class: center, middle

# Open RStudio  

R Studio opens an R session

---

.left-column[
The Console is your window to R.  

You can code directly in the console…  

pi*2 <kbd> Enter </kbd>  
37/12 <kbd> Enter <kbd>  
… but there is a better way…
]

.right-column[

<img src="img/session01/rstudio_console.PNG"/>

]

---

.left-column[

#### The Editor  

If you don’t see the Editor pane, click top right button  

And choose "R Script" from the drop down.  

Or, shortcut:  
<kbd> Ctrl + Shift + N </kbd>  

.blue[The cloud shortcut is <kbd> Ctrl + Shift + Alt + N </kbd>]
]

.pull-right[

<img src="img/session01/new_file.PNG"/>

]
---

.left-column[
The Editor is just like any other text  
editor: you can copy, paste, and save text.  

<kbd> Ctrl + Z </kbd> undoes *but*  
<kbd> Ctrl + Shift + Z </kbd> to redo   
(.blue[not <kbd> Ctrl + y</kbd>])  

Different text is coloured  
(the console is uniform)  

Autocomplete  

<kbd>Ctrl + Enter </kbd>  
(sends line of  
code to Console)
]

.right-column[
<img src="img/session01/editor.PNG"/>
]

---

.left-column[
Comment code with a #  

E.g # this was a bad idea

Comment frequently, at least in the beginning

]

.right-column[
<img src="img/session01/editor.PNG"/>
]

---

# Tools -> Options

[Reasons why this is default](https://community.rstudio.com/t/defaults-of-saving-and-restoring-workspace/939)

<img class="center" src="img/session01/global_options.PNG"/>

---

# Tools -> Options

Accessbility and comfort for all

<img class="center" src="img/session01/appearance.PNG"/>

---

class: center, middle

# Packages  

### R packages are like apps for your phone:


--

Extend the capabilities of the basic or "base R"  
with extra functions, datasets, documentation.

---

<img class="center" src="img/session01/app_analogy.PNG"/>

---

# Packages

Quotations in R can be either "" or '' but cannot be mixed:

```{r echo=TRUE}

# either
install.packages("tidyverse")

# or
install.packages('tidyverse')
```


will download a package to your personal library. Then:  

```{r echo=TRUE}
library(tidyverse) 
```

This tells R to load the package from your personal library and is .blue[needed for every new session/script]

---

class: center, middle

## CRAN repository

[Comprehensive R Archive Network](https://cran.r-project.org/web/packages/)  

18,903 packages (April 2022). Free. Peer reviewed.  


(Manifold possibilities) eg. interactive graphics and  

dashboards, machine learning, mine twitter data,  

create PowerPoint docs, maps…  


## GitHub

Many useful packages in development or subject to a lot of change are not on CRAN and are available through GitHub including [{NHSRtheme}](https://github.com/nhs-r-community/NHSRtheme). These won't be peer reviewed.

## ROpenSci

ROpenSci offer a peer reviewed ecosystem of R packages through GitHub including UKHSA's [{fingertipsR}](https://github.com/ropensci/fingertipsR)

---

<img class="center" src="img/session01/tidyverse.PNG"/>

---

class: center, middle

## What is the tidyverse?  

The [tidyverse package](https://www.tidyverse.org/) collects (some of) the most popular  
R packages into one.  

All have the same underlying principles:

Provide simple tools (with consistent structure) which may  
be used together to help solve complex problems.

---

class: center, middle

## What is the tidyverse?

During the workshop we will use the [ggplot2](https://ggplot2.tidyverse.org/), [dplyr](https://dplyr.tidyverse.org/),  
and [readr](https://readr.tidyverse.org/) packages. These are bundled up in the  
tidyverse package. Load it by running:  


```{r, echo=TRUE}
library(tidyverse)
```

---

# Output

Information - what was loaded and potential conflicts

```
-- Attaching packages ------------------------------------------ tidyverse 1.3.0 --
v ggplot2 3.3.3     v purrr   0.3.4
v tibble  3.1.0     v dplyr   1.0.4
v tidyr   1.1.2     v stringr 1.4.0
v readr   1.4.0     v forcats 0.5.1
-- Conflicts --------------------------------------------- tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
```

Warnings - not errors, just information on versions

```
Warning messages:
1: package ‘tidyverse’ was built under R version 4.0.4 
2: package ‘tidyr’ was built under R version 4.0.3 
3: package ‘readr’ was built under R version 4.0.3 
4: package ‘purrr’ was built under R version 4.0.3 
5: package ‘dplyr’ was built under R version 4.0.3 
6: package ‘stringr’ was built under R version 4.0.3 
```

---

#### This work is licensed as  
Creative Commons  
Attribution  
ShareAlike 4.0  
International  
To view a copy of this license, visit  
https://creativecommons.org/licenses/by/4.0/  

---

name: goodbye
class: middle, inverse

# **Thank you!**  

Acknowledgements: for creating the original training slides and delivering training:

Andrew Jones | Ozayr Mohammed  
Healthcare Analysts | The Strategy Unit

[`r icons::fontawesome("paper-plane")` andrew.jones40@nhs.net](mailto:andrew.jones40@nhs.net)  

[`r icons::fontawesome("paper-plane")` ozayr.mohammed@nhs.net](mailto:ozayr.mohammed@nhs.net)

And to Silvia Canelón who created the Xaringan presentation using NHS and NHR-R colour branding and shared this at the 2020 [NHS-R Community conference](https://spcanelon.github.io/xaringan-basics-and-beyond/index.html).  

Details of the workshops she ran at the [NHS-R Community conference](https://spcanelon.github.io/xaringan-basics-and-beyond/index.html).

And to Zoë Turner who converted the presentation to Xaringan. [`r icons::fontawesome("paper-plane")` zoe.turner2@notthshc.nhs.uk](mailto:zoe.turner2@nottshc.nhs.uk)