TeachingScript_final.Rmd

---
title: "MyFirstRmarkdown"
author: "Ashley Sawle"
date: "2th April 2025"
output:
  html_document:
    toc: false
    toc_float: true
---

```{r setup, message=FALSE}
library(tidyverse)
library(patchwork)
library(knitr)
library(kableExtra)
library(DT)
library(readr)
opts_chunk$set(warning = FALSE, echo = TRUE, cache = TRUE)
```


## The `mtcars` data set

### Description of the data set

There is a popular built-in data set in R called "**mtcars**" (Motor Trend Car
Road Tests), which is retrieved from the 1974 Motor Trend US Magazine. The
dataset contains measurements on *11 different* attributes for *32 different*
cars.

## More inline formatting {#inline_section}

Superscript: 32 = 2^5^

Subscript: Burning petrol creates CO~2~

Code: Later we will used the `tidyverse` package

## Using tab sets {.tabset}

### Bold

This is **bold**.

It is not ~subscript~.

### Italics

This is *italics*

### Strikethrough

This is ~~strikethrough~~

## End the tabs

To end the tabs, start a new section at the same level (or higher) as before.

## A note on linebreaks

Rmarkdown does not recognise a new line as a "line break". This is the next line, but it will stay in the same line of text.

Rmarkdown does not recognise a new line as a "line break".\
To create a break add two (or more) spaces at the end of the previous line.

## Lists (bullet points)

To create an unordered list (bullet points):

* Use an asterisk as the beginning of the line
* Each asterisk is a new bullet
* You can also use "+" or "-"
    - you can create sublists by indenting
    - using the different symbols at different levels is clearer but not 
    necessary
    
To create an ordered list use a number, a lower case letter or "i" for roman
numerals

Some animals:

1. Cat
1. Ferret
1. Dog
    a. Terriers
        i. Jack Russell
        ii. Airedale
    b. Spaniels
48. Goldfish

## Links

Basic syntax is the link text surrounded by square brackes, followed by the link
surrounded by round brackets.

### External links

[Link to the BBC home page](https://www.bbc.co.uk)

### Internal links

These are links within the document. First we need to create a tag for
the header we want to link to by adding `{#tag_name}` after the header.

[Go to inline section](#inline_section)

## Inserting images

Similar syntax to the links, but precede it with an `!`. The first part
becomes a caption

![Vectors in R](images/Vectors-in-R.jpg){width=50%}

## Manual tables

| Name        | Band        |
| :---------: | ----------: |
| Mick        | Stones      |
| John        | Beatles     |
| Paul        | Beatles     |       

## Blockquotes

> There is a popular built-in data set in R called "**mtcars**" (Motor Trend Car
> Road Tests), which is retrieved from the 1974 Motor Trend US Magazine. The
> dataset contains measurements on *11 different* attributes for *32 different*
> cars.

## R code chunks

They look like this

```{r}
x <- 15
y <- 20
x + y
```

## Chunk options

```{r, echo=FALSE}
x <- 19
y <- 20
x + y
```

```{r, include=FALSE}
x <- 19
y <- 90
a <- x + y
```


```{r, eval=FALSE}
x <- 19
y <- 190
a <- x + y
```

## Chunk labels

```{r label}
z <- 10
z^8
```

## The "setup" chunk

Put this at the very start of your script. It should load all necessary packages
and set any global options (see the chunk).

## Tabular output from chunk

```{r smallTable}
smallTable <- mtcars %>%
  rownames_to_column("car") %>%
  select(car, mpg, cyl, wt) %>%
  slice(1:5)
smallTable
```

### The `kable` function

```{r}
smallTable %>%
  kable(digits = 2, align = "c")
```

### The `kableExtra` package

```{r}
smallTable %>%
  kbl() %>%
  kable_styling(bootstrap_options = c("striped")) %>%
  column_spec(column = 1, bold = TRUE, border_right = TRUE)
```


Built in "themes"

```{r}
smallTable %>%
  kbl() %>%
  kable_classic(full_width = F)
```

### Interactive tables with `DT`

```{r}
longTable <- mtcars %>%
  rownames_to_column("car")
longTable %>%
  datatable()
```

Let's:

* remove the search box
* change the number of rows displayed to 5
* add buttons to allow the table to be downloaded
* customize the column names

```{r}
longTable %>%
    datatable(
        extensions = "Buttons",
        options = list(
            dom = "Btip",
            buttons = c("csv", "excel"),
            pageLength = 5),
        colnames = c("Car", "Miles per gallon", "Cylinders", "Weight")
    )
```

```
`dom`:

* l - length changing input control (how many rows to display)
* f - filtering input (search box)
* t - table
* i - table information summary (e.g. “Showing 1 to 10 of 57 entries”)
* p - pagination control (next/previous buttons)
* B - buttons (export buttons)
* r - processing display element (loading indicator)
```

## Plots

If a code chunk generates a plot it will be displayed in the rendered document.
We can control the size of the figure and add a caption using the chunk options.

```{r plot, fig.with=5, fig.height=3, fig.cap=figCap}
figCap <- "Scatter plot of weight vs miles per gallon"
mtcars %>%
    ggplot(aes(x = mpg, y = wt)) +
    geom_point() +
    labs(title = "Scatter plot of weight vs miles per gallon",
         x = "Miles per gallon",
         y = "Weight") +
    theme_minimal()
```

### Combining multiple plots with `patchwork`

```{r, patchwork}
p1 <- mtcars %>%
    mutate(across(cyl, factor)) %>%
    ggplot(aes(x = mpg, y = wt)) +
    geom_point(aes(colour = cyl)) +
    geom_text(label = "A", x = 22.5, y = 3.5, size = 50)
p2 <- mtcars %>%
    mutate(across(cyl, factor)) %>%
    ggplot(aes(x = gear, y = hp)) +
    geom_point(aes(colour = cyl)) +
    geom_text(label = "B", x = 4, y = 195, size = 50)
p1 + p2 
```

We can use `+`, `/` and `|` with brackets to control the layout of the plots.

We can also add annotation(e.g title, subtitle, plot labels).

We can also combine the legends.

```{r}
((p1 + p2) / (p2 + p1 + p2) | (p1 / p2 / p1)) +
    plot_layout(guides = "collect") +
    plot_annotation(title = "Patchwork example",
                    subtitle = "Combining plots with patchwork")
```
 
## Inline code
 
 Finally, it's possible to include inline within markdown sections. 
 
 Useful if we can to include a value from a variable in the text.
 
```{r inline}
six_cyl_mean_mpg <- mtcars %>%
    filter(cyl == 6) %>%
    summarise(mpg = mean(mpg)) %>%
    pull(mpg)
```

The mean mpg of cars with 6 cylinders was **`r six_cyl_mean_mpg`**.

## Session info

Good practice....

```{r}
devtools::session_info()
```