Prework.knit

# Modelling and quantifying mortality and longevity risk 
## Prework

### Katrien Antonio, Torsten Kleinow, Frank van Berkum, Michel Vellekoop and Jens Robben
### <a href="https://gitfront.io/r/jensrobben/mUZ8CcDz5x1L/Lausanne-summer-school/">35th International Summer School of the Swiss Association of Actuaries </a> | June 3-7, 2024
###  <a> </a>

---

# Introduction

### Workshop

<img align="left" src="img/gitfront.png" width="35" hspace="10"/> https://gitfront.io/r/jensrobben/mUZ8CcDz5x1L/Lausanne-summer-school/

The workshop's landing page on GitFront, where we upload slide decks, R code and data sets.

### Us

[Katrien Antonio](https://katrienantonio.github.io) [<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#106EB6;overflow:visible;position:relative;"><path d="M64 112c-8.8 0-16 7.2-16 16v22.1L220.5 291.7c20.7 17 50.4 17 71.1 0L464 150.1V128c0-8.8-7.2-16-16-16H64zM48 212.2V384c0 8.8 7.2 16 16 16H448c8.8 0 16-7.2 16-16V212.2L322 328.8c-38.4 31.5-93.7 31.5-132 0L48 212.2zM0 128C0 92.7 28.7 64 64 64H448c35.3 0 64 28.7 64 64V384c0 35.3-28.7 64-64 64H64c-35.3 0-64-28.7-64-64V128z"/></svg>](mailto:katrien.antonio@kuleuven.be) &nbsp; &nbsp; &nbsp; [Michel Vellekoop](https://www.uva.nl/profiel/v/e/m.h.vellekoop/m.h.vellekoop.html) [<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#106EB6;overflow:visible;position:relative;"><path d="M64 112c-8.8 0-16 7.2-16 16v22.1L220.5 291.7c20.7 17 50.4 17 71.1 0L464 150.1V128c0-8.8-7.2-16-16-16H64zM48 212.2V384c0 8.8 7.2 16 16 16H448c8.8 0 16-7.2 16-16V212.2L322 328.8c-38.4 31.5-93.7 31.5-132 0L48 212.2zM0 128C0 92.7 28.7 64 64 64H448c35.3 0 64 28.7 64 64V384c0 35.3-28.7 64-64 64H64c-35.3 0-64-28.7-64-64V128z"/></svg>](mailto:m.h.vellekoop@uva.nl) &nbsp; &nbsp;  [Torsten Kleinow](https://www.uva.nl/profiel/k/l/t.kleinow/t.kleinow.html) [<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#106EB6;overflow:visible;position:relative;"><path d="M64 112c-8.8 0-16 7.2-16 16v22.1L220.5 291.7c20.7 17 50.4 17 71.1 0L464 150.1V128c0-8.8-7.2-16-16-16H64zM48 212.2V384c0 8.8 7.2 16 16 16H448c8.8 0 16-7.2 16-16V212.2L322 328.8c-38.4 31.5-93.7 31.5-132 0L48 212.2zM0 128C0 92.7 28.7 64 64 64H448c35.3 0 64 28.7 64 64V384c0 35.3-28.7 64-64 64H64c-35.3 0-64-28.7-64-64V128z"/></svg>](mailto:t.kleinow@uva.nl) &nbsp; &nbsp; &nbsp; [Frank van Berkum](https://www.uva.nl/profiel/b/e/f.vanberkum/f.vanberkum.html) [<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#106EB6;overflow:visible;position:relative;"><path d="M64 112c-8.8 0-16 7.2-16 16v22.1L220.5 291.7c20.7 17 50.4 17 71.1 0L464 150.1V128c0-8.8-7.2-16-16-16H64zM48 212.2V384c0 8.8 7.2 16 16 16H448c8.8 0 16-7.2 16-16V212.2L322 328.8c-38.4 31.5-93.7 31.5-132 0L48 212.2zM0 128C0 92.7 28.7 64 64 64H448c35.3 0 64 28.7 64 64V384c0 35.3-28.7 64-64 64H64c-35.3 0-64-28.7-64-64V128z"/></svg>](mailto:F.vanBerkum@uva.nl) &nbsp; &nbsp; [Jens Robben](https://jensrobben.github.io) [<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#106EB6;overflow:visible;position:relative;"><path d="M64 112c-8.8 0-16 7.2-16 16v22.1L220.5 291.7c20.7 17 50.4 17 71.1 0L464 150.1V128c0-8.8-7.2-16-16-16H64zM48 212.2V384c0 8.8 7.2 16 16 16H448c8.8 0 16-7.2 16-16V212.2L322 328.8c-38.4 31.5-93.7 31.5-132 0L48 212.2zM0 128C0 92.7 28.7 64 64 64H448c35.3 0 64 28.7 64 64V384c0 35.3-28.7 64-64 64H64c-35.3 0-64-28.7-64-64V128z"/></svg>](mailto:jens.robben@kuleuven.be)

---

# Checklist

---

# What's out there - the R universe

---

# What is R?

> <font size="+2"> <p align="justify">The R environment is an integrated suite of software facilities for data manipulation, calculation and graphical display.</p></font>

</br>

A brief history:

- R is a dialect of the S language.

- R was written by .hi-RCLRbg[R]obert Gentleman and .hi-RCLRbg[R]oss Ihaka in 1992.

- The R source code was first released in 1995.

- In 1998, the Comprehensive R Archive Network [CRAN](http://CRAN.R-project.org/) was established.

- The first official release, R version 1.0.0, dates to 2000-02-29. Currently R 4.4.0 (April, 2024).

- R is open source via the [GNU General Public License](https://en.wikipedia.org/wiki/GNU_General_Public_License).

---

# Explore the R architecture

- R is like a car's engine (source: [https://moderndive.com/1-getting-started.html](https://moderndive.com/1-getting-started.html))

- RStudio is like a car's dashboard, an integrated development environment (IDE) for R.

R: Engine            |  RStudio: Dashboard
:-------------------------:|:-------------------------:
<img src="img/engine.jpg" alt="Drawing" style="height: 300px;"/>  |  <img src="img/dashboard.jpg" alt="Drawing" style="height: 300px;"/>

---

# How do I code in R?

Keep in mind:

- unlike other software like Excel, STATA, or SAS, R is an interpreted language

- no point and click in R!

- .hi-RCLRbg[you have to program in R]!

R .hi-RCLRbg[packages] extend the functionality of R by providing additional functions, and can be downloaded for free from the internet.

R: A new phone           |  R Packages: Apps you can download
:-------------------------:|:-------------------------:
<img src="img/iphone.jpg" alt="Drawing" style="height: 150px;"/>  |  <img src="img/apps.jpg" alt="Drawing" style="height: 150px;"/>

---

# How to install and load an R package?

Install the {ggplot2} package for data visualisation

```r
install.packages("ggplot2")
```

Load the installed package

```r
library(ggplot2)
```

And give it a try

```r
head(diamonds)
ggplot(diamonds, aes(clarity, fill = cut)) + 
  geom_bar() + theme_bw()
```

Packages are developed and maintained by R users worldwide.

They are shared with the R community through CRAN: now 20 770 packages online (on May 25, 2024)!

]

]

---

# Why R and RStudio?

### Data science positivism

- Next to Python, R has become the *de facto* language for data science, with an extensive *machine learning toolbox*.
- See: [The Popularity of Data Science Software](http://r4stats.com/articles/popularity/)
- R is open-source with a very active community of users spanning academia and industry.

### Bridge to actuarial science, econometrics and other tools

- R has all of the statistics and econometrics support, and is adaptable as a “glue” language to other programming languages and APIs.
- Widely used in actuarial undergraduate programs.
- Advantages during the Summer School: allows to use a variety of visualization tools, data handling functions, statistical and machine learning functionalities, and a toolbox for simulations.

### Disclaimer + Read more

- It's also the language that we know best. 
- If you want to read more: [R-vs-Python](https://blog.rstudio.com/2019/12/17/r-vs-python-what-s-the-best-for-language-for-data-science/), [when to use Python or R](https://www.datacamp.com/community/blog/when-to-use-python-or-r) or [Hadley Wickham on the future of R](https://qz.com/1661487/hadley-wickham-on-the-future-of-r-python-and-the-tidyverse/)

---

background-image: url("img/tidyverse2.1.png")
background-size: cover
background-size: 65% 
background-position: center

---

# Welcome to the tidyverse!

><p align="justify">The .hi-RCLRbg[tidyverse] is an opinionated collection of R packages designed for data science. All packages share an underlying design philosophy, grammar, and data structures. </p>

More on: [tidyverse](https://www.tidyverse.org).

Install the packages with `install.packages("tidyverse")`. Then run `library(tidyverse)` to load the core tidyverse.

---

# Principles of tidy data

Three interrelated rules from the [R for data science](https://r4ds.had.co.nz/) book by Garrett Grolemund and Hadley Wickham:

1. Each variable must have its own column.
2. Each observation must have its own row.
3. Each value must have its own cell.

.footnote[This figure is taken from Chapter 12 on Tidy data in [R for data science](https://r4ds.had.co.nz/).]

---

# Workflow of a data scientist

Here is a model of the .hi-pink[tools needed in a typical data science project]:

> <p align="justify"> Together, tidying and transforming are called <b>wrangling</b>, because getting your data in a form that’s natural to work with often feels like a fight! </p>

> <p align="justify"> Models are complementary tools to visualisation. Once you have made your questions sufficiently precise, you can use a model to answer them. Models are a fundamentally <b>mathematical or computational tool</b>, so they generally scale well. But every model makes <b>assumptions</b>, and by its very nature a model cannot question its own assumptions. That means <b>a model cannot fundamentally surprise you</b>.</p>

---

# Data wrangling and visualisation

---

# A tibble instead of a data.frame <img src="img/tibble.png" class="title-hex">

Within the tidyverse `tibble` is a modern take on a `data.frame`:

- keep the features that have stood the test of time

- drop the features that used to be convenient but are now frustrating.

You can use:

- `tibble()` to create a new tibble

- `as_tibble()` transforms an object (e.g., a data frame) into a tibble.

Quick example: explore the differences!

```r
mtcars
# install.packages("tidyverse")
library(tidyverse)
as_tibble(mtcars)
```

---

# Chains with the pipe operator <img src="img/pipe.png" class="title-hex">

In R, the pipe operator is `%>%`.

It takes the output of one statement and makes it the input of the next statement.

When describing it, you can think of it as a “THEN”; with this operator it becomes easy to chain a sequence of calculations.

For example, when you have an input data and want to call functions `foo` and `bar` in sequence, you can write `data %>% foo %>% bar`.

A first example:

- take the `diamonds` data (from the {ggplot2} package)

- then subset

```r
diamonds %>% filter(cut == "Ideal")
```

Some excellent blog posts about this operator: [Pipes in R tutorial for beginners](https://www.datacamp.com/community/tutorials/pipe-r-tutorial) and [how to write this in base R](https://gist.github.com/hadley/c430501804349d382ce90754936ab8ec).

---

# Data manipulation verbs <img src="img/dplyr.png" class="title-hex">

The {dplyr} package holds many useful data manipulation verbs:

- `mutate()` adds new variables that are functions of existing variables

- `select()` picks variables based on their names

- `filter()` picks cases based on their values

- `summarise()` reduces multiple values down to a single summary

- `arrange()` changes the ordering of the rows.

These all combine naturally with `group_by()` which allows you to perform any operation “by group”.

A first example:

```r
diamonds %>% mutate(price_per_carat = price/carat) %>% filter(price_per_carat > 1500)
```

```r
diamonds %>% group_by(cut) %>% summarize(price = mean(price), carat = mean(carat))
```

---

<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css">

## <i class="fa fa-edit"></i> <br> Your turn

]

To get warmed up, let's do some .hi-RCLRbg[basic explorations] of the {tidyverse} instructions. The idea is to get some feel for these functions.

1.1. Create a data frame (with `data.frame(.)`) or tibble (with `tibble(.)`) `df` with two variables `x` and `y`. Enter some values for these variables.

1.2. Create a new variable `z` that is the sum of `x` and `y`. Use `base` R instructions and then use the pipe operator and `mutate(.)`.

2.1. Create a new data vector `v` with some entries, use `c(.)`.

2.2. Try the following instructions:

```r
round(mean(x), 2)
mean(x) %>% round(2)
x %>% mean %>% round(2)
```

]

---

First, you put together the `data.frame`

```r
df <- data.frame(x = c(0, 1), y = c(0, 1))
df 
```

or the `tibble`

```r
df <- tibble(x = c(0, 1), y = c(0, 1))
df 
```

Next, you create a new variable

```r
df$z <- df$x + df$y 
df
```

or with `mutate(.)`

```r
df %>% mutate(z = x+y)
df
```

]

You create a vector `x` with some entries

```r
x <- c(0.157, 0.135, 0.359)
```

and then you evaluate

```r
round(mean(x), 2)
mean(x) %>% round(2)
x %>% mean %>% round(2)
```

These implementations all lead to the same result:

```
## [1] 0.22
```

Which one do you find most intuitive?

]

---

# Plots with ggplot2 <img src="img/ggplot2.png" class="title-hex">

The aim of the {ggplot2} package is to create elegant data visualisations using the .hi-pink[grammar of graphics].

Here are the basic steps:

- begin a plot with the function `ggplot()` creating a coordinate system that you can add layers to

- the first argument of `ggplot()` is the dataset to use in the graph

A first example

```r
library(ggplot2)
ggplot(data = mpg)
ggplot(mpg)
```

creates an empty graph.

You will now add layers to this graph!

---

# Plots with ggplot2 <img src="img/ggplot2.png" class="title-hex">

You complete your graph by adding one or more .hi-pink[layers] to `ggplot()`.

For example:

- `geom_point()` adds a layer of points to your plot, which creates a scatterplot

- `geom_smooth()` adds a smooth line

- `geom_bar` a bar plot

and many more, see [ggplot2 documentation](https://ggplot2.tidyverse.org/).

Each `geom` function in `ggplot2` takes an aesthetic mapping argument:

- maps variables in your dataset to visual properties

- always paired with `aes()` and the `$x$` and `$y$` arguments of `aes()` specify which variables to map to the `$x$` and `$y$` axes.

---

```r
library(ggplot2)
ggplot(mpg, `aes(displ, hwy, colour = class)`) + 
  `geom_point()` + `theme_bw()`

```

]

.pull-right[
  
Extend the empty graph now with (here: global) aesthetic mapping argument `aes(displ, hwy, colour = class)`.

This implies: `displ` on the x-axis, `hwy` on the y-axis and `class` to differentiate the color of the plotting symbol.

With `geom_point` you add a layer of points to the empty graph.

`theme_bw()` changes the `ggtheme` to a simple black-and-white theme.

]

---

# What else is there?

Recall

There are .hi-RCLRbg[(multiple) alternative ways] to do what the packages and functions in the tidyverse do.

For instance:

- base R
- the {data.table} package

You can read more about comparisons on e.g. [how to write this in base R](https://gist.github.com/hadley/c430501804349d382ce90754936ab8ec) or [Base R, the tidyverse, and data.table: a comparison of R dialects to wrangle your data](https://wetlandscapes.com/blog/a-comparison-of-r-dialects/).

---

# Thanks!   <img src="img/xaringan.png" class="title-hex" width="50" height="50" align="right">

Slides created with the R package [xaringan](https://github.com/yihui/xaringan).
<br> <br> <br>
Course material available via 
<br>

<img align="left" src="img/gitfront.png" width="35" hspace="10"/> https://gitfront.io/r/jensrobben/mUZ8CcDz5x1L/Lausanne-summer-school/