---
title: "Introducing eulerr"
author: "Johan Larsson"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Introducing eulerr}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
bibliography: eulerr.bib
---

```{r}
#| label: setup
#| include: false

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

options(digits = 4)
```

## Motivation

**eulerr** generates area-proportional euler diagrams that display set
relationships (intersections, unions, and disjoints) with circles, ellipses, or
axis-aligned rectangles and squares. [Euler
diagrams](https://en.wikipedia.org/wiki/Euler_diagram) are Venn diagrams without
the requirement that all set interactions be present (whether they are empty or
not). That is, depending on input, eulerr will sometimes produce Venn diagrams
but sometimes not.

R features several packages that produce Euler diagrams; some of the more
prominent ones (on CRAN) are

- [eVenn](https://cran.r-project.org/package=eVenn),
- [VennDiagram](https://cran.r-project.org/package=VennDiagram)
- [venn](https://cran.r-project.org/package=venn)
- [colorfulVennPlot](https://cran.r-project.org/package=colorfulVennPlot), and
- [venneuler](https://cran.r-project.org/package=venneuler).

The last of these (**venneuler**) was the primary inspiration for this package,
along with the refinements that Fredrickson has presented on his
[blog](http://www.benfrederickson.com/) and made available in his javascript
[venn.js](https://github.com/benfred/venn.js).
[eulerAPE](https://www.eulerdiagrams.com/eulerAPE/), which was the first program
to uses ellipses instead of circles, has also been instrumental in the design of
**eulerr**. The downside to **eulerAPE** is that it only handles three sets that
all need to intersect.

**venneuler**, on the other hand, will take any number of sets (in theory), yet
has been known to produce [imperfect
solutions](http://benfred.github.io/venn.js/tests/venneuler_comparison/) for set
configurations that have perfect such. And unlike **eulerAPE**, it is restricted
to circles (as is **venn.js**).

## Enter eulerr

**eulerr** is based on the improvements to venneuler that Ben Fredrickson
introduced with **venn.js** but has been programmed from scratch, uses different
optimizers, and returns statistics featured in **venneuler** and **eulerAPE** as
well as allows a range of different inputs and conditioning on additional
variables. Moreover, it can model set relationships with ellipses for any number
of sets involved.

## Input

At the time of writing, it is possible to provide input to **eulerr** as either

- a named numeric vector with set combinations as disjoint set combinations or
  unions (depending on how the argument `type` is set in `euler()`),
- a matrix or data frame of logicals with columns representing sets and rows the
  set relationships for each observation,
- a list of sample spaces, or
- a table.

```{r}
#| label: input

library(eulerr)

# Input in the form of a named numeric vector
fit1 <- euler(c(
  "A" = 25,
  "B" = 5,
  "C" = 5,
  "A&B" = 5,
  "A&C" = 5,
  "B&C" = 3,
  "A&B&C" = 3
))

# Input as a matrix of logicals
set.seed(1)
mat <- cbind(
  A = sample(c(TRUE, TRUE, FALSE), 50, TRUE),
  B = sample(c(TRUE, FALSE), 50, TRUE),
  C = sample(c(TRUE, FALSE, FALSE, FALSE), 50, TRUE)
)
fit2 <- euler(mat)
```

We inspect our results by printing the eulerr object

```{r}
#| label: print

fit2
```

or directly access and plot the residuals.

```{r}
#| label: residual-plot
#| fig-cap: "Residuals for the fit diagram."

# Cleveland dot plot of the residuals
dotchart(resid(fit2))
```

We can also use **eulerr**'s built in `error_plot()` function to diagnose the
fit.

``{r error-plot, fig.cap = "A plot from `error_plot()`."} error_plot(fit2)``

This shows us that the \code{A\&C} intersection is somewhat overrepresented in
\code{fit2}. Given that these residuals are on the scale of the original values,
however, the residuals are arguably of little concern.

As an alternative, we could plot the circles in another program by retrieving
their coordinates and radii.

```{r}
#| label: coefs

coef(fit2)
```

### Goodness-of-fit

To tell if we can trust our solution, we use two goodness-of-fit measures: the
stress statistic from **venneuler**\ [@wilkinson_exact_2012],

$$
  \frac{\sum_{i=1}^{n} (y_i - \hat{y}_i)^2}{\sum_{i=1}^{n} y_i ^ 2}
$$

where $\hat{y}_i$ is an ordinary least squares estimate from the regression of
the fitted areas on the original areas that is being explored during
optimization,

and the *diagError* statistic from **eulerAPE**\ [@Micallef_2014a]:

$$
  \max_{i = 1, 2, \dots, n} \left| \frac{y_i}{\sum y_i} -
  \frac{\hat{y}_i}{\sum \hat{y}_i} \right|
$$

In our example, the diagError is `r fit2$diag_error` and our stress is
`r fit2$stress`, suggesting that the fit is accurate.

We can now be confident that eulerr provides a reasonable representation of our
input using circles. Were it otherwise, we might try a different shape via the
`shape` argument --- `"ellipse"` is the most expressive choice, but axis-aligned
`"rectangle"` and `"square"` fits are also available.\ [@wilkinson_exact_2012]
features a difficult combination that ellipses manage to fit with a reasonably
small error; with **eulerr**, however, we can get rid of that error entirely.

```{r}
#| label: wilkinson2012
#| fig-cap: "A difficult combination from Wilkinson 2012."

wilkinson2012 <- c(
  A = 4,
  B = 6,
  C = 3,
  D = 2,
  E = 7,
  F = 3,
  "A&B" = 2,
  "A&F" = 2,
  "B&C" = 2,
  "B&D" = 1,
  "B&F" = 2,
  "C&D" = 1,
  "D&E" = 1,
  "E&F" = 1,
  "A&B&F" = 1,
  "B&C&D" = 1
)
fit3 <- euler(wilkinson2012, shape = "ellipse")
plot(fit3)
```

If we still lack a good fit after having tried ellipses, we would do best to
stop here and look for another way to visualize our data. (I suggest the
excellent [UpSetR](https://cran.r-project.org/package=UpSetR) package.)

### Visualization

No we get to the fun part: plotting our diagram. This is easy, as well as highly
customizable, with **eulerr**. The default parameters can easily be adjusted to
suit anybody's needs.

```{r}
#| label: eulerr-plot
#| fig-cap: "Customizing Euler plots is a breeze in eulerr."

plot(fit2)

# Switch to squares for the same set combination, customizing borders,
# labels, and quantities. The `shape` argument also accepts `"ellipse"`
# and `"rectangle"`.
plot(
  euler(mat, shape = "square"),
  quantities = TRUE,
  fill = "transparent",
  lty = 1:3,
  labels = list(font = 4)
)
```

Plotting is provided through a custom plotting method built on top of the
excellent facilities made available by the core R package **grid**. **eulerr**'s
default color palette is chosen to be color deficiency-friendly.

## Acknowledgements

**eulerr** would not be possible without Ben Fredrickson's work on **venn.js**
or Leland Wilkinson's **venneuler**.

## References
