This is a package that facilitates hierarchical set analysis on large collections of sets.

*Hierarchical Set Analysis* is a way to investigate large
numbers of sets. It consists of two things: A novel hierarchical
clustering algorithm for sets and a range of visualizations that builds
on top of the resulting clustering.

**The clustering**, in contrast to more traditional
approaches to hierarchical clustering, does not rely on a derived
distance measure between the sets, but instead works directly with the
set data itself using set algebra. This has two results: First, it is
much easier to reason about the result in a set context, and second, you
are not forced to provide a distance if none exists (sets are completely
independent). The clustering is based on a generalization of Jaccard
similarity, called *Set Family Homogeneity*, that, in its
simplest form, is defined as the size of the intersection of the sets in
the family divided by the size of the union of the sets in the family.
The clustering progresses by iteratively merging the set families that
shows the highest set family homogeneity and is terminated once all
remaining set family pairs have a homogeneity of 0. Note that this means
that the clustering does not necessarily end with the all sets in one
overall cluster, but possibly split into several hierarchies - this is
intentional.

**The visualizations** uses the derived clustering as a
scaffold to show e.g. intersection and union sizes of set combinations.
By narrowing the number of set families to visualize to the branch
points of the hierarchy the number of data points to show is linearly
related to the number of sets under investigation, instead of the
exponential if we chose to show everything. This means that hierachical
set visualizations are much more scalable than e.g.Â UpSet and Radial
Sets, at the cost of only showing combinations of the progressively most
similar sets. Apart from intersection and union sizes there is a
secondary analysis build into hierarchical sets that detects the
elements not conforming to the imposed hierarchy. These *outlying
elements* defines a subset of the universe that deviates from the
rest and can be quite interesting - visualizations to investigate these
are of course also provided.

Hierachical set analysis is obviuously sensible for collections of sets where a hierarchical structure makes sense, but even for set collection that does not obviously support a hierarchy, it can be interesting to look at how the different sets do, or do not, relate to each other.

The stable version is available on CRAN with
`install.packages('hierarchicalSets')`

. Alternatively the
development version can be obtained from GitHub using devtools:

```
if (!require(devtools)) {
install.packages('devtools')
}::install_github('thomasp85/hierarchicalSets') devtools
```

hierarchicalSets comes with a toy dataset containing the followers of
100 prolific anonymous twitter users. To create the hierarchical
clustering you use the `create_hierarchy()`

function.

```
library(hierarchicalSets)
data('twitter')
<- create_hierarchy(twitter)
twitSet
twitSet## A HierarchicalSet object
##
## Universe size: 28459
## Number of sets: 100
## Number of independent clusters: 6
```

To simply have a look at the hierarchy you plot it:

`plot(twitSet)`

Here the x axis is encoded with the *Set Family Heterogeneity*
which is the inverse of the homogeneity. It can thus be interpreted as
the ratio of union to intersection size.

Usually we are interested in the direct numbers which can be provided with another plottype - the intersection stact

`plot(twitSet, type = 'intersectStack', showHierarchy = TRUE)`

We see that especially four sets are very similar, incidentally four of the largest sets. The rightmost cluster is interesting as well as we see it is held together by a very small overlap and that each individual set contains a lot of unique followers.

While it is expected that followers share some of the same patterns in terms of who they follow, it cannot be expected that they fully adhere to a single hierarchy. We can look at how sets are connected across the hierarchy by counting the number of elements they have in common that is not part of their closest shared set family. This can be shown using hierarchical edge bundles:

`plot(twitSet, type = 'outlyingElements', quantiles = 0.8, alpha = 0.2)`

It seems our four sets again draws attention to themselves by having strong connections to a range of other sets distant in terms of the clustering. Also it is obvious that there is two seperate groups of sets in terms of their deviation profile. There might be a secondary structure hidden within the outlying elements. Lets create a hierarchical set clustering based only on the outlying elements:

```
<- outlier_hierarchy(twitSet)
twitSet2
twitSet2## A HierarchicalSet object
##
## Universe size: 14657
## Number of sets: 100
## Number of independent clusters: 7
```

In this way it is possible to gradually shave off hierarchical structures, revealing the uncaptured relations of the prior analysisâ€¦ Happy investigation!

Hierarchical Sets is static on purpose. I firmly belive that effective static plots are the foundation for any good visualization. You can always augment a static visualization with interactivity, but not all interactive visualizations can be used in a static way. That being said, it could be fun to experiment with said augmentation within a shiny app. Also, the implementation begins to struggle (just slow down actually) when being used with thousands of sets and millions of elements - some C++ wizardry might be warranted for such huge datasets.

Another nice idea I have in mind is to be able to keep set and element metadata within the HierarchicalSet object and seemlessly use it for plotting.