vtree is a flexible tool for calculating and displaying variable trees — diagrams that show information about nested subsets of a data frame. vtree can be used to:
explore a data set interactively
produce customized figures for reports and publications.
Note, however, that vtree is not designed to build or display decision trees.
Given a data frame and simple specifications, vtree will produce a variable tree and automatically label it with counts, percentages, and other summaries.
The sections below introduce variable trees and provide an overview
of the features of vtree. Or you can skip ahead
and start using the
Subsets play an important role in almost any data analysis.
Imagine a data set of countries that includes variables named
landlocked. Suppose we wish to examine subsets of the data
set based on the
continent variable. Within each of these
subsets, we could examine nested subsets based on the
population variable, for example, countries with
populations under 30 million and over 30 million. We might continue to a
third nesting based on the
Nested subsets are at the heart of questions like the following: Among African countries with a population over 30 million, what percentage are landlocked? The variable tree below provides the answer:
By default, vtree uses the colorful display above (to help distinguish variables and values), but if you prefer a more sedate version, you can specify a single fill color (or simply white):
Even in simple situations like this, it can be a chore to keep track of nested subsets and calculate the corresponding percentages. The denominator used to calculate percentages may also depend on whether the variables have any missing values, as discussed later. Finally, as the number of variables increases, the magnitude of the task balloons, because the number of nested subsets grows exponentially. vtree provides a general solution to the problem of calculating nested subsets and displaying information about them.
Nested subsets arise in all kinds of situations. Consider, for example, flow diagrams for clinical studies, such as the following CONSORT-style diagram, produced by vtree.
Both the structure of this variable tree and the numbers shown were automatically determined. When manual calculation and transcription are instead used to populate diagrams like this, mistakes are likely. And although the errors that make it into published articles are often minor, they can sometimes be disastrous. One motivation for developing vtree was to make flow diagrams reproducible. The ability to reproducibly generate variable trees also means that when a data set is updated, a revised tree can be automatically produced.
At the end of this vignette, there is a collection of examples of variable trees using R datasets that you can try.
The examples that follow use a data set called
which represents 46 fictitious patients. We’ll start by using just two
variables, although variable trees are especially useful with three or
more variables. The variable tree below depicts subsets defined by
Sex (M or F) nested within subsets defined by disease
Severity (Mild, Moderate, Severe, or NA).
A variable tree consists of nodes connected by arrows. At the top of the diagram above, the root node of the tree contains all 46 patients. The rest of the nodes are arranged in successive layers, where each layer corresponds to a specific variable. Note that this highlights one difference between variable trees and some other kinds of trees: each layer of a variable tree corresponds to just one variable. (In a decision tree, by contrast, different branches can have different sequences of variable splits.)
Continuing with the variable tree above, the nodes immediately below
the root represent values of
Severity and are referred to
as the children of the root node. In this case,
Severity was missing (NA) for 6 patients, and there is a
node for these patients. Inside each of the nodes, the number of
patients is displayed and—except for in the missing value node—the
corresponding percentage is also shown. Note that, by default,
vtree displays “valid” percentages, i.e. the denominator
used to calculate the percentage is the total number of
non-missing values, 40.
The final layer of the tree corresponds to values of
Sex. These nodes represent males and females within
subsets defined by each value of
Severity. In each of
these nodes the percentage is calculated in terms of the number of
patients in its parent node.
Like any node, a missing-value node can have children. For example,
of the 6 patients for whom
Severity is missing, 3 are
female and 3 are male. By default,
vtree displays the full
missing-value structure of the specified variables.
Also by default,
vtree automatically assigns a color
palette to the nodes of each variable.
Severity has been
assigned red hues (lightest for Mild, darkest for Severe), while
Sex has been assigned blue hues (light blue for females,
dark blue for males). The node representing missing values of
Severity is colored white to draw attention to it.
A tree with two variables is similar to a two-way contingency table.
In the example above,
Sex is shown within levels of
Severity. This corresponds to the following contingency
table, where the percentages within each column add to 100%. These are
called column percentages.
|F||11 (58%)||11 (69%)||2 (40%)||3 (50%)|
|M||8 (42%)||5 (31%)||3 (60%)||3 (50%)|
Likewise, a tree with
Severity shown within levels of
Sex corresponds to a contingency table with row
While the contingency table above is more compact than the corresponding variable tree, some people find the variable tree more intuitive. When three or more variables are of interest, multi-way contingency tables are often used. These are typically displayed using several two-way tables, but as the number of variables increases, these become increasingly difficult to interpret. Variable trees, on the other hand, have the same simple structure regardless of the number of variables.
Note that contingency tables are not always more compact than variable trees. When most cells of a large contingency table are empty (in which case the table is said to be sparse), the corresponding variable tree may be more compact since empty nodes are not shown.
vtree is designed to be quick and easy to use, so that it is convenient for data exploration, but also flexible enough that it can be used to prepare publication-ready figures. To generate a basic variable tree, it is only necessary to specify a data frame and some variable names. However extra features extend this basic functionality to provide:
flexible pruning to remove parts of the tree that are of lesser interest, which is particularly useful when a tree gets large;
display of information about other variables in each node, including a variety of summary statistics;
automatic generation of PNG image files and embedding in R Markdown documents; and
interactive panning and zooming using the
function to launch a Shiny app.
In many cases, you may wish to generate several different variable trees to investigate a collection of variables in a data frame. For example, it is often useful to change the order of variables, prune parts of the tree, etc.
A formal description of variable trees follows.
The root node of the variable tree represents the entire data frame. The root node has a child for each observed value of the first variable that was specified. Each of these child nodes represents a subset of the data frame with a specific value of the variable, and is labeled with the number of observations in the subset and the corresponding percentage of the number of observations in the entire data frame. The nth layer below the root of the variable tree corresponds to the nth variable specified. Apart from the root node, each node in the variable tree represents the subset of its parent defined by a specific observed value of the variable at that layer of the tree, and is labeled with the number of observations in that subset and the corresponding percentage of the number of observations in its parent node.
Note that a node always represents at least one observation. And unlike a contingency table, which can have empty cells, a variable tree has no empty nodes.
Consider a data frame named
df, which includes discrete
v2. Suppose we wish to
produce a variable tree showing subsets based on values of
v1 as well as subsets of those subsets based on values of
v2. The variable tree can be displayed using the following
Alternatively, you may wish to assign the output of
vtree to an object:
<- vtree(df,"v1 v2")simple_tree
Then it can be displayed later using:
vtree is called without a list of variables:
In this case, only the root node is shown, representing the entire data frame. Although a tree with just one node might not seem very useful, we’ll see later that summary information about the whole data frame can be displayed there.
vtree function has numerous optional parameters. For
example, by default
vtree produces a horizontal tree (that
is, a tree that grows from left to right). To generate a vertical tree,
This section introduces some basic features of the
To display a variable tree for a single variable, say
Severity, use the following command:
By default, next to each layer of the tree, a variable name is shown.
In the example above, “Severity” is shown below the corresponding nodes.
(For a vertical tree, “Severity” would be shown to the left of the
nodes.) If you specify
showvarnames=FALSE, no variable
names will be shown.
vtree can also be used with dplyr. For example, to
Severity variable as
HowBad, we can
pipe the data frame into the
rename function in dplyr, and
then pipe the result into
library(dplyr) %>% rename("HowBad"=Severity) %>% vtree("HowBad")FakeData
vtree also has a built-in
way of renaming variables, which is an alternative to using
Large variable trees can be difficult to display in a readable way. One approach that helps is to display the count and percentage on the same line in each node. For example, in the tree above, the label for the Moderate node is on two lines, like this:
sameline=TRUE results in single-line labels,
Moderate, 16 (40%)
By default, vtree shows “valid percentages”, i.e. percentages
calculated using the total number of non-missing values as
denominator. In the case of
Severity, there are 6 missing
values, so the denominator is 46 - 6, or 40. There are 19 Mild cases,
and 19/40 = 0.475 so the percentage shown is 48%. No percentage is shown
in the NA node since missing values are not included in the
If you prefer the denominator to represent the complete set of
observations (including any missing values), specify
vp=FALSE. A percentage will be shown in each of the nodes,
including any NA nodes.
If you don’t wish to see percentages, specify
showpct=FALSE, and if you don’t wish to see counts, specify
To display a legend, specify
showlegend=TRUE. Next to
each variable name are “legend nodes” representing the values of that
variable and colored accordingly. For each variable, the legend nodes
are grouped within a light gray box. Each legend node also contains a
count (with a percentage) for the value represented by that node in the
whole data frame. This is known as the marginal count (and
When the legend is shown, labels in the nodes of the variable tree
are redundant, since the colors of the nodes identify the values of the
variables (although the labels may aid readability). If you prefer, you
can hide the node labels, by specifying
Severity is the first variable in the tree, it is
not nested within another variable. Therefore the marginal counts and
Severity shown in the legend nodes are
identical to those displayed in the nodes of the variable tree. In
Sex, the marginal counts and percentages are
different from what is shown in the nodes of the variable tree for
Sex since they are nested within levels of
vtree wraps text onto the next line whenever
a space occurs after at least 20 characters. This can be adjusted, for
example, to 15 characters, by specifying
disable line splitting, specify
Inf means infinity, i.e. “do not split”.)
vsplitwidth parameter is similarly used to control
text wrapping in variable names. This is helpful with long variable
names, which may be truncated unless wrapping is used. In this case text
wrapping occurs not only at spaces, but also at any of the following
. - + _ = / (
For example if
vsplitwidth=5, a variable name like
First_Emergency_Visit would be split into
This concludes the mini-tutorial. vtree has many more features, described in the following sections.
This section shows how to remove branches from a variable tree.
When a variable tree gets too big, or you are only interested in certain parts of the tree, it may be useful to remove some nodes along with their descendants. This is known as pruning. For convenience, there are several different ways to prune a tree, described below.
Here’s a variable tree we’ve already seen in various forms:
Suppose you don’t want the tree to show branches for individuals
whose disease is Mild or Moderate. Specifying
prune=list(Severity=c("Mild","Moderate")) removes those
nodes, and all of their descendants:
In general, the argument of the
prune parameter is a
list with an element named for each variable you wish to prune.
In the example above, the list has a single element, named
Severity. In turn, that element is a vector
c("Mild","Moderate") indicating the values of
Severity to prune.
Caution: Once a variable tree has been pruned, it is
no longer complete. This can sometimes be confusing since not all
observations are represented at certain layers of the tree. For example
in the tree above, only 11 observations are shown in the
Severity nodes and their children.
Sometimes it is more convenient to specify which nodes should be
retained rather than which ones should be discarded. The
keep parameter is used for this purpose, and can thus be
considered the complement of the
prune parameter. For
example, to retain the Moderate
Note: In addition to the Moderate node, the missing
value node has also been retained. In general, whenever valid
percentages are used (which is the default), missing value nodes are
keep is used. This is because valid
percentages are difficult to interpret without knowing the denominator,
which requires knowing the number of missing values.
On the other hand, here’s what happens when
As seen above, a disadvantage of pruning is that in the resulting tree, the counts shown in child nodes may not add up to the counts shown in their parent node.
An alternative is to prune below the specified nodes
(i.e. to prune their descendants), so that the counts always add up. In
the present example, this means that the Mild and Moderate nodes will be
shown, but not their descendants. The
is used to do this:
The complement of
Instead of specifying which nodes should be pruned below, this allows
you to specify which nodes should be “followed” (that is, not
This section describes a more flexible way to prune variable trees.
To explain this, first note that the
parameters specify pruning across all branches of the tree. For example,
if you were pruning
Severity nested within levels of
Sex, the pruning would take place in both the M and F
Sometimes, however, it is preferable to perform pruning only in
specified branches of the tree. This is called targeted
pruning, and the parameters
tfollow provide this
functionality. However, their arguments have a more complex form than
those of the corresponding
follow parameters because they
specify the full path from the root of the tree all the way to
the nodes to be pruned. For example to remove every
Severity node except Moderate, but only for males, the
following command can be used:
Note that the argument of
tkeep is a list of lists, one
for each path through the tree. To keep both Moderate and Severe,
Now suppose that, in addition to this, within females,you want to keep
just Mild. Use the following specification to do this:
As a variable tree grows, it can become difficult to see the forest
for the tree. For example, the following tree is hard to read, even when
sameline=TRUE has been specified:
vtree(FakeData,"Severity Sex Age Category",sameline=TRUE)
One solution is to prune nodes that contain small numbers of
observations. For example if you want to only see nodes with at least 3
observations, you can specify
prunesmaller=3, as in this
vtree(FakeData,"Severity Sex Age Category",sameline=TRUE,prunesmaller=3)