This vignette illustrates how to construct fast-and-frugal trees (FFTs) for additional datasets included in the FFTrees package. (See Phillips et al., 2017, for a comparison across 10 real-world datasets.)
The mushrooms
dataset contains data about mushrooms (see
?mushrooms
for details). The goal of our model is to
predict which mushrooms are poisonous
based on 22 cues
ranging from the mushroom’s odor, color, etc.
Here are the first few rows and a subset of 10 potential predictors
of the mushrooms
data:
poisonous | cshape | csurface | ccolor | bruises | odor | vcolor | ringnum | ringtype | sporepc | population | habitat |
---|---|---|---|---|---|---|---|---|---|---|---|
TRUE | x | s | n | t | p | w | o | p | k | s | u |
FALSE | x | s | y | t | a | w | o | p | n | n | g |
FALSE | b | s | w | t | l | w | o | p | n | n | m |
TRUE | x | y | w | t | p | w | o | p | k | s | u |
FALSE | x | s | g | f | n | w | o | e | n | a | g |
FALSE | x | y | y | t | a | w | o | p | k | n | g |
Let’s create some trees using FFTrees()
! We’ll use the
train.p = .50
argument to split the original data into a
\(50\)% training set and a \(50\)% testing set:
# Create FFTs from the mushrooms data:
set.seed(1) # for replicability of the training / test data split
<- FFTrees(formula = poisonous ~.,
mushrooms_fft data = mushrooms,
train.p = .50, # split data into 50:50 training/test subsets
main = "Mushrooms",
decision.labels = c("Safe", "Poison"),
do.comp = FALSE)
Setting the do.comp = FALSE
argument prevents the
evaluation of alternative algorithms (beyond those needed for FFTs).
This can save time, but also avoid error messages stemming from
alternative prediction methods (e.g., rank-deficient fits of linear
models).
Here’s basic information about the best performing FFT (Tree #1):
# Print information about the best tree (during training):
print(mushrooms_fft)
#> Mushrooms
#> FFTrees
#> - Trees: 6 fast-and-frugal trees predicting poisonous
#> - Outcome costs: [hi = 0, fa = 1, mi = 1, cr = 0]
#>
#> FFT #1: Definition
#> [1] If odor != {f,s,y,p,c,m}, decide Safe.
#> [2] If sporepc = {h,w,r}, decide Poison, otherwise, decide Safe.
#>
#> FFT #1: Training Accuracy
#> Training data: N = 4,062, Pos (+) = 1,958 (48%)
#>
#> | | True + | True - | Totals:
#> |----------|----------|----------|
#> | Decide + | hi 1,683 | fa 0 | 1,683
#> | Decide - | mi 275 | cr 2,104 | 2,379
#> |----------|----------|----------|
#> Totals: 1,958 2,104 N = 4,062
#>
#> acc = 93.2% ppv = 100.0% npv = 88.4%
#> bacc = 93.0% sens = 86.0% spec = 100.0%
#>
#> FFT #1: Training Speed, Frugality, and Cost
#> mcu = 1.47, pci = 0.93, E(cost) = 0.068
Let’s look at the individual cue training accuracies with
plot(fft, what = "cues")
:
# Plot the cue accuracies of an FFTrees object:
plot(mushrooms_fft, what = "cues")
#> Plotting cue training statistics:
#> — Cue accuracies ranked by bacc
It looks like the cues oder
and sporepc
are
the best predictors. In fact, the single cue odor
has a hit
rate of \(97\)% and a false alarm rate
of nearly \(0\)%! Based on this, we
should expect the final trees to use just these cues.
Now let’s plot the performance of the best training tree when applied to the test data:
# Plot the best FFT (for test data):
plot(mushrooms_fft, data = "test")
Indeed, it looks like the best tree only uses the odor
and sporepc
cues. In our test dataset, the tree had a
false alarm rate of \(0\)%
(\(1 -\) specificity), and a
sensitivity (aka. hit rate) of \(85\)%.
When considering the implications of our predictions, the fact that
our FFT incurs many misses, but no false alarms, is problematic: Given
our current task, failing to detect poisonous mushrooms has usually more
serious consequences than falsely classifying some as poisonous. To
change the balance between both possible errors, we can select another
tree from the set of FFTs. In this case, FFT #2 would use the same two
cues, but alter their exit structure so that our prediction incurs false
alarms, but no misses. Alternatively, we could re-generate a new set of
FFTs with a higher sensitivity weight value (e.g., increase the default
value of sens.w = .50
to sens.w = .67
) and
optimize the FFTs’ weighted accuracy wacc
.
Let’s assume that a famous mushroom expert insists that our FFT is
using the wrong cues. According to her, the best predictors for
poisonous mushrooms are ringtype
and ringnum
.
To test this, we build a set of FFTs from only these cues and check how
they perform relative to our initial tree:
# Create trees using only the ringtype and ringnum cues:
<- FFTrees(formula = poisonous ~ ringtype + ringnum,
mushrooms_ring_fft data = mushrooms,
train.p = .50,
main = "Mushrooms (ring cues)",
decision.labels = c("Safe", "Poison"),
do.comp = FALSE)
Again, we plot the best training tree, when predicting the cases in the test dataset:
# Plotting the best training FFT (for test data):
plot(mushrooms_ring_fft, data = "test")
As we can see, this tree (in mushrooms_ring_fft
) has
both sensitivity and specificity values of around \(80\)%, but does not perform as well as our
earlier one (in mushrooms_fft
). This suggests that we
should discard the expert’s advice and primarily rely on
the odor
and sporepc
cues.
The iris.v
dataset contains data about 150 flowers (see
?iris.v
). Our goal is to predict which flowers are of the
class Virginica. In this example, we’ll create trees using the
entire dataset (without splitting the available data into explicit
training vs. test subsets), so that we are really fitting the data,
rather than engaging in genuine prediction:
# Create FFTrees object for iris data:
<- FFTrees(formula = virginica ~.,
iris_fft data = iris.v,
main = "Iris",
decision.labels = c("Not-V", "V"))
The FFTrees package provides various functions to
inspect the FFTrees
object iris_fft
. For
summary information on the best training tree, we can print the
FTrees
object (by evaluating iris_fft
or
print(iris_fft)
). Alternatively, we could visualize the
tree (via plot(iris_fft)
) or summarize the
FFTrees
object (via summary(iris_fft)
):
# Inspect resulting FFTs:
print(iris_fft) # summarize best training tree
plot(iris_fft) # visualize best training tree
summary(iris_fft) # summarize FFTrees object
However, let’s first take a look at the individual training cue accuracies…
We can plot the training cue accuracies during training by specifying
what = "cues"
:
# Plot cue values:
plot(iris_fft, what = "cues")
#> Plotting cue training statistics:
#> — Cue accuracies ranked by bacc
It looks like the two cues pet.len
and pet.wid
are the best predictors for this dataset. Based
on this insight, we should expect the final trees will likely use one or
both of these cues.
Now let’s visualize the best tree:
# Plot best FFT:
plot(iris_fft)
Indeed, it turns out that the best tree only uses
the pet.len
and pet.wid
cues (in that order).
For this data, the fitted tree exhibits a performance with a sensitivity
of 100% and a specificity of 94%.
Now, this tree did quite well, but what if someone wanted a tree with the lowest possible false alarm rate? If we inspect the ROC plot in the bottom right corner of the figure, we see that Tree #2 has a specificity close to 100%. Let’s plot this tree:
# Plot FFT #2:
plot(iris_fft, tree = 2)
As we can see, this tree does indeed have a higher specificity (of 98%), but this increase comes at a cost of a lower sensitivity (of 90%). Such trade-offs between conflicting measures are inevitable when fitting and predicting real-world data. Importantly, using FFTs and the FFTrees package help us to render such trade-offs more transparent.
For examples that predict people’s survival of the Titanic
disaster (by growing FFTs for the titanic
data), see the Visualizing FFTs vignette.
Here is a complete list of the vignettes available in the FFTrees package:
Vignette | Description | |
---|---|---|
Main guide: FFTrees overview | An overview of the FFTrees package | |
1 | Tutorial: FFTs for heart disease | An example of using FFTrees() to model
heart disease diagnosis |
2 | Accuracy statistics | Definitions of accuracy statistics used throughout the package |
3 | Creating FFTs with FFTrees() | Details on the main FFTrees()
function |
4 | Manually specifying FFTs | How to directly create FFTs without using the built-in algorithms |
5 | Visualizing FFTs | Plotting FFTrees objects, from full trees
to icon arrays |
6 | Examples of FFTs | Examples of FFTs from different datasets contained in the package |