Examples of FFTrees

Creating FFTs

Let’s create some trees using FFTrees()! We’ll use the train.p = .5 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

mushrooms.fft <- FFTrees(formula = poisonous ~.,
                         data = mushrooms,
                         train.p = .50,   # split data into 50:50 training/test subsets
                         main = "Mushrooms",
                         decision.labels = c("Safe", "Poison"))   

Here’s basic information about the best performing FFT (Tree #1):

# Print information about the best performing tree:
mushrooms.fft

## Mushrooms
## FFTrees 
## - Trees: 6 fast-and-frugal trees predicting poisonous
## - Outcome costs: [hi = 0, mi = 1, fa = 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

Cool beans.

Visualizing cue accuracies

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")

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.

Visualizing FFT performance

Now let’s plot the performance of the best training tree when applied to the test dataset:

# Plot the best FFT for the mushrooms 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 \(85\)%.

An alternative FFT

Now, let’s say that we talk to a mushroom expert who says that we are using the wrong cues. According to her, the best predictors for poisonous mushrooms are ringtype and ringnum. Let’s build a set of trees with these cues and see how they perform relative to our initial tree:

# Create trees using only the ringtype and ringnum cues: 
mushrooms.ring.fft <- FFTrees(formula = poisonous ~ ringtype + ringnum,
                              data = mushrooms,
                              train.p = .50,
                              main = "Mushrooms (ring only)",
                              decision.labels = c("Safe", "Poison"))

Here is the best training tree, when applied to 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 a sensitivity and a specificity 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.

Visualizing cue accuracies

We can plot the training cue accuracies during training by specifying what = "cues":

# Plot cue values: 
plot(iris.fft, what = "cues")

It looks like the two cues pet.wid and pet.len are the best predictors for this dataset. Based on this, we should expect the final trees will likely use one or both of these cues.

Visualizing FFT performance

Now let’s examine the best tree:

# Plot best FFT: 
plot(iris.fft)

Indeed, it turns out that the best tree only uses the pet.wid and pet.len cues. In our test dataset, the tree had a sensitivity of 100% and a specificity of 94%.

Alternative FFTs

Now, this tree did quite well, but what if someone wanted a tree with the lowest possible false alarm rate? If we look at the ROC plot in the bottom left corner of the plot above, we can see that Tree #2 has a specificity close to 100%. Let’s look at that tree:

# Plot FFT #2 in iris FFTrees: 
plot(iris.fft, tree = 2)

As we can see, this tree does indeed have a higher specificity (of 98%). However, this increase comes at a cost of a lower sensitivity (of 90%).

Such trade-offs between measures are typical when fitting and predicting real-world data. Importantly, FFTs (and the FFTrees package) help us to render such trade-offs more transparent.