# Chapter 10 Logistic Regression

In this chapter, we continue our discussion of classification. We introduce our first model for classification, logistic regression. To begin, we return to the `Default`

dataset from the previous chapter.

```
library(ISLR)
library(tibble)
as_tibble(Default)
```

```
## # A tibble: 10,000 x 4
## default student balance income
## <fct> <fct> <dbl> <dbl>
## 1 No No 730. 44362.
## 2 No Yes 817. 12106.
## 3 No No 1074. 31767.
## 4 No No 529. 35704.
## 5 No No 786. 38463.
## 6 No Yes 920. 7492.
## 7 No No 826. 24905.
## 8 No Yes 809. 17600.
## 9 No No 1161. 37469.
## 10 No No 0 29275.
## # ... with 9,990 more rows
```

We also repeat the test-train split from the previous chapter.

```
set.seed(42)
default_idx = sample(nrow(Default), 5000)
default_trn = Default[default_idx, ]
default_tst = Default[-default_idx, ]
```

## 10.1 Linear Regression

Before moving on to logistic regression, why not plain, old, linear regression?

```
default_trn_lm = default_trn
default_tst_lm = default_tst
```

Since linear regression expects a numeric response variable, we coerce the response to be numeric. (Notice that we also shift the results, as we require `0`

and `1`

, not `1`

and `2`

.) Notice we have also copied the dataset so that we can return the original data with factors later.

```
default_trn_lm$default = as.numeric(default_trn_lm$default) - 1
default_tst_lm$default = as.numeric(default_tst_lm$default) - 1
```

Why would we think this should work? Recall that,

\[ \hat{\mathbb{E}}[Y \mid X = x] = X\hat{\beta}. \]

Since \(Y\) is limited to values of \(0\) and \(1\), we have

\[ \mathbb{E}[Y \mid X = x] = P(Y = 1 \mid X = x). \]

It would then seem reasonable that \(\mathbf{X}\hat{\beta}\) is a reasonable estimate of \(P(Y = 1 \mid X = x)\). We test this on the `Default`

data.

`model_lm = lm(default ~ balance, data = default_trn_lm)`

Everything seems to be working, until we plot the results.

```
plot(default ~ balance, data = default_trn_lm,
col = "darkorange", pch = "|", ylim = c(-0.2, 1),
main = "Using Linear Regression for Classification")
abline(h = 0, lty = 3)
abline(h = 1, lty = 3)
abline(h = 0.5, lty = 2)
abline(model_lm, lwd = 3, col = "dodgerblue")
```

Two issues arise. First, all of the predicted probabilities are below 0.5. That means, we would classify every observation as a `"No"`

. This is certainly possible, but not what we would expect.

`all(predict(model_lm) < 0.5)`

`## [1] TRUE`

The next, and bigger issue, is predicted probabilities less than 0.

`any(predict(model_lm) < 0)`

`## [1] TRUE`

## 10.2 Bayes Classifier

Why are we using a predicted probability of 0.5 as the cutoff for classification? Recall, the Bayes Classifier, which minimizes the classification error:

\[ C^B(x) = \underset{g}{\mathrm{argmax}} \ P(Y = g \mid X = x) \]

So, in the binary classification problem, we will use predicted probabilities

\[ \hat{p}(x) = \hat{P}(Y = 1 \mid { X = x}) \]

and

\[ \hat{P}(Y = 0 \mid { X = x}) \]

and then classify to the larger of the two. We actually only need to consider a single probability, usually \(\hat{P}(Y = 1 \mid { X = x})\). Since we use it so often, we give it the shorthand notation, \(\hat{p}(x)\). Then the classifier is written,

\[ \hat{C}(x) = \begin{cases} 1 & \hat{p}(x) > 0.5 \\ 0 & \hat{p}(x) \leq 0.5 \end{cases} \]

This classifier is essentially estimating the Bayes Classifier, thus, is seeking to minimize classification errors.

## 10.3 Logistic Regression with `glm()`

To better estimate the probability

\[ p(x) = P(Y = 1 \mid {X = x}) \] we turn to logistic regression. The model is written

\[ \log\left(\frac{p(x)}{1 - p(x)}\right) = \beta_0 + \beta_1 x_1 + \beta_2 x_2 + \cdots + \beta_p x_p. \]

Rearranging, we see the probabilities can be written as

\[ p(x) = \frac{1}{1 + e^{-(\beta_0 + \beta_1 x_1 + \beta_2 x_2 + \cdots + \beta_p x_p)}} = \sigma(\beta_0 + \beta_1 x_1 + \beta_2 x_2 + \cdots + \beta_p x_p) \]

Notice, we use the sigmoid function as shorthand notation, which appears often in deep learning literature. It takes any real input, and outputs a number between 0 and 1. How useful! (This is actualy a particular sigmoid function called the logistic function, but since it is by far the most popular sigmoid function, often sigmoid function is used to refer to the logistic function)

\[ \sigma(x) = \frac{e^x}{1 + e^x} = \frac{1}{1 + e^{-x}} \]

The model is fit by numerically maximizing the likelihood, which we will let `R`

take care of.

We start with a single predictor example, again using `balance`

as our single predictor.

`model_glm = glm(default ~ balance, data = default_trn, family = "binomial")`

Fitting this model looks very similar to fitting a simple linear regression. Instead of `lm()`

we use `glm()`

. The only other difference is the use of `family = "binomial"`

which indicates that we have a two-class categorical response. Using `glm()`

with `family = "gaussian"`

would perform the usual linear regression.

First, we can obtain the fitted coefficients the same way we did with linear regression.

`coef(model_glm)`

```
## (Intercept) balance
## -10.452182876 0.005367655
```

The next thing we should understand is how the `predict()`

function works with `glm()`

. So, let’s look at some predictions.

`head(predict(model_glm))`

```
## 9149 9370 2861 8302 6415 5189
## -6.9616496 -0.7089539 -4.8936916 -9.4123620 -9.0416096 -7.3600645
```

By default, `predict.glm()`

uses `type = "link"`

.

`head(predict(model_glm, type = "link"))`

```
## 9149 9370 2861 8302 6415 5189
## -6.9616496 -0.7089539 -4.8936916 -9.4123620 -9.0416096 -7.3600645
```

That is, `R`

is returning

\[ \hat{\beta}_0 + \hat{\beta}_1 x_1 + \hat{\beta}_2 x_2 + \cdots + \hat{\beta}_p x_p \] for each observation.

Importantly, these are **not** predicted probabilities. To obtain the predicted probabilities

\[ \hat{p}(x) = \hat{P}(Y = 1 \mid X = x) \]

we need to use `type = "response"`

`head(predict(model_glm, type = "response"))`

```
## 9149 9370 2861 8302 6415
## 9.466353e-04 3.298300e-01 7.437969e-03 8.170105e-05 1.183661e-04
## 5189
## 6.357530e-04
```

Note that these are probabilities, **not** classifications. To obtain classifications, we will need to compare to the correct cutoff value with an `ifelse()`

statement.

```
model_glm_pred = ifelse(predict(model_glm, type = "link") > 0, "Yes", "No")
# model_glm_pred = ifelse(predict(model_glm, type = "response") > 0.5, "Yes", "No")
```

The line that is run is performing

\[ \hat{C}(x) = \begin{cases} 1 & \hat{f}(x) > 0 \\ 0 & \hat{f}(x) \leq 0 \end{cases} \]

where

\[ \hat{f}(x) =\hat{\beta}_0 + \hat{\beta}_1 x_1 + \hat{\beta}_2 x_2 + \cdots + \hat{\beta}_p x_p. \]

The commented line, which would give the same results, is performing

\[ \hat{C}(x) = \begin{cases} 1 & \hat{p}(x) > 0.5 \\ 0 & \hat{p}(x) \leq 0.5 \end{cases} \]

where

\[ \hat{p}(x) = \hat{P}(Y = 1 \mid X = x). \]

Once we have classifications, we can calculate metrics such as the trainging classification error rate.

```
calc_class_err = function(actual, predicted) {
mean(actual != predicted)
}
```

`calc_class_err(actual = default_trn$default, predicted = model_glm_pred)`

`## [1] 0.0278`

As we saw previously, the `table()`

and `confusionMatrix()`

functions can be used to quickly obtain many more metrics.

```
train_tab = table(predicted = model_glm_pred, actual = default_trn$default)
library(caret)
train_con_mat = confusionMatrix(train_tab, positive = "Yes")
c(train_con_mat$overall["Accuracy"],
train_con_mat$byClass["Sensitivity"],
train_con_mat$byClass["Specificity"])
```

```
## Accuracy Sensitivity Specificity
## 0.9722000 0.2738095 0.9964818
```

We could also write a custom function for the error for use with trained logist regression models.

```
get_logistic_error = function(mod, data, res = "y", pos = 1, neg = 0, cut = 0.5) {
probs = predict(mod, newdata = data, type = "response")
preds = ifelse(probs > cut, pos, neg)
calc_class_err(actual = data[, res], predicted = preds)
}
```

This function will be useful later when calculating train and test errors for several models at the same time.

```
get_logistic_error(model_glm, data = default_trn,
res = "default", pos = "Yes", neg = "No", cut = 0.5)
```

`## [1] 0.0278`

To see how much better logistic regression is for this task, we create the same plot we used for linear regression.

```
plot(default ~ balance, data = default_trn_lm,
col = "darkorange", pch = "|", ylim = c(-0.2, 1),
main = "Using Logistic Regression for Classification")
abline(h = 0, lty = 3)
abline(h = 1, lty = 3)
abline(h = 0.5, lty = 2)
curve(predict(model_glm, data.frame(balance = x), type = "response"),
add = TRUE, lwd = 3, col = "dodgerblue")
abline(v = -coef(model_glm)[1] / coef(model_glm)[2], lwd = 2)
```

This plot contains a wealth of information.

- The orange
`|`

characters are the data, \((x_i, y_i)\). - The blue “curve” is the predicted probabilities given by the fitted logistic regression. That is, \[ \hat{p}(x) = \hat{P}(Y = 1 \mid { X = x}) \]
- The solid vertical black line represents the
**decision boundary**, the`balance`

that obtains a predicted probability of 0.5. In this case`balance`

= 1947.252994.

The decision boundary is found by solving for points that satisfy

\[ \hat{p}(x) = \hat{P}(Y = 1 \mid { X = x}) = 0.5 \]

This is equivalent to point that satisfy

\[
\hat{\beta}_0 + \hat{\beta}_1 x_1 = 0.
\]
Thus, for logistic regression with a single predictor, the decision boundary is given by the *point*

\[ x_1 = \frac{-\hat{\beta}_0}{\hat{\beta}_1}. \]

The following is not run, but an alternative way to add the logistic curve to the plot.

```
grid = seq(0, max(default_trn$balance), by = 0.01)
sigmoid = function(x) {
1 / (1 + exp(-x))
}
lines(grid, sigmoid(coef(model_glm)[1] + coef(model_glm)[2] * grid), lwd = 3)
```

Using the usual formula syntax, it is easy to add or remove complexity from logistic regressions.

```
model_1 = glm(default ~ 1, data = default_trn, family = "binomial")
model_2 = glm(default ~ ., data = default_trn, family = "binomial")
model_3 = glm(default ~ . ^ 2 + I(balance ^ 2),
data = default_trn, family = "binomial")
```

Note that, using polynomial transformations of predictors will allow a linear model to have non-linear decision boundaries.

```
model_list = list(model_1, model_2, model_3)
train_errors = sapply(model_list, get_logistic_error, data = default_trn,
res = "default", pos = "Yes", neg = "No", cut = 0.5)
test_errors = sapply(model_list, get_logistic_error, data = default_tst,
res = "default", pos = "Yes", neg = "No", cut = 0.5)
```

Here we see the misclassification error rates for each model. The train decreases, and the test decreases, until it starts to increases. Everything we learned about the bias-variance tradeoff for regression also applies here.

`diff(train_errors)`

`## [1] -0.0058 -0.0002`

`diff(test_errors)`

`## [1] -0.0068 0.0004`

We call `model_2`

the **additive** logistic model, which we will use quite often.

## 10.4 ROC Curves

Let’s return to our simple model with only balance as a predictor.

`model_glm = glm(default ~ balance, data = default_trn, family = "binomial")`

We write a function which allows use to make predictions based on different probability cutoffs.

```
get_logistic_pred = function(mod, data, res = "y", pos = 1, neg = 0, cut = 0.5) {
probs = predict(mod, newdata = data, type = "response")
ifelse(probs > cut, pos, neg)
}
```

\[ \hat{C}(x) = \begin{cases} 1 & \hat{p}(x) > c \\ 0 & \hat{p}(x) \leq c \end{cases} \]

Let’s use this to obtain predictions using a low, medium, and high cutoff. (0.1, 0.5, and 0.9)

```
test_pred_10 = get_logistic_pred(model_glm, data = default_tst, res = "default",
pos = "Yes", neg = "No", cut = 0.1)
test_pred_50 = get_logistic_pred(model_glm, data = default_tst, res = "default",
pos = "Yes", neg = "No", cut = 0.5)
test_pred_90 = get_logistic_pred(model_glm, data = default_tst, res = "default",
pos = "Yes", neg = "No", cut = 0.9)
```

Now we evaluate accuracy, sensitivity, and specificity for these classifiers.

```
test_tab_10 = table(predicted = test_pred_10, actual = default_tst$default)
test_tab_50 = table(predicted = test_pred_50, actual = default_tst$default)
test_tab_90 = table(predicted = test_pred_90, actual = default_tst$default)
test_con_mat_10 = confusionMatrix(test_tab_10, positive = "Yes")
test_con_mat_50 = confusionMatrix(test_tab_50, positive = "Yes")
test_con_mat_90 = confusionMatrix(test_tab_90, positive = "Yes")
```

```
metrics = rbind(
c(test_con_mat_10$overall["Accuracy"],
test_con_mat_10$byClass["Sensitivity"],
test_con_mat_10$byClass["Specificity"]),
c(test_con_mat_50$overall["Accuracy"],
test_con_mat_50$byClass["Sensitivity"],
test_con_mat_50$byClass["Specificity"]),
c(test_con_mat_90$overall["Accuracy"],
test_con_mat_90$byClass["Sensitivity"],
test_con_mat_90$byClass["Specificity"])
)
rownames(metrics) = c("c = 0.10", "c = 0.50", "c = 0.90")
metrics
```

```
## Accuracy Sensitivity Specificity
## c = 0.10 0.9404 0.77575758 0.9460186
## c = 0.50 0.9738 0.31515152 0.9962771
## c = 0.90 0.9674 0.01818182 0.9997932
```

We see then sensitivity decreases as the cutoff is increased. Conversely, specificity increases as the cutoff increases. This is useful if we are more interested in a particular error, instead of giving them equal weight.

Note that usually the best accuracy will be seen near \(c = 0.50\).

Instead of manually checking cutoffs, we can create an ROC curve (receiver operating characteristic curve) which will sweep through all possible cutoffs, and plot the sensitivity and specificity.

```
library(pROC)
test_prob = predict(model_glm, newdata = default_tst, type = "response")
test_roc = roc(default_tst$default ~ test_prob, plot = TRUE, print.auc = TRUE)
```

`as.numeric(test_roc$auc)`

`## [1] 0.9515076`

A good model will have a high AUC, that is as often as possible a high sensitivity and specificity.

## 10.5 Multinomial Logistic Regression

What if the response contains more than two categories? For that we need multinomial logistic regression.

\[ P(Y = k \mid { X = x}) = \frac{e^{\beta_{0k} + \beta_{1k} x_1 + \cdots + + \beta_{pk} x_p}}{\sum_{g = 1}^{G} e^{\beta_{0g} + \beta_{1g} x_1 + \cdots + \beta_{pg} x_p}} \]

We will omit the details, as ISL has as well. If you are interested, the Wikipedia page provides a rather thorough coverage. Also note that the above is an example of the softmax function.

As an example of a dataset with a three category response, we use the `iris`

dataset, which is so famous, it has its own Wikipedia entry. It is also a default dataset in `R`

, so no need to load it.

Before proceeding, we test-train split this data.

```
set.seed(430)
iris_obs = nrow(iris)
iris_idx = sample(iris_obs, size = trunc(0.50 * iris_obs))
iris_trn = iris[iris_idx, ]
iris_test = iris[-iris_idx, ]
```

To perform multinomial logistic regression, we use the `multinom`

function from the `nnet`

package. Training using `multinom()`

is done using similar syntax to `lm()`

and `glm()`

. We add the `trace = FALSE`

argument to suppress information about updates to the optimization routine as the model is trained.

```
library(nnet)
model_multi = multinom(Species ~ ., data = iris_trn, trace = FALSE)
summary(model_multi)$coefficients
```

```
## (Intercept) Sepal.Length Sepal.Width Petal.Length Petal.Width
## versicolor 26.81602 -6.983313 -16.24574 20.35750 3.218787
## virginica -34.24228 -8.398869 -17.03985 31.94659 11.594518
```

Notice we are only given coefficients for two of the three class, much like only needing coefficients for one class in logistic regression.

A difference between `glm()`

and `multinom()`

is how the `predict()`

function operates.

`head(predict(model_multi, newdata = iris_trn))`

```
## [1] setosa virginica setosa setosa virginica setosa
## Levels: setosa versicolor virginica
```

`head(predict(model_multi, newdata = iris_trn, type = "prob"))`

```
## setosa versicolor virginica
## 23 1.000000e+00 2.607782e-19 3.891079e-44
## 106 4.461651e-38 2.328295e-09 1.000000e+00
## 37 1.000000e+00 1.108222e-18 1.620112e-42
## 40 1.000000e+00 5.389221e-15 1.525649e-37
## 145 1.146554e-28 9.816687e-07 9.999990e-01
## 36 1.000000e+00 6.216549e-16 7.345269e-40
```

Notice that by default, classifications are returned. When obtaining probabilities, we are given the predicted probability for **each** class.

Interestingly, you’ve just fit a neural network, and you didn’t even know it! (Hence the `nnet`

package.) Later we will discuss the connections between logistic regression, multinomial logistic regression, and simple neural networks.

## 10.6 `rmarkdown`

The `rmarkdown`

file for this chapter can be found **here**. The file was created using `R`

version 3.5.1. The following packages (and their dependencies) were loaded when knitting this file:

`## [1] "nnet" "pROC" "caret" "ggplot2" "lattice" "tibble" "ISLR"`