We will begin by examining some numerical and graphical summaries of
the Smarket data, which is part of the ISLR2
library. This data set consists of percentage returns for the S&P
500 stock index over \(1,250\) days,
from the beginning of 2001 until the end of 2005. For each date, we have
recorded the percentage returns for each of the five previous trading
days, lagone through lagfive. We have also
recorded volume (the number of shares traded on the
previous day, in billions), Today (the percentage return on
the date in question) and direction (whether the market was
Up or Down on this date). Our goal is to
predict direction (a qualitative response) using the other
features.
library(ISLR2)## Error in library(ISLR2): there is no package called 'ISLR2'names(Smarket)## Error: object 'Smarket' not founddim(Smarket)## Error: object 'Smarket' not foundsummary(Smarket)## Error: object 'Smarket' not foundpairs(Smarket)## Error: object 'Smarket' not foundThe cor() function produces a matrix that contains all
of the pairwise correlations among the predictors in a data set. The
first command below gives an error message because the
direction variable is qualitative.
cor(Smarket)## Error: object 'Smarket' not foundcor(Smarket[, -9])## Error: object 'Smarket' not foundAs one would expect, the correlations between the lag variables and
today’s returns are close to zero. In other words, there appears to be
little correlation between today’s returns and previous days’ returns.
The only substantial correlation is between Year and
volume. By plotting the data, which is ordered
chronologically, we see that volume is increasing over
time. In other words, the average number of shares traded daily
increased from 2001 to 2005.
attach(Smarket)## Error: object 'Smarket' not foundplot(Volume)## Error: object 'Volume' not foundNext, we will fit a logistic regression model in order to predict
direction using lagone through
lagfive and volume. The glm()
function can be used to fit many types of generalized linear models,
including logistic regression. The syntax of the glm()
function is similar to that of lm(), except that we must
pass in the argument family = binomial in order to tell
R to run a logistic regression rather than some other type
of generalized linear model.
glm.fits <- glm(
Direction ~ Lag1 + Lag2 + Lag3 + Lag4 + Lag5 + Volume,
data = Smarket, family = binomial
)## Error in eval(mf, parent.frame()): object 'Smarket' not foundsummary(glm.fits)## Error: object 'glm.fits' not foundThe smallest \(p\)-value here is
associated with lagone. The negative coefficient for this
predictor suggests that if the market had a positive return yesterday,
then it is less likely to go up today. However, at a value of \(0.15\), the \(p\)-value is still relatively large, and so
there is no clear evidence of a real association between
lagone and direction.
We use the coef() function in order to access just the
coefficients for this fitted model. We can also use the
summary() function to access particular aspects of the
fitted model, such as the \(p\)-values
for the coefficients.
coef(glm.fits)## Error: object 'glm.fits' not foundsummary(glm.fits)$coef## Error: object 'glm.fits' not foundsummary(glm.fits)$coef[, 4]## Error: object 'glm.fits' not foundThe predict() function can be used to predict the
probability that the market will go up, given values of the predictors.
The type = "response" option tells R to output
probabilities of the form \(P(Y=1|X)\),
as opposed to other information such as the logit. If no data set is
supplied to the predict() function, then the probabilities
are computed for the training data that was used to fit the logistic
regression model. Here we have printed only the first ten probabilities.
We know that these values correspond to the probability of the market
going up, rather than down, because the contrasts()
function indicates that R has created a dummy variable with
a 1 for Up.
glm.probs <- predict(glm.fits, type = "response")## Error: object 'glm.fits' not foundglm.probs[1:10]## Error: object 'glm.probs' not foundcontrasts(Direction)## Error: object 'Direction' not foundIn order to make a prediction as to whether the market will go up or
down on a particular day, we must convert these predicted probabilities
into class labels, Up or Down. The following
two commands create a vector of class predictions based on whether the
predicted probability of a market increase is greater than or less than
\(0.5\).
glm.pred <- rep("Down", 1250)
glm.pred[glm.probs > .5] = "Up"## Error: object 'glm.probs' not foundThe first command creates a vector of 1,250 Down
elements. The second line transforms to Up all of the
elements for which the predicted probability of a market increase
exceeds \(0.5\). Given these
predictions, the table() function can be used to produce a
confusion matrix in order to determine how many observations were
correctly or incorrectly classified.
table(glm.pred, Direction)## Error: object 'Direction' not found(507 + 145) / 1250## [1] 0.5216mean(glm.pred == Direction)## Error: object 'Direction' not foundThe diagonal elements of the confusion matrix indicate correct
predictions, while the off-diagonals represent incorrect predictions.
Hence our model correctly predicted that the market would go up on \(507\) days and that it would go down on
\(145\) days, for a total of \(507+145 = 652\) correct predictions. The
mean() function can be used to compute the fraction of days
for which the prediction was correct. In this case, logistic regression
correctly predicted the movement of the market \(52.2\) % of the time.
At first glance, it appears that the logistic regression model is working a little better than random guessing. However, this result is misleading because we trained and tested the model on the same set of \(1,250\) observations. In other words, \(100\%-52.2\%=47.8\%\), is the training error rate. As we have seen previously, the training error rate is often overly optimistic—it tends to underestimate the test error rate. In order to better assess the accuracy of the logistic regression model in this setting, we can fit the model using part of the data, and then examine how well it predicts the held out data. This will yield a more realistic error rate, in the sense that in practice we will be interested in our model’s performance not on the data that we used to fit the model, but rather on days in the future for which the market’s movements are unknown.
To implement this strategy, we will first create a vector corresponding to the observations from 2001 through 2004. We will then use this vector to create a held out data set of observations from 2005.
train <- (Year < 2005)## Error: object 'Year' not foundSmarket.2005 <- Smarket[!train, ]## Error: object 'Smarket' not founddim(Smarket.2005)## Error: object 'Smarket.2005' not foundDirection.2005 <- Direction[!train]## Error: object 'Direction' not foundThe object train is a vector of \(1{,}250\) elements, corresponding to the
observations in our data set. The elements of the vector that correspond
to observations that occurred before 2005 are set to TRUE,
whereas those that correspond to observations in 2005 are set to
FALSE. The object train is a Boolean
vector, since its elements are TRUE and FALSE.
Boolean vectors can be used to obtain a subset of the rows or columns of
a matrix. For instance, the command Smarket[train, ] would
pick out a submatrix of the stock market data set, corresponding only to
the dates before 2005, since those are the ones for which the elements
of train are TRUE. The ! symbol
can be used to reverse all of the elements of a Boolean vector. That is,
!train is a vector similar to train, except
that the elements that are TRUE in train get
swapped to FALSE in !train, and the elements
that are FALSE in train get swapped to
TRUE in !train. Therefore,
Smarket[!train, ] yields a submatrix of the stock market
data containing only the observations for which train is
FALSE—that is, the observations with dates in 2005. The
output above indicates that there are 252 such observations.
We now fit a logistic regression model using only the subset of the
observations that correspond to dates before 2005, using the
subset argument. We then obtain predicted probabilities of
the stock market going up for each of the days in our test set—that is,
for the days in 2005.
glm.fits <- glm(
Direction ~ Lag1 + Lag2 + Lag3 + Lag4 + Lag5 + Volume,
data = Smarket, family = binomial, subset = train
)## Error in eval(mf, parent.frame()): object 'Smarket' not foundglm.probs <- predict(glm.fits, Smarket.2005,
type = "response")## Error: object 'glm.fits' not foundNotice that we have trained and tested our model on two completely separate data sets: training was performed using only the dates before 2005, and testing was performed using only the dates in 2005. Finally, we compute the predictions for 2005 and compare them to the actual movements of the market over that time period.
glm.pred <- rep("Down", 252)
glm.pred[glm.probs > .5] <- "Up"## Error: object 'glm.probs' not foundtable(glm.pred, Direction.2005)## Error: object 'Direction.2005' not foundmean(glm.pred == Direction.2005)## Error: object 'Direction.2005' not foundmean(glm.pred != Direction.2005)## Error: object 'Direction.2005' not foundThe != notation means not equal to, and so the
last command computes the test set error rate. The results are rather
disappointing: the test error rate is \(52\) %, which is worse than random
guessing! Of course this result is not all that surprising, given that
one would not generally expect to be able to use previous days’ returns
to predict future market performance. (After all, if it were possible to
do so, then the authors of this book would be out striking it rich
rather than writing a statistics textbook.)
We recall that the logistic regression model had very underwhelming
\(p\)-values associated with all of the
predictors, and that the smallest \(p\)-value, though not very small,
corresponded to lagone. Perhaps by removing the variables
that appear not to be helpful in predicting direction, we
can obtain a more effective model. After all, using predictors that have
no relationship with the response tends to cause a deterioration in the
test error rate (since such predictors cause an increase in variance
without a corresponding decrease in bias), and so removing such
predictors may in turn yield an improvement. Below we have refit the
logistic regression using just lagone and
lagtwo, which seemed to have the highest predictive power
in the original logistic regression model.
glm.fits <- glm(Direction ~ Lag1 + Lag2, data = Smarket,
family = binomial, subset = train)## Error in eval(mf, parent.frame()): object 'Smarket' not foundglm.probs <- predict(glm.fits, Smarket.2005,
type = "response")## Error: object 'glm.fits' not foundglm.pred <- rep("Down", 252)
glm.pred[glm.probs > .5] <- "Up"## Error: object 'glm.probs' not foundtable(glm.pred, Direction.2005)## Error: object 'Direction.2005' not foundmean(glm.pred == Direction.2005)## Error: object 'Direction.2005' not found106 / (106 + 76)## [1] 0.5824176Now the results appear to be a little better: \(56\%\) of the daily movements have been correctly predicted. It is worth noting that in this case, a much simpler strategy of predicting that the market will increase every day will also be correct \(56\%\) of the time! Hence, in terms of overall error rate, the logistic regression method is no better than the naive approach. However, the confusion matrix shows that on days when logistic regression predicts an increase in the market, it has a \(58\%\) accuracy rate. This suggests a possible trading strategy of buying on days when the model predicts an increasing market, and avoiding trades on days when a decrease is predicted. Of course one would need to investigate more carefully whether this small improvement was real or just due to random chance.
Suppose that we want to predict the returns associated with
particular values of lagone and lagtwo. In
particular, we want to predict direction on a day when
lagone and lagtwo equal 1.2 and~1.1,
respectively, and on a day when they equal 1.5 and $-$0.8. We do this
using the predict() function.
predict(glm.fits,
newdata =
data.frame(Lag1 = c(1.2, 1.5), Lag2 = c(1.1, -0.8)),
type = "response"
)## Error: object 'glm.fits' not foundNow we will perform LDA on the Smarket data. In
R, we fit an LDA model using the lda()
function, which is part of the MASS library. Notice that
the syntax for the lda() function is identical to that of
lm(), and to that of glm() except for the
absence of the family option. We fit the model using only
the observations before 2005.
library(MASS)
lda.fit <- lda(Direction ~ Lag1 + Lag2, data = Smarket,
subset = train)## Error in eval(expr, p): object 'Smarket' not foundlda.fit## Error: object 'lda.fit' not foundplot(lda.fit)## Error: object 'lda.fit' not foundThe LDA output indicates that \(\hat\pi_1=0.492\) and \(\hat\pi_2=0.508\); in other words, \(49.2\) % of the training observations
correspond to days during which the market went down. It also provides
the group means; these are the average of each predictor within each
class, and are used by LDA as estimates of \(\mu_k\). These suggest that there is a
tendency for the previous 2~days’ returns to be negative on days when
the market increases, and a tendency for the previous days’ returns to
be positive on days when the market declines. The coefficients of
linear discriminants output provides the linear combination of
lagone and lagtwo that are used to form the
LDA decision rule. In other words, these are the multipliers of the
elements of \(X=x\) in (4.24). If
$-0.642 \(`lagone`\) - 0.514
$lagtwo is large, then the LDA classifier will predict a
market increase, and if it is small, then the LDA classifier will
predict a market decline.
The plot() function produces plots of the linear
discriminants, obtained by computing $-0.642 \(`lagone`\) - 0.514 $lagtwo for
each of the training observations. The Up and
Down observations are displayed separately.
The predict() function returns a list with three
elements. The first element, class, contains LDA’s
predictions about the movement of the market. The second element,
posterior, is a matrix whose \(k\)th column contains the posterior
probability that the corresponding observation belongs to the \(k\)th class, computed from (4.15). Finally,
x contains the linear discriminants, described earlier.
lda.pred <- predict(lda.fit, Smarket.2005)## Error: object 'lda.fit' not foundnames(lda.pred)## Error: object 'lda.pred' not foundAs we observed in Section 4.5, the LDA and logistic regression predictions are almost identical.
lda.class <- lda.pred$class## Error: object 'lda.pred' not foundtable(lda.class, Direction.2005)## Error: object 'lda.class' not foundmean(lda.class == Direction.2005)## Error: object 'lda.class' not foundApplying a \(50\) % threshold to the
posterior probabilities allows us to recreate the predictions contained
in lda.pred$class.
sum(lda.pred$posterior[, 1] >= .5)## Error: object 'lda.pred' not foundsum(lda.pred$posterior[, 1] < .5)## Error: object 'lda.pred' not foundNotice that the posterior probability output by the model corresponds to the probability that the market will decrease:
lda.pred$posterior[1:20, 1]## Error: object 'lda.pred' not foundlda.class[1:20]## Error: object 'lda.class' not foundIf we wanted to use a posterior probability threshold other than \(50\) % in order to make predictions, then we could easily do so. For instance, suppose that we wish to predict a market decrease only if we are very certain that the market will indeed decrease on that day—say, if the posterior probability is at least \(90\) %.
sum(lda.pred$posterior[, 1] > .9)## Error: object 'lda.pred' not foundNo days in 2005 meet that threshold! In fact, the greatest posterior probability of decrease in all of 2005 was \(52.02\) %.
We will now fit a QDA model to the Smarket data. QDA is
implemented in R using the qda() function,
which is also part of the MASS library. The syntax is
identical to that of lda().
qda.fit <- qda(Direction ~ Lag1 + Lag2, data = Smarket,
subset = train)## Error in eval(expr, p): object 'Smarket' not foundqda.fit## Error: object 'qda.fit' not foundThe output contains the group means. But it does not contain the
coefficients of the linear discriminants, because the QDA classifier
involves a quadratic, rather than a linear, function of the predictors.
The predict() function works in exactly the same fashion as
for LDA.
qda.class <- predict(qda.fit, Smarket.2005)$class## Error: object 'qda.fit' not foundtable(qda.class, Direction.2005)## Error: object 'qda.class' not foundmean(qda.class == Direction.2005)## Error: object 'qda.class' not foundInterestingly, the QDA predictions are accurate almost \(60\) % of the time, even though the 2005 data was not used to fit the model. This level of accuracy is quite impressive for stock market data, which is known to be quite hard to model accurately. This suggests that the quadratic form assumed by QDA may capture the true relationship more accurately than the linear forms assumed by LDA and logistic regression. However, we recommend evaluating this method’s performance on a larger test set before betting that this approach will consistently beat the market!
Next, we fit a naive Bayes model to the Smarket data.
Naive Bayes is implemented in R using the
naiveBayes() function, which is part of the
e1071 library. The syntax is identical to that of
lda() and qda(). By default, this
implementation of the naive Bayes classifier models each quantitative
feature using a Gaussian distribution. However, a kernel density method
can also be used to estimate the distributions.
library(e1071)
nb.fit <- naiveBayes(Direction ~ Lag1 + Lag2, data = Smarket,
subset = train)## Error: object 'Smarket' not foundnb.fit## Error: object 'nb.fit' not foundThe output contains the estimated mean and standard deviation for
each variable in each class. For example, the mean for
lagone is \(0.0428\)
for
Direction=Down, and the standard deviation is \(1.23\). We can easily verify this:
mean(Lag1[train][Direction[train] == "Down"])## Error: object 'Lag1' not foundsd(Lag1[train][Direction[train] == "Down"])## Error: object 'Lag1' not foundThe predict() function is straightforward.
nb.class <- predict(nb.fit, Smarket.2005)## Error: object 'nb.fit' not foundtable(nb.class, Direction.2005)## Error: object 'nb.class' not foundmean(nb.class == Direction.2005)## Error: object 'nb.class' not foundNaive Bayes performs very well on this data, with accurate predictions over \(59\%\) of the time. This is slightly worse than QDA, but much better than LDA.
The predict() function can also generate estimates of
the probability that each observation belongs to a particular class.
%
nb.preds <- predict(nb.fit, Smarket.2005, type = "raw")## Error: object 'nb.fit' not foundnb.preds[1:5, ]## Error: object 'nb.preds' not foundWe will now perform KNN using the knn() function, which
is part of the class library. This function works rather
differently from the other model-fitting functions that we have
encountered thus far. Rather than a two-step approach in which we first
fit the model and then we use the model to make predictions,
knn() forms predictions using a single command. The
function requires four inputs.
train.X below.test.X
below.train.Direction below.We use the cbind() function, short for column
bind, to bind the lagone and lagtwo
variables together into two matrices, one for the training set and the
other for the test set.
library(class)
train.X <- cbind(Lag1, Lag2)[train, ]## Error: object 'Lag1' not foundtest.X <- cbind(Lag1, Lag2)[!train, ]## Error: object 'Lag1' not foundtrain.Direction <- Direction[train]## Error: object 'Direction' not foundNow the knn() function can be used to predict the
market’s movement for the dates in 2005. We set a random seed before we
apply knn() because if several observations are tied as
nearest neighbors, then R will randomly break the tie.
Therefore, a seed must be set in order to ensure reproducibility of
results.
set.seed(1)
knn.pred <- knn(train.X, test.X, train.Direction, k = 1)## Error: object 'train.X' not foundtable(knn.pred, Direction.2005)## Error: object 'knn.pred' not found(83 + 43) / 252## [1] 0.5The results using \(K=1\) are not very good, since only \(50\) % of the observations are correctly predicted. Of course, it may be that \(K=1\) results in an overly flexible fit to the data. Below, we repeat the analysis using \(K=3\).
knn.pred <- knn(train.X, test.X, train.Direction, k = 3)## Error: object 'train.X' not foundtable(knn.pred, Direction.2005)## Error: object 'knn.pred' not foundmean(knn.pred == Direction.2005)## Error: object 'knn.pred' not foundThe results have improved slightly. But increasing \(K\) further turns out to provide no further improvements. It appears that for this data, QDA provides the best results of the methods that we have examined so far.
KNN does not perform well on the Smarket data but it
does often provide impressive results. As an example we will apply the
KNN approach to the Insurance data set, which is part of
the ISLR2 library. This data set includes \(85\) predictors that measure demographic
characteristics for 5,822 individuals. The response variable is
Purchase, which indicates whether or not a given individual
purchases a caravan insurance policy. In this data set, only \(6\) % of people purchased caravan
insurance.
dim(Caravan)## Error: object 'Caravan' not foundattach(Caravan)## Error: object 'Caravan' not foundsummary(Purchase)## Error: object 'Purchase' not found348 / 5822## [1] 0.05977327Because the KNN classifier predicts the class of a given test
observation by identifying the observations that are nearest to it, the
scale of the variables matters. Variables that are on a large scale will
have a much larger effect on the distance between the
observations, and hence on the KNN classifier, than variables that are
on a small scale. For instance, imagine a data set that contains two
variables, salary and age (measured in dollars
and years, respectively). As far as KNN is concerned, a difference of
\(\$1,000\) in salary is enormous
compared to a difference of \(50\)
years in age. Consequently, salary will drive the KNN
classification results, and age will have almost no effect.
This is contrary to our intuition that a salary difference of \(\$1,000\) is quite small compared to an age
difference of \(50\) years.
Furthermore, the importance of scale to the KNN classifier leads to
another issue: if we measured salary in Japanese yen, or if
we measured age in minutes, then we’d get quite different
classification results from what we get if these two variables are
measured in dollars and years.
A good way to handle this problem is to standardize the data
so that all variables are given a mean of zero and a standard deviation
of one. Then all variables will be on a comparable scale. The
scale() function does just this. In standardizing the data,
we exclude column \(86\), because that
is the qualitative Purchase variable.
standardized.X <- scale(Caravan[, -86])## Error: object 'Caravan' not foundvar(Caravan[, 1])## Error: object 'Caravan' not foundvar(Caravan[, 2])## Error: object 'Caravan' not foundvar(standardized.X[, 1])## Error: object 'standardized.X' not foundvar(standardized.X[, 2])## Error: object 'standardized.X' not foundNow every column of standardized.X has a standard
deviation of one and a mean of zero.
We now split the observations into a test set, containing the first 1,000 observations, and a training set, containing the remaining observations. We fit a KNN model on the training data using \(K=1\), and evaluate its performance on the test data.%
test <- 1:1000
train.X <- standardized.X[-test, ]## Error: object 'standardized.X' not foundtest.X <- standardized.X[test, ]## Error: object 'standardized.X' not foundtrain.Y <- Purchase[-test]## Error: object 'Purchase' not foundtest.Y <- Purchase[test]## Error: object 'Purchase' not foundset.seed(1)
knn.pred <- knn(train.X, test.X, train.Y, k = 1)## Error: object 'train.X' not foundmean(test.Y != knn.pred)## Error: object 'test.Y' not foundmean(test.Y != "No")## Error: object 'test.Y' not foundThe vector test is numeric, with values from \(1\) through \(1,000\). Typing
standardized.X[test, ] yields the submatrix of the data
containing the observations whose indices range from \(1\) to \(1,000\), whereas typing
standardized.X[-test, ] yields the submatrix containing
the observations whose indices do not range from \(1\) to \(1,000\). The KNN error rate on the 1,000
test observations is just under \(12\)
%. At first glance, this may appear to be fairly good. However, since
only \(6\) % of customers purchased
insurance, we could get the error rate down to \(6\) % by always predicting No
regardless of the values of the predictors!
Suppose that there is some non-trivial cost to trying to sell insurance to a given individual. For instance, perhaps a salesperson must visit each potential customer. If the company tries to sell insurance to a random selection of customers, then the success rate will be only \(6\) %, which may be far too low given the costs involved. Instead, the company would like to try to sell insurance only to customers who are likely to buy it. So the overall error rate is not of interest. Instead, the fraction of individuals that are correctly predicted to buy insurance is of interest.
It turns out that KNN with \(K=1\) does far better than random guessing among the customers that are predicted to buy insurance. Among \(77\) such customers, \(9\), or \(11.7\) %, actually do purchase insurance. This is double the rate that one would obtain from random guessing.
table(knn.pred, test.Y)## Error: object 'knn.pred' not found9 / (68 + 9)## [1] 0.1168831Using \(K=3\), the success rate increases to \(19\) %, and with \(K=5\) the rate is \(26.7\) %. This is over four times the rate that results from random guessing. It appears that KNN is finding some real patterns in a difficult data set!
knn.pred <- knn(train.X, test.X, train.Y, k = 3)## Error: object 'train.X' not foundtable(knn.pred, test.Y)## Error: object 'knn.pred' not found5 / 26## [1] 0.1923077knn.pred <- knn(train.X, test.X, train.Y, k = 5)## Error: object 'train.X' not foundtable(knn.pred, test.Y)## Error: object 'knn.pred' not found4 / 15## [1] 0.2666667However, while this strategy is cost-effective, it is worth noting that only 15 customers are predicted to purchase insurance using KNN with \(K=5\). In practice, the insurance company may wish to expend resources on convincing more than just 15 potential customers to buy insurance.
As a comparison, we can also fit a logistic regression model to the data. If we use \(0.5\) as the predicted probability cut-off for the classifier, then we have a problem: only seven of the test observations are predicted to purchase insurance. Even worse, we are wrong about all of these! However, we are not required to use a cut-off of \(0.5\). If we instead predict a purchase any time the predicted probability of purchase exceeds \(0.25\), we get much better results: we predict that 33 people will purchase insurance, and we are correct for about \(33\) % of these people. This is over five times better than random guessing!
glm.fits <- glm(Purchase ~ ., data = Caravan,
family = binomial, subset = -test)## Error in eval(mf, parent.frame()): object 'Caravan' not foundglm.probs <- predict(glm.fits, Caravan[test, ],
type = "response")## Error: object 'glm.fits' not foundglm.pred <- rep("No", 1000)
glm.pred[glm.probs > .5] <- "Yes"## Error: object 'glm.probs' not foundtable(glm.pred, test.Y)## Error: object 'test.Y' not foundglm.pred <- rep("No", 1000)
glm.pred[glm.probs > .25] <- "Yes"## Error: object 'glm.probs' not foundtable(glm.pred, test.Y)## Error: object 'test.Y' not found11 / (22 + 11)## [1] 0.3333333Finally, we fit a Poisson regression model to the
Bikeshare data set, which measures the number of bike
rentals (bikers) per hour in Washington, DC. The data can
be found in the ISLR2 library.
attach(Bikeshare)## Error: object 'Bikeshare' not founddim(Bikeshare)## Error: object 'Bikeshare' not foundnames(Bikeshare)## Error: object 'Bikeshare' not foundWe begin by fitting a least squares linear regression model to the data.
mod.lm <- lm(
bikers ~ mnth + hr + workingday + temp + weathersit,
data = Bikeshare
)## Error in eval(mf, parent.frame()): object 'Bikeshare' not foundsummary(mod.lm)## Error: object 'mod.lm' not foundDue to space constraints, we truncate the output of
summary(mod.lm). In mod.lm, the first level of
hr (0) and mnth (Jan) are treated as the
baseline values, and so no coefficient estimates are provided for them:
implicitly, their coefficient estimates are zero, and all other levels
are measured relative to these baselines. For example, the Feb
coefficient of \(6.845\) signifies
that, holding all other variables constant, there are on average about 7
more riders in February than in January. Similarly there are about 16.5
more riders in March than in January.
The results seen in Section 4.6.1 used a slightly different coding of
the variables hr and mnth, as follows:
contrasts(Bikeshare$hr) = contr.sum(24)## Error: object 'Bikeshare' not foundcontrasts(Bikeshare$mnth) = contr.sum(12)## Error: object 'Bikeshare' not foundmod.lm2 <- lm(
bikers ~ mnth + hr + workingday + temp + weathersit,
data = Bikeshare
)## Error in eval(mf, parent.frame()): object 'Bikeshare' not foundsummary(mod.lm2)## Error: object 'mod.lm2' not foundWhat is the difference between the two codings? In
mod.lm2, a coefficient estimate is reported for all but the
last level of hr and mnth. Importantly, in
mod.lm2, the coefficient estimate for the last level of
mnth is not zero: instead, it equals the negative of
the sum of the coefficient estimates for all of the other levels.
Similarly, in mod.lm2, the coefficient estimate for the
last level of hr is the negative of the sum of the
coefficient estimates for all of the other levels. This means that the
coefficients of hr and mnth in
mod.lm2 will always sum to zero, and can be interpreted as
the difference from the mean level. For example, the coefficient for
January of \(-46.087\) indicates that,
holding all other variables constant, there are typically 46 fewer
riders in January relative to the yearly average.
It is important to realize that the choice of coding really does not matter, provided that we interpret the model output correctly in light of the coding used. For example, we see that the predictions from the linear model are the same regardless of coding:
sum((predict(mod.lm) - predict(mod.lm2))^2)## Error: object 'mod.lm' not foundThe sum of squared differences is zero. We can also see this using
the all.equal() function:
all.equal(predict(mod.lm), predict(mod.lm2))## Error: object 'mod.lm' not foundTo reproduce the left-hand side of Figure 4.13, we must first obtain
the coefficient estimates associated with mnth. The
coefficients for January through November can be obtained directly from
the mod.lm2 object. The coefficient for December must be
explicitly computed as the negative sum of all the other months.
coef.months <- c(coef(mod.lm2)[2:12],
-sum(coef(mod.lm2)[2:12]))## Error: object 'mod.lm2' not foundTo make the plot, we manually label the \(x\)-axis with the names of the months.
plot(coef.months, xlab = "Month", ylab = "Coefficient",
xaxt = "n", col = "blue", pch = 19, type = "o")## Error: object 'coef.months' not foundaxis(side = 1, at = 1:12, labels = c("J", "F", "M", "A",
"M", "J", "J", "A", "S", "O", "N", "D"))## Error in axis(side = 1, at = 1:12, labels = c("J", "F", "M", "A", "M", : plot.new has not been called yetReproducing the right-hand side of Figure 4.13 follows a similar process.
coef.hours <- c(coef(mod.lm2)[13:35],
-sum(coef(mod.lm2)[13:35]))## Error: object 'mod.lm2' not foundplot(coef.hours, xlab = "Hour", ylab = "Coefficient",
col = "blue", pch = 19, type = "o")## Error: object 'coef.hours' not foundNow, we consider instead fitting a Poisson regression model to the
Bikeshare data. Very little changes, except that we now use
the function glm() with the argument
family = poisson to specify that we wish to fit a Poisson
regression model:
mod.pois <- glm(
bikers ~ mnth + hr + workingday + temp + weathersit,
data = Bikeshare, family = poisson
)## Error in eval(mf, parent.frame()): object 'Bikeshare' not foundsummary(mod.pois)## Error: object 'mod.pois' not foundWe can plot the coefficients associated with mnth and
hr, in order to reproduce Figure 4.15:
coef.mnth <- c(coef(mod.pois)[2:12],
-sum(coef(mod.pois)[2:12]))## Error: object 'mod.pois' not foundplot(coef.mnth, xlab = "Month", ylab = "Coefficient",
xaxt = "n", col = "blue", pch = 19, type = "o")## Error: object 'coef.mnth' not foundaxis(side = 1, at = 1:12, labels = c("J", "F", "M", "A", "M", "J", "J", "A", "S", "O", "N", "D"))## Error in axis(side = 1, at = 1:12, labels = c("J", "F", "M", "A", "M", : plot.new has not been called yetcoef.hours <- c(coef(mod.pois)[13:35],
-sum(coef(mod.pois)[13:35]))## Error: object 'mod.pois' not foundplot(coef.hours, xlab = "Hour", ylab = "Coefficient",
col = "blue", pch = 19, type = "o")## Error: object 'coef.hours' not foundWe can once again use the predict() function to obtain
the fitted values (predictions) from this Poisson regression model.
However, we must use the argument type = "response" to
specify that we want R to output \(\exp(\hat\beta_0 + \hat\beta_1 X_1 + \ldots
+\hat\beta_p X_p)\) rather than \(\hat\beta_0 + \hat\beta_1 X_1 + \ldots +
\hat\beta_p X_p\), which it will output by default.
plot(predict(mod.lm2), predict(mod.pois, type = "response"))## Error: object 'mod.lm2' not foundabline(0, 1, col = 2, lwd = 3)## Error in int_abline(a = a, b = b, h = h, v = v, untf = untf, ...): plot.new has not been called yetThe predictions from the Poisson regression model are correlated with those from the linear model; however, the former are non-negative. As a result the Poisson regression predictions tend to be larger than those from the linear model for either very low or very high levels of ridership.
In this section, we used the glm() function with the
argument family = poisson in order to perform Poisson
regression. Earlier in this lab we used the glm() function
with family = binomial to perform logistic regression.
Other choices for the family argument can be used to fit
other types of GLMs. For instance, family = Gamma fits a
gamma regression model.