R Language Frequently Asked Questions

The article is about the use and application of Logistic Regression Models in R Language. In logistic regression models, the response variable ($y$) is of categorical (binary, dichotomous) values such as 1 or 0 (TRUE/ FALSE). It measures the probability of a binary response variable based on a mathematical equation relating the values of the response variable with the predictor(s). The built-in glm() function in R can be used to perform logistic regression analysis.

Probability and Odds Ratio

The odds are used in logistic regression. If $p$ is the probability of success, the odds of in favour of success are, $\frac{p}{q}=\frac{p}{1-p}$.

Note that probability can be converted to odds and odds can also be converted to likelihood (probability). However, unlike probability, odds can exceed 1. For example, if the likelihood of an event is 0.25, the odds in favour of that event are $\frac{0.25}{0.75}=0.33$. And the odds against the same event are $\frac{0.75}{0.25}=3$.

Logistic Regression Models in R (Example)

In built-in dataset (“mtcars“), the column (am) describes the transmission mode (automatic or manual) which is of binary value (0 or 1). Let us perform logistic regression models between the response variable “am” and other regressors: “hp”, “wt”, and “cyl” as given:

Logistic Regression with one Dichotomous Predictor

logmodel1 <- glm(am ~ vs, family = "binomial")
summary(logmodel1)

Logistic Regression with one Continuous Predictor

If the prediction variable is continuous then the logistic regression formula in R would be as given below:

logmodel2 <- glm(am ~ wt, family = "binomial")
summary(logmodel2)

Multiple Predictors in Logistic Regression

The following is an example of a logistic regression model with more than one predictor. For the model diagnostic plots are also drawn.

logmodel3 <- glm(am ~ cyl + hp + wt, family = "binomial")
summary(logmodel3)
plot(logmodel3)

Note: in the logistic regression model, dichotomous and continuous variables can be used as predictors.

In R language, the coefficients returned by logistic regression are a logit, or the log of the odds. To convert logits to odds ratio exponentiates it and to convert logits to probability use $\frac{e^\beta}{1-e^\beta}$. For example,

logmodel1 <- glm(am ~ vs, family = "binomial", data = mtcars)
logit_coef <- logmodel1$coef
exp(logmodel1$coef)
exp(logit_coef)/(1 + exp(logmodel1$coef))

The generalized linear models (GLM) can be used when the distribution of the response variable is non-normal or when the response variable is transformed into linearity. The GLMs are flexible extensions of linear models that are used to fit the regression models to non-Gaussian data.

One can classify a regression model as linear or non-linear regression models.

The basic form of a Generalized linear model is
\begin{align*}
g(\mu_i) &= X_i’ \beta \\
&= \beta_0 + \sum\limits_{j=1}^p x_{ij} \beta_j
\end{align*}
where $\mu_i=E(U_i)$ is the expected value of the response variable $Y_i$ given the predictors, $g(\cdot)$ is a smooth and monotonic link function that connects $\mu_i$ to the predictors, $X_i’=(x_{i0}, x_{i1}, \cdots, x_{ip})$ is the known vector having $i$th observations with $x_{i0}=1$, and $\beta=(\beta_0, \beta_1, \cdots, \beta_p)’$ is the unknown vector of regression coefficients.

Fitting Generalized Linear Models

The glm() is a function that can be used to fit a generalized linear model, using the generic form of the model below. The formula argument is similar to that used in the lm() function for the linear regression model.

mod <- glm(formula, family = gaussian, data = data.frame)

The family argument is a description of the error distribution and link function to be used in the model.

The class of generalized linear models is specified by giving a symbolic description of the linear predictor and a description of the error distribution. The link functions for different families of the probability distribution of the response variables are given below. The family name can be used as an argument in the glm( ) function.

Generalized Linear Models Example in R

Consider the “cars” dataset available in R. Let us fit a generalized linear regression model on the data set by assuming the “dist” variable as the response variable, and the “speed” variable as the predictor. Both the linear and generalized linear models are performed in the example below.

data(cars)
head(cars)
attach(cars)

scatter.smooth(x=speed, y=dist, main = "Dist ~ Speed")

# Linear Model
lm(dist ~ speed, data = cars)
summary(lm(dist ~ speed, data = cars)

# Generalized Linear Model
glm(dist ~ speed, data=cars, family = "gaussian")
plot(glm(dist ~ speed, data = cars))
summary(glm(dist ~ speed, data = cars))

Diagnostic Plots of Generalized Linear Models

https://gmstat.com