ggplot(newdata3, aes(x = gre, y = PredictedProb)) + geom_ribbon(aes(ymin = LL,
ymax = UL, fill = rank), alpha = 0.2) + geom_line(aes(colour = rank),
size = 1)
Logistic regression, also called a logit model, is used to model dichotomous outcome variables. In the logit model the log odds of the outcome is modeled as a linear combination of the predictor variables.
library(aod) library(ggplot2)
Example 1. Suppose that we are interested in the factors that influence whether a political candidate wins an election. The outcome (response) variable is binary (0/1); win or lose. The predictor variables of interest are the amount of money spent on the campaign, the amount of time spent campaigning negatively and whether or not the candidate is an incumbent.
Example 2. A researcher is interested in how variables, such as GRE (Graduate Record Exam scores), GPA (grade point average) and prestige of the undergraduate institution, effect admission into graduate school. The response variable, admit/don't admit, is a binary variable.
Logistic regression is a special type of the Generalized Linear Models (GLM; will be explained later). Here, the bivariate outcome \(Y\) has a Bernoulli distribution with parameter \(p\) (success probability \(p\in(0,1)\)). Recall that \(\mathsf{E}Y=p\). The logit link function \[ logit(\mathsf{E}Y)=\log\frac{p}{1-p}=\log\frac{\mathsf{P}[Y=1]}{\mathsf{P}[Y=0]} \] is used to transform the expectation of this 0/1 dependent variable. Then, the logit of the mean (aka log odds) is modelled as a linear combination of the covariates (regressors) \({\boldsymbol X}\), i.e., we have a linear predictor \[ logit(\mathsf{E}{\bf Y})={\boldsymbol X}{\boldsymbol\beta}, \] where \({\boldsymbol\beta}\) is a vector of unknown parameters. The maximum likelihood based approach is used for the parameter estimation, where a version of the IRLS algorithm is applied (Newton???Raphson method, Fisher's scoring method, ...).
Predicted probability can be obtained by the expit (inverse of logit) transformation \[ \widehat{\mathsf{P}}[Y_i=1]=\frac{1}{1+\exp\{-{\boldsymbol X}_{i,\bullet}\widehat{\boldsymbol\beta}\}}. \]
For our data analysis below, we are going to expand on Example 2 about getting into graduate school. We have generated hypothetical data.
mydata <- read.csv("http://www.karlin.mff.cuni.cz/~pesta/prednasky/NMFM404/Data/binary.csv")
## view the first few rows of the data
head(mydata)
## admit gre gpa rank ## 1 0 380 3.61 3 ## 2 1 660 3.67 3 ## 3 1 800 4.00 1 ## 4 1 640 3.19 4 ## 5 0 520 2.93 4 ## 6 1 760 3.00 2
This dataset has a binary response (outcome, dependent) variable called admit. There are three predictor variables: gre, gpa and rank. We will treat the variables gre and gpa as continuous. The variable rank takes on the values 1 through 4. Institutions with a rank of 1 have the highest prestige, while those with a rank of 4 have the lowest. We can get basic descriptives for the entire data set by using summary. To get the standard deviations, we use sapply to apply the sd function to each variable in the dataset.
summary(mydata)
## admit gre gpa rank ## Min. :0.0000 Min. :220.0 Min. :2.260 Min. :1.000 ## 1st Qu.:0.0000 1st Qu.:520.0 1st Qu.:3.130 1st Qu.:2.000 ## Median :0.0000 Median :580.0 Median :3.395 Median :2.000 ## Mean :0.3175 Mean :587.7 Mean :3.390 Mean :2.485 ## 3rd Qu.:1.0000 3rd Qu.:660.0 3rd Qu.:3.670 3rd Qu.:3.000 ## Max. :1.0000 Max. :800.0 Max. :4.000 Max. :4.000
sapply(mydata, sd)
## admit gre gpa rank ## 0.4660867 115.5165364 0.3805668 0.9444602
## two-way contingency table of categorical outcome and predictors we want ## to make sure there are not 0 cells xtabs(~admit + rank, data = mydata)
## rank ## admit 1 2 3 4 ## 0 28 97 93 55 ## 1 33 54 28 12
Below is a list of some analysis methods you may have encountered. Some of the methods listed are quite reasonable while others have either fallen out of favor or have limitations.
The code below estimates a logistic regression model using the glm (generalized linear model) function. First, we convert rank to a factor to indicate that rank should be treated as a categorical variable.
mydata$rank <- factor(mydata$rank) mylogit <- glm(admit ~ gre + gpa + rank, data = mydata, family = "binomial")
mylogit), R will not produce any output from our regression. In order to get the results we use the summary command:
summary(mylogit)
## ## Call: ## glm(formula = admit ~ gre + gpa + rank, family = "binomial", ## data = mydata) ## ## Deviance Residuals: ## Min 1Q Median 3Q Max ## -1.6268 -0.8662 -0.6388 1.1490 2.0790 ## ## Coefficients: ## Estimate Std. Error z value Pr(>|z|) ## (Intercept) -3.989979 1.139951 -3.500 0.000465 *** ## gre 0.002264 0.001094 2.070 0.038465 * ## gpa 0.804038 0.331819 2.423 0.015388 * ## rank2 -0.675443 0.316490 -2.134 0.032829 * ## rank3 -1.340204 0.345306 -3.881 0.000104 *** ## rank4 -1.551464 0.417832 -3.713 0.000205 *** ## --- ## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 ## ## (Dispersion parameter for binomial family taken to be 1) ## ## Null deviance: 499.98 on 399 degrees of freedom ## Residual deviance: 458.52 on 394 degrees of freedom ## AIC: 470.52 ## ## Number of Fisher Scoring iterations: 4
gre and gpa are statistically significant, as are the three terms for rank. The logistic regression coefficients give the change in the log odds of the outcome for a one unit increase in the predictor variable.gre, the log odds of admission (versus non-admission) increases by 0.002.gpa, the log odds of being admitted to graduate school increases by 0.804.rank have a slightly different interpretation. For example, having attended an undergraduate institution with rank of 2, versus an institution with a rank of 1, changes the log odds of admission by -0.675.We can use the confint function to obtain confidence intervals for the coefficient estimates. Note that for logistic models, confidence intervals are based on the profiled log-likelihood function. We can also get CIs based on just the standard errors by using the default method.
## CIs using profiled log-likelihood confint(mylogit)
## 2.5 % 97.5 % ## (Intercept) -6.2716202334 -1.792547080 ## gre 0.0001375921 0.004435874 ## gpa 0.1602959439 1.464142727 ## rank2 -1.3008888002 -0.056745722 ## rank3 -2.0276713127 -0.670372346 ## rank4 -2.4000265384 -0.753542605
## CIs using standard errors confint.default(mylogit)
## 2.5 % 97.5 % ## (Intercept) -6.2242418514 -1.755716295 ## gre 0.0001202298 0.004408622 ## gpa 0.1536836760 1.454391423 ## rank2 -1.2957512650 -0.055134591 ## rank3 -2.0169920597 -0.663415773 ## rank4 -2.3703986294 -0.732528724
We can test for an overall effect of rank using the wald.test function of the aod library. The order in which the coefficients are given in the table of coefficients is the same as the order of the terms in the model. This is important because the wald.test function refers to the coefficients by their order in the model. We use the wald.test function. b supplies the coefficients, while Sigma supplies the variance covariance matrix of the error terms, finally Terms tells R which terms in the model are to be tested, in this case, terms 4, 5, and 6, are the three terms for the levels of rank.
wald.test(b = coef(mylogit), Sigma = vcov(mylogit), Terms = 4:6)
## Wald test: ## ---------- ## ## Chi-squared test: ## X2 = 20.9, df = 3, P(> X2) = 0.00011
20.9, with three degrees of freedom is associated with a p-value of 0.00011 indicating that the overall effect of rank is statistically significant.
We can also test additional hypotheses about the differences in the coefficients for the different levels of rank. Below we test that the coefficient for rank=2 is equal to the coefficient for rank=3. The first line of code below creates a vector l that defines the test we want to perform. In this case, we want to test the difference (subtraction) of the terms for rank=2 and rank=3 (i.e., the 4th and 5th terms in the model). To contrast these two terms, we multiply one of them by 1, and the other by -1. The other terms in the model are not involved in the test, so they are multiplied by 0. The second line of code below uses L=l to tell R that we wish to base the test on the vector l (rather than using the Terms option as we did above).
l <- cbind(0, 0, 0, 1, -1, 0) wald.test(b = coef(mylogit), Sigma = vcov(mylogit), L = l)
## Wald test: ## ---------- ## ## Chi-squared test: ## X2 = 5.5, df = 1, P(> X2) = 0.019
5.5 with 1 degree of freedom is associated with a p-value of 0.019, indicating that the difference between the coefficient for rank=2 and the coefficient for rank=3 is statistically significant.
You can also exponentiate the coefficients and interpret them as odds-ratios. R will do this computation for you. To get the exponentiated coefficients, you tell R that you want to exponentiate (exp), and that the object you want to exponentiate is called coefficients and it is part of mylogit (coef(mylogit)). We can use the same logic to get odds ratios and their confidence intervals, by exponentiating the confidence intervals from before. To put it all in one table, we use cbind to bind the coefficients and confidence intervals column-wise.
## odds ratios only exp(coef(mylogit))
## (Intercept) gre gpa rank2 rank3 rank4 ## 0.0185001 1.0022670 2.2345448 0.5089310 0.2617923 0.2119375
## odds ratios and 95% CI exp(cbind(OR = coef(mylogit), confint(mylogit)))
## OR 2.5 % 97.5 % ## (Intercept) 0.0185001 0.001889165 0.1665354 ## gre 1.0022670 1.000137602 1.0044457 ## gpa 2.2345448 1.173858216 4.3238349 ## rank2 0.5089310 0.272289674 0.9448343 ## rank3 0.2617923 0.131641717 0.5115181 ## rank4 0.2119375 0.090715546 0.4706961
gpa, the odds of being admitted to graduate school (versus not being admitted) increase by a factor of 2.23. Note that while R produces it, the odds ratio for the intercept is not generally interpreted.
You can also use predicted probabilities to help you understand the model. Predicted probabilities can be computed for both categorical and continuous predictor variables. In order to create predicted probabilities we first need to create a new data frame with the values we want the independent variables to take on to create our predictions.
We will start by calculating the predicted probability of admission at each value of rank, holding gre and gpa at their means. First we create and view the data frame.
newdata1 <- with(mydata, data.frame(gre = mean(gre), gpa = mean(gpa), rank = factor(1:4))) ## view data frame newdata1
## gre gpa rank ## 1 587.7 3.3899 1 ## 2 587.7 3.3899 2 ## 3 587.7 3.3899 3 ## 4 587.7 3.3899 4
gre must be named gre). Now that we have the data frame we want to use to calculate the predicted probabilities, we can tell R to create the predicted probabilities. The first line of code below is quite compact, we will break it apart to discuss what various components do. The newdata1$rankP tells R that we want to create a new variable in the dataset (data frame) newdata1 called rankP, the rest of the command tells R that the values of rankP should be predictions made using the predict( ) function. The options within the parentheses tell R that the predictions should be based on the analysis mylogit with values of the predictor variables coming from newdata1 and that the type of prediction is a predicted probability (type="response"). The second line of the code lists the values in the data frame newdata1. Although not particularly pretty, this is a table of predicted probabilities.
newdata1$rankP <- predict(mylogit, newdata = newdata1, type = "response") newdata1
## gre gpa rank rankP ## 1 587.7 3.3899 1 0.5166016 ## 2 587.7 3.3899 2 0.3522846 ## 3 587.7 3.3899 3 0.2186120 ## 4 587.7 3.3899 4 0.1846684
0.52 for students from the highest prestige undergraduate institutions (rank=1), and 0.18 for students from the lowest ranked institutions (rank=4), holding gre and gpa at their means. We can do something very similar to create a table of predicted probabilities varying the value of gre and rank. We are going to plot these, so we will create 100 values of gre between 200 and 800, at each value of rank (i.e., 1, 2, 3, and 4).
newdata2 <- with(mydata, data.frame(gre = rep(seq(from = 200, to = 800, length.out = 100),
4), gpa = mean(gpa), rank = factor(rep(1:4, each = 100))))
newdata3 <- cbind(newdata2, predict(mylogit, newdata = newdata2, type = "link",
se = TRUE))
newdata3 <- within(newdata3, {
PredictedProb <- plogis(fit)
LL <- plogis(fit - (1.96 * se.fit))
UL <- plogis(fit + (1.96 * se.fit))
})
## view first few rows of final dataset
head(newdata3)
## gre gpa rank fit se.fit residual.scale UL ## 1 200.0000 3.3899 1 -0.8114870 0.5147714 1 0.5492064 ## 2 206.0606 3.3899 1 -0.7977632 0.5090986 1 0.5498513 ## 3 212.1212 3.3899 1 -0.7840394 0.5034491 1 0.5505074 ## 4 218.1818 3.3899 1 -0.7703156 0.4978239 1 0.5511750 ## 5 224.2424 3.3899 1 -0.7565919 0.4922237 1 0.5518545 ## 6 230.3030 3.3899 1 -0.7428681 0.4866494 1 0.5525464 ## LL PredictedProb ## 1 0.1393812 0.3075737 ## 2 0.1423880 0.3105042 ## 3 0.1454429 0.3134499 ## 4 0.1485460 0.3164108 ## 5 0.1516973 0.3193867 ## 6 0.1548966 0.3223773
ggplot2 package for graphing. Below we make a plot with the predicted probabilities, and 95% confidence intervals.
ggplot(newdata3, aes(x = gre, y = PredictedProb)) + geom_ribbon(aes(ymin = LL,
ymax = UL, fill = rank), alpha = 0.2) + geom_line(aes(colour = rank),
size = 1)
We may also wish to see measures of how well our model fits. This can be particularly useful when comparing competing models. The output produced by summary(mylogit) included indices of fit (shown below the coefficients), including the null and deviance residuals and the AIC. One measure of model fit is the significance of the overall model. This test asks whether the model with predictors fits significantly better than a model with just an intercept (i.e., a null model). The test statistic is the difference between the residual deviance for the model with predictors and the null model. The test statistic is distributed chi-squared with degrees of freedom equal to the differences in degrees of freedom between the current and the null model (i.e., the number of predictor variables in the model). To find the difference in deviance for the two models (i.e., the test statistic) we can use the command:
with(mylogit, null.deviance - deviance)
## [1] 41.45903
with(mylogit, df.null - df.residual)
## [1] 5
with(mylogit, pchisq(null.deviance - deviance, df.null - df.residual, lower.tail = FALSE))
## [1] 7.578194e-08
logLik(mylogit)
## 'log Lik.' -229.2587 (df=6)