Logistic Regression
The ASTA team
Introduction to logistic regression
Binary response
- We consider a binary response \(y\) with outcome \(1\) or \(0\). This might be a code indicating whether a person is able or unable to perform a given task.
- Furthermore, we are given an explanatory variable \(x\), which is numeric, e.g. age.
- We shall study models for \[P(y=1\, |\, x)\] i.e. the probability that a person of age \(x\) is able to complete the task.
- We shall see methods for determining whether or not age actually influences the probability, i.e. is \(y\) independent of \(x\)?
A linear model
\[P(y=1\, |\, x)=\alpha+\beta x\] is simple, but often inappropiate. If \(\beta\) is positive and \(x\) sufficiently large, then the probability exceeds \(1\).
Simple logistic regression
Logistic model
Instead we consider the odds that the person is able to complete the task \[\mathtt{Odds}(y=1\, |\, x)=\frac{P(y=1\, |\, x)}{P(y=0\, |\, x)}=
\frac{P(y=1\, |\, x)}{1-P(y=1\, |\, x)}\] which can have any positive value.
The logistic model is defined as: \[\mathtt{logit}(P(y=1\, |\, x))=\log(\mathtt{Odds}(y=1\, |\, x))=\alpha+\beta x\] The function \(\mathtt{logit}(p)=\log(\frac{p}{1-p})\) - i.e. log of odds - is termed the logistic transformation.
Remark that log odds can be any number, where zero corresponds to \(P(y=1\,|\, x)=0.5\). Solving \(\alpha+\beta x=0\) shows that at age \(x_0=-\alpha/\beta\) you have fifty-fifty chance of solving the task.
Odds-ratio
Interpretation of \(\beta\):
What happens to odds, if we increase age by 1 year?
Consider the so-called odds-ratio: \[\frac{\mathtt{Odds}(y=1\, |\, x+1)}{\mathtt{Odds}(y=1\, |\, x)}=
\frac{\exp(\alpha+\beta(x+1))}{\exp(\alpha+\beta x)}=\exp(\beta)\] where we see, that \(\exp(\beta)\) equals the odds for age \(x+1\) relative to odds at age \(x\).
This means that when age increase by 1 year, then the relative change \[ \frac{\exp(\alpha+\beta(x+1))-\exp(\alpha+\beta x)}{\exp(\alpha+\beta x)}\] in odds is given by \(100(\exp(\beta)-1)\%\).
Simple logistic regression
Examples of logistic curves for \(P(y=1|x)\). The black curve has a positive \(\beta\)-value (=10), whereas the red has a negative \(\beta\) (=-3).
In addition we note that:
- Increasing the absolute value of \(\beta\) yields a steeper curve.
- When \(P(y=1\, |\, x)=\frac{1}{2}\) then logit is zero, i.e. \(\alpha+\beta x=0\).
This means that at age \(x=-\frac{\alpha}{\beta}\) you have 50% chance to perform the task.
Example: Credit card data
We shall investigate if income is a good predictor of whether or not you have a credit card.
- Data structure: For each level of income, we let
n denote the number of persons with that income, and credit how many of these that carries a credit card.
creInc <- read.csv("https://asta.math.aau.dk/datasets?file=income-credit.csv")
## Income n credit
## 1 12 1 0
## 2 13 1 0
## 3 14 8 2
## 4 15 14 2
## 5 16 9 0
## 6 17 8 2
Example: Fitting the model
modelFit <- glm(cbind(credit,n-credit) ~ Income, data = creInc, family = binomial)
cbind gives a matrix with two column vectors: credit and n-credit, where the latter is the vector counting the number of persons without a credit card.
The response has the form cbind(credit,n-credit).
We need to use the function glm (generalized linear model).
The argument family=binomial tells the function that the data has binomial variation. Leaving out this argument will lead R to believe that data follows a normal distribution - as with lm.
The function coef extracts the coefficients (estimates of parameters) from the model summary:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -3.5179469 0.71033573 -4.952513 7.326117e-07
## Income 0.1054089 0.02615743 4.029788 5.582714e-05
Test of no effect
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -3.5179469 0.71033573 -4.952513 7.326117e-07
## Income 0.1054089 0.02615743 4.029788 5.582714e-05
Our model for dependence of odds of having a credit card related to income(\(x\)) is \[\mathtt{logit}(x)=\alpha+\beta x\] The hypothesis of no relation between income and ability to obtain a credit card corresponds to \[H_0:\ \ \beta=0\] with the alternative \(\beta\not=0\). Inspecting the summary reveals that \(\hat{\beta}=0.1054\) is more than 4 standard errors away from zero.
With a z-score equal to 4.03 we get the tail probability
ptail <- 2*(1-pdist("norm",4.03,xlim=c(-5,5)))
## [1] 5.577685e-05
Which is very significant - as reflected by the p-value.
Confidence interval for odds ratio
From the summary:
\(\hat{\beta}=0.10541\) and hence \(\exp(\hat{\beta})-1=0.11\). If income increases by 1000 euro, then odds increases by 11%.
Standard error on \(\hat{\beta}\) is \(0.02616\) and hence a 95% confidence interval for log-odds ratio is \(\hat{\beta}\pm 1.96\times 0.02616=(0.054;0,157)\).
Corresponding interval for odds ratio: \(\exp((0.054;0,157))=(1.056;1.170)\),
i.e. the increase in odds is - with confidence 95% - between 5.6% and 17%.
Plot of model predictions against actual data
- Tendency is fairly clear and very significant.
- Due to low sample size at some income levels, the deviations are quite large.
Multiple logistic regression
Several numeric predictors
We generalize the model to the case, where we have \(k\) predictors \(x_1,x_2,\ldots,x_k\). Where some might be dummies for a factor. \[\mathtt{logit}(P(y=1\, |\, x_1,x_2,\ldots,x_k))=
\alpha+\beta_1 x_1+\cdots+\beta_k x_k\] Interpretation of \(\beta\)-values is unaltered: If we fix \(x_2,\ldots,x_k\) and increase \(x_1\) by one unit, then the relative change in odds is given by \(\exp(\beta_1)-1\).
Example
Wisconsin Breast Cancer Database covers 683 observations of 10 variables in relation to examining tumors in the breast.
- Nine clinical variables with a score between 0 and 10.
- The binary variable
Class with levels benign/malignant.
- By default
R orders the levels lexicografically and chooses the first level as reference (\(y=0\)). Hence benign is reference, and we model odds of malignant.
We shall work with only 4 of the predictors, where two of these have been discretized.
BC <- read.table("https://asta.math.aau.dk/datasets?file=BC0.dat",header=TRUE)
head(BC)
## nuclei cromatin Size.low Size.medium Shape.low Class
## 1 1 3 TRUE FALSE TRUE benign
## 2 10 3 FALSE TRUE FALSE benign
## 3 2 3 TRUE FALSE TRUE benign
## 4 4 3 FALSE FALSE FALSE benign
## 5 1 3 TRUE FALSE TRUE benign
## 6 10 9 FALSE FALSE FALSE malignant
Global test of no effects
First we fit the model mainEffects with main effect of all predictors - remember the notation ~ . for all predictors. Then we fit the model noEffects with no predictors.
mainEffects <- glm(factor(Class)~., data=BC, family=binomial)
noEffects <- glm(factor(Class)~1, data=BC, family=binomial)
First we want to test, whether there is any effect of the predictors, i.e the null hypothesis \[H_0:\ \ \beta_1=\beta_2=\beta_3=\beta_4=\beta_5=0\]
Example
Similarly to lm we can use the function anova to compare mainEffects and noEffects. Only difference is that we need to tell the function that the test is a chi-square test and not an F-test.
anova(noEffects, mainEffects, test="Chisq")
## Analysis of Deviance Table
##
## Model 1: factor(Class) ~ 1
## Model 2: factor(Class) ~ nuclei + cromatin + Size.low + Size.medium +
## Shape.low
## Resid. Df Resid. Dev Df Deviance Pr(>Chi)
## 1 682 884.35
## 2 677 135.06 5 749.29 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
mainEffects is a much better model.
The test statistic is the Deviance (749.29), which should be small.
It is evaluated in a chi-square with 5 (the number of parameters equal to zero under the nul hypothesis) degrees of freedom.
The 95%-critical value for the \(\chi^2(5)\) distribution is 11.07 and the p-value is in practice zero.
Test of influence of a given predictor
round(coef(summary(mainEffects)),4)
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.7090 0.8570 -0.8274 0.4080
## nuclei 0.4403 0.0823 5.3484 0.0000
## cromatin 0.5058 0.1444 3.5026 0.0005
## Size.lowTRUE -3.6154 0.8081 -4.4740 0.0000
## Size.mediumTRUE -2.3773 0.7188 -3.3074 0.0009
## Shape.lowTRUE -2.1490 0.6054 -3.5496 0.0004
For each predictor \(p\) can we test the hypothesis: \[H_0:\ \ \beta_p=0\]
- Looking at the
z-values, there is a clear effect of all 5 predictors. Which of course is also supported by the p-values.
Prediction and classification
BC$pred <- round(predict(mainEffects,type="response"),3)
- We add the column
pred to our dataframe BC.
pred is the final model’s estimate of the probability of malignant.
head(BC[,c("Class","pred")])
## Class pred
## 1 benign 0.011
## 2 benign 0.945
## 3 benign 0.017
## 4 benign 0.929
## 5 benign 0.011
## 6 malignant 1.000
Not good for patients 2 and 4.
We may classify by round(BC$pred):
- 0 to denote
benign (probability BC$pred less than 0.5)
- 1 to denote
malignant (probability BC$pred more than 0.5)
tally(~ Class + round(pred), data = BC)
## round(pred)
## Class 0 1
## benign 433 11
## malignant 11 228
22 patients are misclassified.
sort(BC$pred[BC$Class=="malignant"])[1:5]
## [1] 0.035 0.037 0.089 0.190 0.205
There is a malignant woman with a predicted probability of malignancy, which is only 3.5%.
If we assign all women with predicted probability of malignancy above 5% to further investigation, then we only miss two malignant.
tally(~ Class + I(pred>.05), data = BC)
## I(pred > 0.05)
## Class TRUE FALSE
## benign 50 394
## malignant 237 2
The expense is that the number of false positive increases from 11 to 50.
tally(~ Class + I(pred>.1), data = BC)
## I(pred > 0.1)
## Class TRUE FALSE
## benign 27 417
## malignant 236 3
- If we instead set the alarm to 10%, then the number of false positives decreases from 50 to 27.
- But at the expense of 3 false negative.
