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Example 1 Case Study 20.1: Survival in the Donner Party. What is the relationship between age

and sex of individuals in the Donner Party and whether or not they survived?

Example 2 Birthweight data: birthweights of 189 newborns were recorded along with a number

of other variables concerning the mother: weight, smoker or not, race, etc. Suppose we were

interested only in whether the baby was underweight (defined to be under 2500 gms) or not and

what characteristics of the mother, if any, are associated with having underweight babies.

Example 3 Pronghorn data: In a study of winter habitat selection by pronghorn in the Red Rim

area in south-central Wyoming (Source: Manly, McDonald, and Thomas 1993, Resource

Selection by Animals, Chapman and Hall, pp. 16-24; data from Ryder 1983), presence/absence of

pronghorn during winters of 1980-81 and 1981-82 were recorded for a systematic sample of 256

plots of 4 ha. each Other variables recorded for each plot were: density (in thousands/ha) of

sagebrush, black greasewood, Nuttal’s saltbrush, and Douglas rabbitbrush, and the slope,

distance to water, and aspect. What variables are most strongly associated with

presence/absence of pronghorn and can you formulate a model to predict the probability that

pronghorn will be present on a plot?

Could use linear regression to regress 0/1 response on quantitative and categorical explanatory

variables. What are the problems with this approach?

X 1 ,..., X p : explanatory variables

page 2

• Rather than model µ (Y ) = π as a linear function of the explanatory variables, model

⎛ π ⎞

logit(π) = ln⎜ ⎟ as a linear function of the explanatory variables; that is:

⎝1− π ⎠

logit(π) = β 0 + β1 X 1 + … + β p X p

eη

π=

1 + eη

Example 3: In the pronghorn example, suppose, hypothetically, the true relationship between

probability of use and distance to water (in meters) followed the logit model:

logit(π) = 3 - .0015Water

e 3 − .0015 Water

Then π = .

1 + e 3 − .0015Water

Calculate π for the following distances (note that it might be easier to compute 1-π =

1

, then subtract from 1),

3 − .0015Water

1+ e

page 3

1.0 0.8

Probability of use

0.4 0.6

0.2

0.0

Distance to water (m)

• What is the interpretation of the coefficient -.0015 for the variable distance to water?

For every 1 m. increase in the distance to water, the log-odds of use decrease by .0015;

for every 1 km. increase in distance to water, log-odds of use decrease by 1.5.

• More meaningful: for every 1 m. increase in the distance to water, the odds of use change

by a multiplicative factor of e −.0015 = .999; for every 1 km. increase in distance to water,

the odds of use change by a multiplicative factor of e −1.5 = .223 (we could also reverse

these statements; for example, the odds of use increase by a factor of e1.5 = 4.48 for

every km. closer to water a plot is.)

Variance

µ (Y X 1 ,…, X p ) = π

SD( Y X 1 , …, X p ) = π (1 − π )

The logistic regression model is an example of a generalized linear model (in contrast to a

general linear model which is the usual regression model with normal errors and constant

variance). A generalized linear model is specified by:

In logistic regression, the link function is the logit function.

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2. the distribution of Y for a fixed set of values of X 1 , … , X p . In the logit model, this is the

Bernoulli distribution.

The usual linear regression model is also a generalized linear model. The link function is the

identity: that is, f ( µ ) = µ , and the distribution is normal with constant variance.

There are other generalized linear models which are useful (e.g., Poisson response distribution

with log link function). A general methodology has been developed to fit and analyze these

models.

Estimation of parameters in linear regression model was by least squares. If we assume normal

errors with constant variance, the least squares estimators are the same as the maximum

likelihood estimators (MLE’s).

Maximum likelihood estimation is based on a simple principle: the estimates of the parameters in

a model are the values which maximize the probability (likelihood) of observing the sample data

we have.

proportion of students own a car. We find that 6 out of the 10 own a car. What is the MLE of

the proportion p of all students who won a car? What do we think it should turn out to be?

We model the responses from the students as 10 independent Bernoulli trials with probability of

success p on each trial. Then the total number of successes, say Y, in 10 trials follows a binomial

model:

⎛10 ⎞

Pr(Y = y ) = ⎜⎜ ⎟⎟ p y (1 − p)10− y , y = 0,1,…,10

⎝ y⎠

The maximum likelihood principle says to find the value of p which maximizes the probability

of observing the number of successes we actually observed in the sample; that is, find p to

maximize:

⎛10 ⎞

Pr(Y = 4) = ⎜⎜ ⎟⎟ p 4 (1 − p) 6

⎝4⎠

This is called the likelihood function. The following is a graph of Pr(Y=4) versus p. At what

value of p does it appear to be maximized?

page 5

0.25

0.20

0.15

Pr(Y = 4)

0.10

0.05

0.0

p

We can also find the exact solution using calculus. Note that finding the value of p to maximize

Pr(Y = 4) is equivalent to finding the value of p which maximizes

⎡⎛10 ⎞⎤

[ ⎡⎛10 ⎞⎤

]

ln[Pr(Y = 4)] = ln ⎢⎜⎜ ⎟⎟⎥ + ln p 4 (1 − p ) 6 = ln ⎢⎜⎜ ⎟⎟⎥ + 4 ln p + 6 ln(1 − p )

⎣⎝ 4 ⎠⎦ ⎣⎝ 4 ⎠⎦

By repeating this process but replacing 10 by n (the number of trials) and 4 by y (the number of

successes), we find a general expression for the MLE of p in n independent Bernoulli trials:

y

pˆ =

n

• Back to logistic regression: we use the maximum likelihood principle to find estimators of

the β’s in the logistic regression model. The likelihood function is the probability of

observing the particular set of failures and successes that we observed in the sample. But

there’s a difference from the binomial model above: the model says that the probability of

success is possibly different for each subject because it depends on the explanatory

variables X 1 , … , X p . Dropping the subscript i to avoid confusion, the probability of

success for an individual is:

page 6

β 0 + β1 X 1 +…+ β p X p

e

Pr(Y = 1) = π where π = β 0 + β1 X 1 +…+ β p X p

.

1+ e

• Note that we can also write the model for a single individual as

Pr(Y = y ) = π y (1 − π )1− y , y = 0, 1.

• If the responses are independent, then the probability of observing the set of 0/1 responses

we observed is

n

Pr(Y1 = y1 , Y2 = y2 , …, Yn = yn ) = π 1y1 (1 − π 1 ) y1 π 2y2 (1 − π 2 ) y2 …π nyn (1 − π n ) yn = ∏ π iyi (1 − π i ) yi

i =1

where each of the π i ’s is, in turn, a function of the β i ’s. Therefore, we maximize this

likelihood function as a function of the β i ’s. This cannot be done analytically and must be

done numerically using a computer program.

binary dependent variable and all the covariates.

• If any of the covariates are categorical then click Categorical to tell SPSS how to create

indicator variables (or other way of coding) for each categorical variable. If a binary

covariate is already coded as 0-1, it’s not necessary to identify it as categorical.

• Interaction terms can be added when specifying the covariates in the logistic regression

command in SPSS. Select two or more variables (keep the Ctrl key pressed while

selecting the second and subsequent variables), then press the “a*b>” button.

Example: Birthweight data. The response variable was the 0/1 variable “low” which was an

indicator of low birthweight, An additive model with all the covariates was fit. The variables

were:

Name Meaning

low Birthweight < 2500 gm.

age Age (years)

lwt Weight at last menstrual period (lbs)

race Race (1=White, 2=Black, 3=Other)

smoke Smoke (0/1)

ptl Number of premature labors

ht Hypertension (0.1)

ui Uterine irritability (0/1)

ftv Number of physician visits in first trimester

page 7

There is a lot of SPSS out put. For now, we’re interested in only two tables: one that indicates

how the categorical variable Race was coded, and the final table of model coefficients (under

Block 1).

Parameter coding

Frequency (1) (2)

Race (1=White, White 96 .000 .000

2=Black, 3=Other) Black 26 1.000 .000

Other 67 .000 1.000

I chose Indicator coding for Race with the first category (White) as the reference category. The

two columns of this table are the two indicator variables for Race.

B S.E. Wald df Sig. Exp(B) Lower Upper

Step

a

age -.030 .037 .637 1 .425 .971 .903 1.044

1 lwt -.015 .007 4.969 1 .026 .985 .971 .998

race 7.116 2 .028

race(1) 1.272 .527 5.820 1 .016 3.569 1.270 10.033

race(2) .880 .441 3.990 1 .046 2.412 1.017 5.723

smoke .939 .402 5.450 1 .020 2.557 1.163 5.624

ptl .543 .345 2.474 1 .116 1.722 .875 3.388

ht 1.863 .698 7.136 1 .008 6.445 1.642 25.291

ui .768 .459 2.793 1 .095 2.155 .876 5.301

ftv .065 .172 .143 1 .705 1.067 .761 1.497

Constant .481 1.197 .161 1 .688 1.617

a. Variable(s) entered on step 1: age, lwt, race, smoke, ptl, ht, ui, ftv.

2. S.E. The standard errors (SE’s) for the estimated coefficients (the β i ’s) are estimated

using asymptotic results for maximum likelihood estimators. An approximate confidence

interval for each coefficient can be calculated using β i ± z SE where z is the appropriate

percentile of the standard normal distribution. We don’t use the t-distribution; that only

applies to the linear regression model with normal errors.

2

⎛ βˆi ⎞

3. Wald: the Wald statistic is ⎜ ⎟ . It is used as a two-sided test of the hypothesis

⎜ SE ( βˆ ) ⎟

⎝ i ⎠

H 0 : β i = 0 given that all the other variables are in the model. Under this null

hypothesis βˆ / SE ( βˆ ) has approximately a N(0,1) distribution. The square of a N(0,1)

i i

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is a chi-square distribution with 1 d.f. so the Wald statisic can be compared to a χ 2 (1) to

get a test of H 0 : β i = 0 .

4. df: The d.f. for the chi-square distribution which the Wald statistic is compared to. It is 1

except for categorical explanatory variables with more than 2 levels (however, the test for

each indicator variable involved in the categorical variable still has 1 d.f.).

5. Sig.: The P-value for the test of H 0 : β i = 0 using the Wald statistic. This is the area to

the right of the Wald statistic in a χ 2 (1) distribution.

6. Exp(B): exp(β i ) has the interpretation that it represents how many times the odds of a

positive response increase for every one-unit increase in xi , given that the values of the

other variables in the model remain the same. For example, the coefficient for Smoke is

2.557. Since Smoke is 0/1, this means that, according to this model, the odds that a

smoker will have a low birthweight baby are estimated to be 2.557 times higher (95% CI:

1.163 to 5.624; see next column) than the odds a non-smoker will, even after adjusting

for Last weight, Race and the other variables in the model. Similarly, every one-year

increase in age reduces the odds of a low birthweight baby to .971 of what they were

(95% CI: .903 to 1.044), after adjusting for the other variables.

7. 95.0% C.I. for Exp(B): A confidence interval for exp(β i ) (the true value) can be

[ ( ) ( )]

calculated as exp β i − z SE ,exp β i + z SE . SPSS will calculate a confidence interval

for each exp(β i ) in the model if, under Options, you select “CI for exp(B).”

In linear regression, we used the extra sum-of-squares F test to compare two nested models (two

models are nested if one is a special case of the other). The analogous test in logistic regression

compares the values of –2ln(Maximized likelihood function). What is this quantity? Recall that

page 9

the MLE’s of the β i ’s are the values that maximize the likelihood function of the data (defined a

couple of pages ago). So, we find that maximum value of the likelihood function, take the

natural log and multiply by –2.

• The quantity –2 ln(Maximized likelihood) is also called the deviance of a model since

larger values indicate greater deviation from the assumed model. Comparing two nested

models by the difference in deviances is a drop-in-deviance test.

SPSS gives the value of –2 ln(Maximized likelihood) in the output. For the full model for low

birthweight examined previously:

Model Summary

Step likelihood R Square R Square

1 201.285a .162 .228

a. Estimation terminated at iteration number 5 because

parameter estimates changed by less than .001.

• The difference between the values of –2ln(Maximized likelihood function) for a full and

reduced model has approximately a chi-square distribution if the null hypothesis that the

extra parameters are all 0 is true. The d.f. is the difference in the number of parameters

for the two models.

Example:

Compare the full birthweight model to one without Smoke. The value of –2ln(Maximized

likelihood function) for the model without Smoke is:

Model Summary

Step likelihood R Square R Square

1 206.906a .137 .192

a. Estimation terminated at iteration number 5 because

parameter estimates changed by less than .001.

The P-value is the area to the right of 5.621 in χ 2 (1) distribution (since there is one less

parameter in the reduced model). Thus, P =.018, which indicates moderately strong evidence of

an effect of smoking on the probability of having a low-birthweight baby after adjusting for the

other variables in the model.

• The drop-in-deviance test is a likelihood ratio test (LR test) because it is based on the

natural log of the ratio of the maximized likelihoods (the difference of logs is the log of

the ratio). The extra sum-of squares F-test in linear regression also turns out to be a

likelihood ratio test.

page 10

• If the full and reduced models differ by only one parameter, as in this example, then the

likelihood ratio test is testing the same thing as the Wald test above. In this example, the

test statistic is slightly different than the Wald test value of 5.450 and P = .020. The

likelihood ratio test is preferred. The two tests will generally give similar results, but not

always.

• The relationship between the Wald test and the likelihood ratio test is analogous to

relationship between the t-test for a single coefficient and the F-test in linear regression.

However, in linear regression, the two tests are exactly equivalent. Not so in logistic

regression.

One can obtain a LR test for each coefficient in SPSS by selecting “Backward-LR” under

Method. Also be sure that Display: At each step is checked under Options. This performs a

backward stepwise logistic regression. All we are using it for, though, is the output at the first

step where it reports a likelihood ratio test for each variable with all the other variables in the

model. The table we are looking for looks like this. The LR test for each term is listed under

Step 1.

Model if Term Removed

Change in

Model Log -2 Log Sig. of the

Variable Likelihood Likelihood df Change

Step age -100.965 .645 1 .422

1 lwt -103.402 5.520 1 .019

race -104.376 7.468 2 .024

smoke -103.453 5.621 1 .018

ptl -101.916 2.546 1 .111

ht -104.403 7.521 1 .006

ui -102.014 2.742 1 .098

ftv -100.713 .142 1 .706

Step age -100.993 .559 1 .455

2 lwt -103.404 5.381 1 .020

race -104.386 7.344 2 .025

smoke -103.458 5.489 1 .019

ptl -101.974 2.521 1 .112

ht -104.406 7.384 1 .007

ui -102.053 2.680 1 .102

Step lwt -104.056 6.126 1 .013

3 race -105.155 8.325 2 .016

smoke -103.864 5.743 1 .017

ptl -102.108 2.231 1 .135

ht -104.732 7.479 1 .006

ui -102.449 2.912 1 .088

Step lwt -105.583 6.949 1 .008

4 race -106.413 8.609 2 .014

smoke -105.755 7.293 1 .007

ht -105.957 7.698 1 .006

ui -104.124 4.031 1 .045

Model Selection

Both AIC and BIC can be used as model selection criteria. As with linear regression models,

they are only relative measures of fit, not absolute measures of fit.

AIC = Deviance + 2p

page 11

where p is the number of parameters in the model. Stepwise model selection methods are

available in SPSS using likelihood ratio tests or Wald’s test. The LR methods are preferred.

Other software programs, like S-Plus, have stepwise procedures using AIC or BIC.

Interactions

Interaction terms can be added when specifying the covariates in the logistic regression

command in SPSS. Select two or more variables (keep the Ctrl key pressed while selecting the

second and subsequent variables), then press the “a*b>” button.

Residuals

There are two standard ways to define a residual in logistic regression.

yi − πˆ i

1. Pearson residual = .

πˆ i (1 − πˆ i )

Logistic in SPSS, but it is labeled “Normalized Residual” in the data sheet. The Pearson

residual is the raw (unstandardized) residual y i − πˆ i standardized by its estimated standard

deviation.

⎧ − 2 ln πˆ i if yi = 1

⎪

2. Deviance residual = ⎨

⎪− − 2 ln(1 − πˆ ) if y = 0

⎩ i i

This is called the “Deviance Residual” in SPSS. The deviance residuals have the property

that the sum of the deviance residuals squared is the deviance D (= -2 ln(maximized

likelihood)) for the model.

The Pearson residual is more easily understood, but the deviance residual directly gives the

contribution of each point to the lack of fit of the model.

There is also a “Studentized residual” in SPSS (but labeled “Standard residual” in the data sheet).

It’s usually almost identical to the deviance residual so we won’t consider it here.

The residuals in a logistic regression (either Pearson or deviance) are not as useful as in a linear

regression unless the data are grouped (see Chapter 21). The residuals are not assumed to have a

normal distribution, as in linear regression. Since the residuals don’t have a normal distribution,

the usual ±2 or ±3 cutoffs don’t necessarily apply. Instead, we can simply look for outliers

among the distribution of Pearson or deviance residuals. We can plot the values against the

predicted probabilities.

Measures of influence

Measures of influence attempt to measure how much individual observations influence the

model. Observations with high influence merit special examination. Many measures of

influence have been suggested and are used for linear regression. Some of these have analogies

page 12

for logistic regression. However, the guidelines for deciding what is a big enough value of an

influence measure to merit special attention are less developed for logistic regression than for

linear regression and the guidelines developed there are sometimes not appropriate for logistic

regression.

Cook’s Distance: This is a measure of how much the residuals change when the case is deleted.

Large values indicate a large change when the observation is left out. Plot Di against case

number or against πˆ i and look for outliers.

The leverage is a measure of the potential influence of an observation. In linear regression, the

leverage is a function of how far its covariate vector x i is from the average. It is a function only

of the covariate vector. In logistic regression, the leverage is a function of x i and of π i (which

must be estimated) – it isn’t necessarily the observations which have the most extreme x i ’s

which have the most leverage.

Assessing the fit of a logistic regression model is difficult. Since the response is 0/1, plots of the

response versus explanatory variables are not as useful as when the response is continuous.

There is no good measure analogous to R2; SPSS will report a couple of R2-like measures that

have been proposed for logistic regression, but these don’t have the same interpretation as in

linear regression and are not particularly good measures of fit.

In theory, a chi-square goodness-of-fit test could be carried out by comparing the observed count

in each category (meaning each combination of the values of the explanatory variables) against

the expected count. However, unless there are multiple subjects in each combination of the

values of the covariates (the explanatory variables), the observed counts are 0’s and 1’s; the

expected counts are simply the πˆ i ’s. But the chi-square approximation for the goodness-of-fit

statistic does not hold when the expected counts are all less than 1 (most of them should be

above 5 to use the chi-square approximation). A way around this difficulty is to group the data.

The Hosmer-Lemeshow test groups individuals by their value of πˆ i into ten groups of about

equal size. That is, the tenth of the observations with the lowest values of πˆ i are put in the first

group, the next tenth lowest values in the second, and so on. It then totals the πˆ i ’s for everyone

in each group (that is, it totals the expected number of successes) and does the same for the

1 − πˆ i ’s (the expected number of failures). It then compares the observed and expected counts in

the 20 cells using Pearson’s X2 and compares the result to a chi-square with 8 d.f. The expected

counts still need to be large enough for the chi-square approximation to hold, but this is much

more likely to happen since we group the data. Since the cases are grouped, this test is “crude”

in a sense, but it is a useful tool.

Another goodness-of-fit tool is the classification table. Each observation is classified according

to its estimated π: if πˆ i > .5, then its classified as a “success” (a 1), otherwise as a “failure” (a 0).

The table of actual group versus predicted group is used to assess how well the classifier does.

This is a very crude way of assessing how well the model fits since it does not measure how far

πˆ i is from yi ; only whether it is on the same side of .5. as yi . In addition, if yi =1 is rare, then

page 13

the estimated probabilities may all be less than 1 and the classification table isn’t useful in

assessing fit (the same is true if yi =0 is rare).

page 14

Example

Birthweight data: using only LastWeight, Race, Smoke

Model Summary

Step likelihood R Square R Square

1 210.491a .120 .169

a. Estimation terminated at iteration number 5 because

parameter estimates changed by less than .001.

Step

a

lwt -.012 .045 .073 1 .786 .988

1 race 1.733 2 .420

race(1) -3.481 2.717 1.642 1 .200 .031

race(2) -2.969 2.907 1.043 1 .307 .051

smoke -.679 1.933 .123 1 .726 .507

lwt * race 1.271 2 .530

lwt by race(1) .017 .021 .634 1 .426 1.017

lwt by race(2) .025 .022 1.269 1 .260 1.026

lwt by smoke .008 .016 .257 1 .612 1.008

race * smoke 1.911 2 .385

race(1) by smoke 1.308 .953 1.882 1 .170 3.698

race(2) by smoke .667 1.180 .320 1 .572 1.949

lwt2 .000 .000 .167 1 .683 1.000

Constant 1.849 3.131 .349 1 .555 6.353

a. Variable(s) entered on step 1: lwt, race, smoke, lwt * race , lwt * smoke , race * smoke , lwt2.

Model Summary

Step likelihood R Square R Square

1 215.015a .099 .139

a. Estimation terminated at iteration number 4 because

parameter estimates changed by less than .001.

Step

a

lwt -.013 .006 4.415 1 .036 .987

1 race 8.730 2 .013

race(1) -.971 .412 5.543 1 .019 .379

race(2) .320 .526 .370 1 .543 1.377

smoke 1.060 .378 7.850 1 .005 2.886

Constant .861 .797 1.168 1 .280 2.366

a. Variable(s) entered on step 1: lwt, race, smoke.

page 15

Parameter coding

Frequency (1) (2)

Race (1=White, White 96 1.000 .000

2=Black, 3=Other) Black 26 .000 1.000

Other 67 .000 .000

The largest difference is between White and Other. The difference between Black and Other is

smaller and not statistically significant. We might consider coding race as simply

White/Nonwhite.

Model Summary

Step likelihood R Square R Square

1 215.383a .097 .136

a. Estimation terminated at iteration number 4 because

parameter estimates changed by less than .001.

B S.E. Wald df Sig. Exp(B) Lower Upper

Step

a

lwt -.0122 .0060 4.118 1 .042 .988 .976 1.000

1 Nonwhite 1.077 .373 8.342 1 .004 2.937 1.414 6.102

smoke 1.103 .372 8.775 1 .003 3.013 1.452 6.252

Constant -.275 .834 .109 1 .742 .760

a. Variable(s) entered on step 1: lwt, Nonwhite, smoke.

1 7.071 8 .529

Some residual analysis should also be done to see that there are not any outliers or particularly

influential points.

• Write the logit equation from the last model for each of the four groups represented by the

two categorical explanatory variables:

page 16

Compare the odds of a low birthweight baby for a nonwhite smoking mother who weighs 150

pounds versus a white, nonsmoking mother who weighs 120 pounds.

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