Logistic regression model does not converge

Question

I've got some data about airline flights (in a data frame called flights) and I would like to see if the flight time has any effect on the probability of a significantly delayed arrival (meaning 10 or more minutes). I figured I'd use logistic regression, with the flight time as the predictor and whether or not each flight was significantly delayed (a bunch of Bernoullis) as the response. I used the following code...

flights$BigDelay <- flights$ArrDelay >= 10
delay.model <- glm(BigDelay ~ ArrDelay, data=flights, family=binomial(link="logit"))
summary(delay.model)

...but got the following output.

> flights$BigDelay <- flights$ArrDelay >= 10
> delay.model <- glm(BigDelay ~ ArrDelay, data=flights, family=binomial(link="logit"))
Warning messages:
1: In glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart,  :
  algorithm did not converge
2: In glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart,  :
  fitted probabilities numerically 0 or 1 occurred
> summary(delay.model)

Call:
glm(formula = BigDelay ~ ArrDelay, family = binomial(link = "logit"),
    data = flights)

Deviance Residuals:
       Min          1Q      Median          3Q         Max
-3.843e-04  -2.107e-08  -2.107e-08   2.107e-08   3.814e-04

Coefficients:
            Estimate Std. Error z value Pr(>|z|)
(Intercept)  -312.14     170.26  -1.833   0.0668 .
ArrDelay       32.86      17.92   1.833   0.0668 .
---
Signif. codes:  0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1

(Dispersion parameter for binomial family taken to be 1)

    Null deviance: 2.8375e+06  on 2291292  degrees of freedom
Residual deviance: 9.1675e-03  on 2291291  degrees of freedom
AIC: 4.0092

Number of Fisher Scoring iterations: 25

What does it mean that the algorithm did not converge? I thought it be because the BigDelay values were TRUE and FALSE instead of 0 and 1, but I got the same error after I converted everything. Any ideas?

Answer 1

glm() uses an iterative re-weighted least squares algorithm. The algorithm hit the maximum number of allowed iterations before signalling convergence. The default, documented in ?glm.control is 25. You pass control parameters as a list in the glm call:

delay.model <- glm(BigDelay ~ ArrDelay, data=flights, family=binomial,
                   control = list(maxit = 50))

As @Conjugate Prior says, you seem to be predicting the response with the data used to generate it. You have complete separation as any ArrDelay < 10 will predict FALSE and any ArrDelay >= 10 will predict TRUE. The other warning message tells you that the fitted probabilities for some observations were effectively 0 or 1 and that is a good indicator you have something wrong with the model.

The two warnings can go hand in hand. The likelihood function can be quite flat when some $\hat{\beta}_i$ get large, as in your example. If you allow more iterations, the model coefficients will diverge further if you have a separation issue.

Answer 2

You could try to check if Firth's bias reduction works with your dataset. It is a penalized likelihood approach that can be useful for datasets which produce divergences using the standard glm package. Sometimes it can be used instead of eliminating that variable which produces complete/almost complete separation.

For the formulation of the bias reduction (the $O(n^{-1})$-term in the asymptotic expansion of the bias of the maximum likelihood estimator is removed using classical cumulants expansion as motivating example) please check http://biomet.oxfordjournals.org/content/80/1/27.abstract

Firth's bias reduction is implemented in the R-package logistf: http://cran.r-project.org/web/packages/logistf/logistf.pdf