[R] Warning message as a result of logistic regression performed
gavin.simpson at ucl.ac.uk
Wed May 27 16:24:35 CEST 2009
Try reading this thread:
especially the posts by I Kosmidis which show you how to diagnose
problems in logit model fits like this.
There is a statement about this warning in ?glm as well and a pointer to
a reference which discusses a source of the warning.
On Wed, 2009-05-27 at 11:22 +0100, Winter, Katherine wrote:
> I am sorry if this question sounds basic but I am having trouble understanding a warning message I have been receiving in R after attempting logistic regression.
> I have been using the logistic regression function in R to analyse a simulated data set. The dependent variable "failure" has an outcome of either 0 (success) or 1 (failure). Both the independent variables have been previously generated in a mathematical model and stored in a data.frame for analysis. I am currently using a sample size of 1000 and I use the following commands in R:
> log.reg.1 <- glm(failure ~ age +weight +init.para.log.value +k.d1,family=binomial(logit), data=test)
> log.reg.1.summary <- summary(log.reg.1); print(log.reg.1.summary)
> log.reg.1.exp <- exp(log.reg.1$coef); print(log.reg.1.exp)
> When I execute these commands I get the following warning message:
> "In glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart, :fitted probabilities numerically 0 or 1 occurred"
> I am unsure what this warning is referring to. I have tried using google to answer this question but have had no luck.
> I have been on the following website https://stat.ethz.ch/pipermail/r-sig-ecology/2008-July/000278.html but found it was not helpful as I when I ran the example given I received no warning message (I am using R version 2.8.1).
> I am working with simulated data so there are no missing values in the data set.
> I have also looked at the following website http://tolstoy.newcastle.edu.au/R/help/05/07/7759.html they suggest that the warning is as a result of "perfect separation" of the results (a possibility with simulated data). However, when I added an extra row to my data.frame of results that I knew to be false and hence to prevent "perfect separation" subsequent logistic regression still resulted in the same warning message.
> I am still at a loss as to the meaning of this message and any help in understanding this warning would be much appreciated.
> R-help at r-project.org mailing list
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
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