[R] warnings about factor levels dropped from predict.glm

Bert Gunter bgunter.4567 at gmail.com
Tue Dec 5 21:37:47 CET 2017

A guess (treat accordingly):

Different BLAS versions are in use on the two different machines/versions.
In one, near singularities are handled, and in the other they are not,
percolating up to warnings at the R level.

You can check this by seeing whether the estimated fit is the same on the 2
machines. If so, ignore the above.

-- Bert

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Tue, Dec 5, 2017 at 12:17 PM, Cade, Brian <cadeb at usgs.gov> wrote:

> I am helping a student with some logistic regression analyses and we are
> getting some strange inconsistencies regarding a warning about factor
> levels being dropped when running predict.glm(, newdata = ournewdata) on
> the logistic regression model object.  We have checked multiple times that
> the factor levels have been defined similarly on both data sets (one used
> to estimate model and the newdata) and that values occur for all factor
> levels in both data sets.  When I run these commands on my version of R
> (3.2.5) on a Windows 7 OS I do not get the warnings.  When the student runs
> them on her version of R (not sure what number hers is) on her Mac, she
> gets these warnings constantly.  I've checked some records manually by
> doing the algebra and the predict.glm() function is working correctly
> incorporating the factor levels on my machine.  Any thoughts???
> Brian
> Brian S. Cade, PhD
> U. S. Geological Survey
> Fort Collins Science Center
> 2150 Centre Ave., Bldg. C
> Fort Collins, CO  80526-8818
> email:  cadeb at usgs.gov <brian_cade at usgs.gov>
> tel:  970 226-9326
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