[R] Different output for lm Mac vs PC

Duncan Mackay dulcalma at bigpond.com
Tue Jan 14 23:24:12 CET 2014

```I think this is a case of using dput to make sure that the datasets are the
same.

I was bitten once by this and now dput between machines.

Regards

Duncan

Duncan Mackay
Department of Agronomy and Soil Science
University of New England
Armidale NSW 2351
Email: home: mackay at northnet.com.au

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On
Behalf Of Marc Schwartz
Sent: Wednesday, 15 January 2014 07:29
To: CASENHISER, DEVIN M
Cc: r-help at r-project.org
Subject: Re: [R] Different output for lm Mac vs PC

On Jan 14, 2014, at 2:23 PM, CASENHISER, DEVIN M <devin at uthsc.edu> wrote:

> I've noticed that I get different output when running a linear model on my
Mac versus on my PC. Same effect, but the Mac assumes the predictor as a 0
level whereas the PC uses the first category (alphabetically).
>
> So for example (using Bodo Winter's example from his online linear models
tutorial):
>
> pitch = c(233,204,242,130,112,142)
> sex=c(rep("female",3),rep("male",3))
>
> summary(lm(pitch~sex))
>
> My Mac, running R 3.0.2, outputs:
>
> Residuals:
>      1       2       3       4       5       6
>  6.667 -22.333  15.667   2.000 -16.000  14.000
>
> Coefficients:
>            Estimate Std. Error t value Pr(>|t|)
> (Intercept)  177.167      7.201  24.601 1.62e-05 ***
> sex1          49.167      7.201   6.827  0.00241 **
> ---
> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
>
> Residual standard error: 17.64 on 4 degrees of freedom Multiple
> R-squared:  0.921, Adjusted R-squared:  0.9012
> F-statistic: 46.61 on 1 and 4 DF,  p-value: 0.002407
>
> But my PC, running R 3.0.2, outputs:
>
> Residuals:
>      1       2       3       4       5       6
>  6.667 -22.333  15.667   2.000 -16.000  14.000
>
> Coefficients:
>            Estimate Std. Error t value Pr(>|t|)
> (Intercept)   226.33      10.18  22.224 2.43e-05 ***
> sexmale       -98.33      14.40  -6.827  0.00241 **
> ---
> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
>
> Residual standard error: 17.64 on 4 degrees of freedom
> Multiple R-squared:  0.921,     Adjusted R-squared:  0.9012
> F-statistic: 46.61 on 1 and 4 DF,  p-value: 0.002407
>
>
> I understand that these are the same (correct) answer, but it does make it
a little more challenging to follow examples (when learning or teaching)
given that the coefficient outputs are calculated differently.
>
> I don't suppose that there is way to easily change either output so that
they correspond (some setting I've overlooked perhaps)?
>
> Thanks and Cheers!
> Devin

On my Mac with R 3.0.2, I get the same output as you get on your Windows
machine.

Something on your Mac is amiss, resulting in the recoding of 'sex' into a
factor with presumably 0/1 levels rather than the default textual factor
levels. If you try something like:

model.frame(pitch ~ sex)

the output should give you an indication of the actual data that is being
used for your model in each case.

Either you have other code on your Mac that you did not include above, which
is modifying the contents of 'sex', or you have some other behavior going on
in the default workspace.

I would check for other objects in your current workspace on the Mac, using
ls() for example, that might be conflicting. If you are running some type of
GUI on your Mac (eg. the default R.app or perhaps RStudio), try running R
from a terminal session, using 'R --vanilla' from the command line, to be
sure that you are not loading a default workspace containing objects that
are resulting in the altered behavior. Then re-try the example code. If that
resolves the issue, you may want to delete, or at least rename/move the
.RData file contained in your default working directory.

Regards,

Marc Schwartz

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