[R] Different output for lm Mac vs PC
CASENHISER, DEVIN M
devin at uthsc.edu
Wed Jan 15 14:17:06 CET 2014
Yes that's it!
My mac has:
> options('contrasts')
$contrasts
[1] "contr.sum" "contr.poly"
whereas the PC has
$contrasts
unordered ordered
"contr.treatment" "contr.poly"
I've changed the mac with
options(contrasts=c('contr.treatment','contr.poly'))
and that has solved the issue.
Thanks Greg and Marc!
Cheers!
Devin
On 1/14/14 5:35 PM, "Marc Schwartz" <marc_schwartz at me.com> wrote:
>Good catch Greg.
>
>The Mac output observed can result from either:
>
> options(contrasts = c("contr.helmert", "contr.poly"))
>
>or
>
> options(contrasts = c("contr.sum", "contr.poly"))
>
>being run first, before calling the model code.
>
>I checked the referenced tutorial and did not see any steps pertaining to
>altering the default contrasts. So either code along the lines of the
>above was manually entered on the Mac at some point or perhaps there is a
>change to the defaults on Devin's Mac system? The latter perhaps in
>~/.Rprofile to mimic S-PLUS' behavior, in the case of Helmert contrasts?
>
>Devin, note that the model output lines for both the intercept and sex,
>beyond the way in which 'sex' is displayed (sex1 versus sexmale), are
>rather different and are consistent with the use of non-default contrasts
>on the Mac, as Greg noted.
>
>Regards,
>
>Marc
>
>
>On Jan 14, 2014, at 3:55 PM, Greg Snow <538280 at gmail.com> wrote:
>
>> I would suggest running the code:
>>
>> options('contrasts')
>>
>> on both machines to see if there is a difference. Having the default
>> contrasts set differently would be one explanation.
>>
>> On Tue, Jan 14, 2014 at 2:28 PM, Marc Schwartz <marc_schwartz at me.com>
>>wrote:
>>>
>>> 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 Œ***¹ 0.001 Œ**¹ 0.01 Œ*¹ 0.05 Œ.¹ 0.1 Œ 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 Œ***¹ 0.001 Œ**¹ 0.01 Œ*¹ 0.05 Œ.¹ 0.1 Œ 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
>
More information about the R-help
mailing list