[R] Different output for lm Mac vs PC

[CASENHISER, DEVIN M]

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
>