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_schwa...@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 <538...@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_schwa...@me.com> >>wrote: >>> >>> On Jan 14, 2014, at 2:23 PM, CASENHISER, DEVIN M <de...@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 ***¹ 0.001 **¹ 0.01 *¹ 0.05 .¹ 0.1 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 ***¹ 0.001 **¹ 0.01 *¹ 0.05 .¹ 0.1 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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