[R] scatter3d() model.summary coefficients?

[John Fox]

Dear Anja,

As you suggest, models in scatter3d() are fit via lm() and also mgcv().
scatter3d() rescales the three variables to fit in the unit cube;  I believe
that the new version of rgl makes the rescaling unnecessary, so eventually
I'll probably rework scatter3d() to avoid it. It would be better if
?scatter3d mentioned this; I've made that change in the development version
of the package.

BTW, a nice thing about R is that the source code is there, so you can look
to see what a function does.

I hope this helps,
 John

--------------------------------
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox 
-------------------------------- 

> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of angela baldo
> Sent: Friday, September 29, 2006 5:23 PM
> To: r-help at stat.math.ethz.ch
> Subject: [R] scatter3d() model.summary coefficients?
> 
> Hello All,
> 
> I am a R newbie and am probably misinterpreting something 
> really obvious...
> 
> In the Rcmdr package there is a scatter3d() function that can 
> fit a curve and also provide coefficients for the model.  If 
> I'm understanding this right, I think it's calling the lower 
> level stats package function lm(), which is the part that 
> actually does the curve fitting.
> 
> Anyway, what has me perplexed is that the model summary from 
> scatter3d() has different coefficients than the one generated 
> by lm().  However, the actual surface plotted by scatter3d() 
> looks like the function generated by lm().
> 
> In the scatter3d() docs I didn't see anything about 
> transforming the coefficients or changing them somehow - 
> perhaps I have not been looking in the right place?
> 
> I'm using a Linux box: 2.6.17-1.2187_FC5smp, R version 2.3.1, 
> Rcmdr version 1.2-0, in case that helps.
> 
> Thanks very much for any enlightenment!
> 
> anja
> 
> 
> Here's an example of the output on the same data by both 
> functions.  If anyone wants the dataset, let me know:
> 
> > scatter3d(samples$x1, samples$y, samples$x2, fit="linear",
> residuals=TRUE, bg="white", axis.scales=TRUE, grid=TRUE, 
> ellipsoid=FALSE, xlab="x1", ylab="y", zlab="x2", 
> model.summary=TRUE) $linear
> 
> Call:
> lm(formula = y ~ x + z)
> 
> Residuals:
>       Min        1Q    Median        3Q       Max 
> -0.096984 -0.022303  0.004758  0.029354  0.091188 
> 
> Coefficients:
>              Estimate Std. Error t value Pr(>|t|)    
> (Intercept)  0.708945   0.007005  101.20   <2e-16 ***
> x            0.278540   0.011262   24.73   <2e-16 ***
> z           -0.688175   0.011605  -59.30   <2e-16 ***
> ---
> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 
> 
> Residual standard error: 0.03936 on 105 degrees of freedom
> Multiple R-Squared: 0.972,	Adjusted R-squared: 0.9715 
> F-statistic:  1822 on 2 and 105 DF,  p-value: < 2.2e-16 
> 
> > summary(lm(formula=samples$y~samples$x1+samples$x2))
> 
> Call:
> lm(formula = samples$y ~ samples$x1 + samples$x2)
> 
> Residuals:
>     Min      1Q  Median      3Q     Max 
> -7865.0 -1808.6   385.8  2380.5  7394.9 
> 
> Coefficients:
>              Estimate Std. Error t value Pr(>|t|)    
> (Intercept) 92204.502   1323.217   69.68   <2e-16 ***
> samples$x1    225.882      9.133   24.73   <2e-16 ***
> samples$x2   -558.076      9.411  -59.30   <2e-16 ***
> ---
> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 
> 
> Residual standard error: 3192 on 105 degrees of freedom
> Multiple R-Squared: 0.972,	Adjusted R-squared: 0.9715 
> F-statistic:  1822 on 2 and 105 DF,  p-value: < 2.2e-16 
> 
> --
> Angela M. Baldo
> Computational Biologist
> USDA, ARS
> Plant Genetic Resources Unit
> & Grape Genetics Research Unit
> New York State Agricultural Experiment Station 630 W. North 
> Street Geneva, NY  14456-0462 USA
> 
> voice 315 787-2413 or 607 254-9413
> fax   315 787-2339 or 607 254-9339
> 
> angela.baldo at ars.usda.gov
> http://www.ars.usda.gov/NAA/Geneva
> 
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