[R] Change sum of squares type for ANOVA

Fox, John jfox at mcmaster.ca
Fri May 20 14:58:27 CEST 2016


Dear Michael and Michael,

I took a quick look at the Statistica website, and their definition of "types" of sums of squares doesn't appear to be the same as the common definition, which originated with SAS. As I read their materials, what they call "Type VI" sums of squares would correspond to the "Type III" tests provided by Anova() in the car package by setting type=3. 

As well, the reference to "sigma-restricted coding" in the Statistica documentation corresponds to contrasts provided by contr.sum() in R. This is important for Type III tests because it produces a row-basis for the model matrix with orthogonal effects. One way to do this is via options(contrasts=c("contr.sum", "contr.poly")). See ?Anova for more information.

I hope this helps,
 John

-----------------------------
John Fox, Professor
McMaster University
Hamilton, Ontario
Canada L8S 4M4
Web: socserv.mcmaster.ca/jfox



> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Michael 
> Friendly
> Sent: May 20, 2016 8:50 AM
> To: michael.eisenring at agroscope.admin.ch; r-help at r-project.org
> Subject: Re: [R] Change sum of squares type for ANOVA
> 
> Use car::Anova() for type II and type III sums of squares and F-tests.
> The sequential type I tests computed by anova() are rarely sensible
> 
> On 5/20/2016 3:11 AM, michael.eisenring at agroscope.admin.ch wrote:
> > Dear R-list members,
> >
> > I compared my statistics with my supervisor yesterday. He is using
> STATISTICA, I am using R. We both loaded the same data-file and did a two-way
> ANOVA with treatment and trial as factors; treatment means were then
> compared to the untreated control using Dunnett's test. Surprisingly, we got
> different values, especially the F values differed. In the following Dunnett's test,
> some treatments were significant in R, but not in STATISTICA. We checked the
> basic settings of the programs and found out, that STATISTICA is using "sigma-
> restricted parametrization" and "type VI sum of squares" for the calculations,
> but so far, I could not find any information about the sum of squares type,
> which is applied in R. Is it possible, that these settings are the reason for the
> different values we got? And how can I change in R these settings?
> >
> > Here the code I used:
> > bt_assay_devtime_Model <-
> > aov(developmenttime~treatment+run+treatment*run, data=bt_assay)
> > summary(bt_assay_devtime_Model)
> > postHocs_bt_assay_devtime <- glht(bt_assay_devtime_Model,
> > linfct=mcp(treatment="Dunnett"), base=1)
> > summary(postHocs_bt_assay_devtime)
> > confint(postHocs_bt_assay_devtime)
> >
> > Thanks a lot for your help!
> > Simone
> >
> > Eisenring Michael, Msc.
> > PhD Student
> >
> > Federal Department of Economic Affairs, Education and Research EAER
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> > e.admin.ch> www.agroscope.ch<http://www.agroscope.ch/>
> >
> >
> > 	[[alternative HTML version deleted]]
> >
> >
> >
> 
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