[R] Change sum of squares type for ANOVA

Michael Friendly friendly at yorku.ca
Fri May 20 14:49:40 CEST 2016

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
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