[R] Change sum of squares type for ANOVA

Michael Dewey lists at dewey.myzen.co.uk
Fri May 20 15:01:53 CEST 2016

Dear Michael F

What you say is of course true but Michael E (or possibly Simone) seems 
to be using a function glht from an unnamed package. Since we do not 
have the data or the offending output it is hard to be sure though.

Michael D

On 20/05/2016 13:49, Michael Friendly wrote:
> 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
>> Institute of Sustainability Sciences ISS
>> Biosafety
>> Reckenholzstrasse 191, CH-8046 Z�rich
>> Tel. +41 44 37 77181
>> Fax +41 44 37 77201
>> michael.eisenring at agroscope.admin.ch<mailto:michael.eisenring at agroscope.admin.ch>
>> www.agroscope.ch<http://www.agroscope.ch/>
>>     [[alternative HTML version deleted]]
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