[R] ANOVA results in R conflicting with results in other software packages

Simon Blomberg s.blomberg1 at uq.edu.au
Thu Apr 26 04:28:31 CEST 2007

R uses "treatment" contrasts for factors (ie 0/1 coding) by default.
Systat is using "sum" (ie sum to zero) contrasts:  Try this:

options(contrasts=c("contr.sum", "contr.poly")
Anova(fm, type="III")

I won't discuss the dangers of "types" of sums of squares and different
contrast codings. That would be tempting the wrath of the gods. See
section 7.18 in the R FAQ. John Fox's "Companion" book also has a brief
discussion (p. 140).



Simon Blomberg, BSc (Hons), PhD, MAppStat. 
Lecturer and Consultant Statistician 
Faculty of Biological and Chemical Sciences 
The University of Queensland 
St. Lucia Queensland 4072 

Room 320, Goddard Building (8)
T: +61 7 3365 2506 
email: S.Blomberg1_at_uq.edu.au 

The combination of some data and an aching desire for 
an answer does not ensure that a reasonable answer can 
be extracted from a given body of data. - John Tukey.

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