[R] lme gives different results to SAS Proc Mixed

[Metconnection]

http://www.nabble.com/file/p24211204/repeated.csv repeated.csv 

Dear all, 
I'm currently trying to replicate some Proc Mixed results using lme() and
have a curious result I can't explain. 

The dataset is a repeated measures example where patients (each on one of
several treatments) are measured over a number of days. Putting aside issues
of the error covariance structure I'm using the simple compound symmetry. 

The SAS code I'm using is:
Proc mixed ;
class dose day animal  ;
model blood=dose|day / htype=1,3;
repeated day / subject = animal type = cs;
run;  

and the lme code is
testmain<-lme(blood~dose*day, random=~1|animal, data=sasdata, na.action =
(na.omit))
anova(testmain)

The overall test of the fixed effects agree as expected, but when I tried
Blood2 (which has missing data) only the Day*Dose interaction agrees. I
tried sequential and marginal options in the anove.lme code but to no
effect. I suspect this is something to do with the "non-orthogonality"
induced by the missing data but I am not sure.

Not being an expert in this area  I was wondering if anyone knew why I'm
seeing these differences and if I can tweak the R code to get agreement? 

Any thoughts would be most appreciated!

Simon


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