contrasts in lm and lme
"Peter B. Mandeville" <mandevip at deimos.tc.uaslp.mx> writes:
SAS treatment helmert sum sdif
Pr(>F) 3.073e-05 3.073e-05 3.073e-05 3.073e-05 3.073e-05
the probabilities of the different contrasts were
SAS treatment helmert sum sdif
A-B 0.072635 0.072635 0.072635
A-C 8.69e-06 8.69e-06 0.000322
B-C 0.00875 0.637971 0.00875
Why does the contrast contr.sum have distinct results from the other
contrasts? Which ones are confiable?
Are you reading the output correctly? Sum contrasts are the ones that sum to zero, so you get k-1 values and the k-th one is minus the sum of the others. One result of this is that the test of each individual coefficient is meaningless (whether a group level is equal to the average of all group levels). If the process is repeated with lme in place of lm with
res <- lm(dbp~Treatment+Visit+dbp1,random=~1|Patient)
in place of
res <- lm(dbp~Treatment+Visit+dbp1)
...
SAS treatment helmert sum sdif AIC 7501.212 7501.212 7511.151 7506.182 7501.212 BIC 7546.116 7546.116 7556.055 7551.086 7546.116 logLik -3741.606 -3741.606 -3746.576 -3744.091 -3741.606 Given that AIC and BIC are calculated logLik, it is reasonable that they differ given the different values of the logLik, but is it reasonable that the logLik's are different?
I think the model is contrast independent when specified like that. (But you have a typo in the command, so that's not what you ran...) Looks like there might a convergence problem with the sum and helmert contrasts, although they are the ones normally considered numerically more stable. Do the variance estimates look similar?
SAS treatment helmert sum sdif A-B 0.2330 0.2330 0.2330 A-C 0.0033 0.0033 0.0168 B-C 0.0850 0.7553 0.0850 Again, why does the contrast contr.sum have distinct results from the other contrasts? Which ones are confiable?
Same as before I think.
O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._