a question of conducting contrast in lme4 (not pairwise contrast)
On 16-09-02 02:18 PM, Gu Hao wrote:
Hello, I am trying to do some contrasts using a mixed model, but don?t know how to use it in lme4. I've done the multiple contrast, but I believe the power of this method is lower than ideal. I think contrast in lme4 would be a better option. I searched the question on stackoverflow and found one post. However, the question asked wasn't our situation. In our case, there are five treatments. Let?s call them AA, BB, CC, DD, and EE. I have the following hypotheses: the response to AA will be higher than the average of BB, CC and DD. the response to AA will be higher than EE the average response to BB, CC and DD will be higher than EE.
Some notes on linear contrasts: http://ms.mcmaster.ca/~bolker/classes/s4c03/notes/week2B.Rnw http://ms.mcmaster.ca/~bolker/classes/s4c03/notes/week2B.pdf The three contrasts you've set up are collinear: let's code them as c1 = c(1, -1/3, -1/3, -1/3, 0) ## AA vs (BB,CC,DD) c2 = c(1, 0, 0, 0, -1) ## AA vs EE c3 = c(0, 1/3, 1/3, 1/3, -1) ## (BB,CC,DD) vs EE then you can see that c1 + c3 is equal to c2. Therefore, you can't use these three contrasts as part of a full set of 5 contrasts that span the space of possibilities. Before I saw that you said you've already tried multcomp I wrote the following down; it might be useful to someone else. Adapted from the examples in ?multcomp::glht z <- gl(5,10,labels=LETTERS[1:5]) y <- rnorm(50) library(multcomp) K <- rbind("A - BCD" = c( 1, -1/3, -1/3, -1/3, 0), "A - E" = c( 1, 0, 0, 0, -1), "BCD-E" = c( 0, 1/3, 1/3, 1/3, -1)) m <- lm(y~z) mc <- glht(m, linfct = mcp(z = K), alternative = "less") summary(mc) If you want to live dangerously I think summary(mc,test=univariate()) will give you the unadjusted p-values ...
The model is being run in lme4 as a mixed model: response (binomial, 0 or 1) ~ treatment (the 5 levels above) + (1|tape) + (1|round) + (1|location). Do anybody know how to code this? Please kindly find the data in the attachment. With thanks and best wishes, Hao