# Mixed model specification in R

I have nested structure design with the following model:

Yijklt = m + ai + bij + rijk + sikl + (bs)ijkl + eijkl

where i = 1, 2, ..................., s; number of sets
j = 1, 2, ........................, r; number of replications
k = 1, 2, ........................., m; males
l = 1,2,............................, f; females
t = 1, 2, ................, n; progeny

where m is the general mean
ai is the effect of the ith set
bij is effect of jth replication in the ith set
rik is the effect of kth male in the ith set
sikl is the the effect of the lth female to kth male in the ith set
(bs)ijkl is the interaction term


The "non-mixed" model formula in R is as follows:

 model <- lm(y ~ set + replication %in% set + male %in%
set + female %in% male %in% set + replication %in%
female %in% male %in% set)
model <- lm(y ~ set + replication:set + male:set + female:male:set + replication:
female:male:set)


What would be its corresponding model in mixed model using lme4 or nlme package in R?

I want to do it right.

Please note that all terms in the new mixed model are random, I just want to estimate variance components associated.

Edits: work out example based on the answers below by @Aaron

library(lme4)
set.seed(5)
d <- expand.grid(set=factor(1:3), male=factor(1:3),female=factor(1:3),
progeny = factor(1:3), replication=factor(1:4))
d\$y <- rnorm(nrow(d))

• As I am not getting any responses in this statistical forum, I am not sure if this is proper forum to post this question, or somebody (suggest) migrate this question to stackoverflow
– John
Nov 15 '11 at 11:00
• Could you provide some sample data (preferably generated with just a few lines of code)? It's not clear to me how the (bs)ijkl term is different from the eijkl term, or what role the t variable plays. (I'll post an example as an answer.) Nov 15 '11 at 15:41

library(lme4)
model <- lmer(y ~ (1|set) + (1|replication:set) + (1|male:set) +
(1|female:male:set) +
(1|replication:female:male:set), data=d)

• you need to add another factor progeny, which can be 1:3, this will add term to calculate error df (not 0). thanks;
– John
Nov 15 '11 at 16:08
• Done; data creation code now moved to the question. Nov 15 '11 at 16:37
• thank you so much, I still wonder difference between ":", "/", and "|" notation in modelling in lme4
– John
Nov 15 '11 at 17:36
• proably this question can be different question in itself, too much in the same post
– John
Nov 15 '11 at 17:42
• @Wayne: No, it doesn't seem to be in the internal documentation. But see section 11.1 of An Introduction to R. Nov 15 '11 at 20:16

I would recommend that you look at the text book "Linear Mixed Models: a practical guide using statistical software" by West, Welch and Galecki. It goes through step-wise the process of model specification, testing, intrepretation for real world datasets for a variety of software packages. the R component is using nlme. I found it very helpful at developing my code. I haven't seen variance component estimates within the book, but have seen this discussed in "the R book", by Crawley.
Good luck Natasha