[R] Help with lme

[Annie Hoen]

Hi, 

This is my first time posting to the list so please forgive any breeches
of etiquette!
I am new to mixed-effects modeling.

This is my dataset:

   subject treatment day replicate outcome
       1         1   1         1     0.0
       1         1   4         1     0.0
       1         1   8         1    14.5
       1         1   8         2    15.4
       2         1   2         1     0.0
       2         1   4         1     0.0
       2         1   7         1    12.1
       2         1   7         2    11.9
       3         1   2         1     0.0
       3         1   4         1     0.0
       3         1   7         1     0.0
       4         1   2         1     4.2
       4         1   2         2     5.0
       4         1   4         1     8.5
       4         1   4         2    10.0
       4         1   6         1    16.4
       4         1   6         2    18.1
       5         1   2         1     0.0
       5         1   4         1     0.0
       5         1   7         1     0.0
       6         2   2         1     0.0
       6         2   4         1     9.1
       6         2   4         2     9.7
       6         2   7         1    12.6
       6         2   7         2    10.3
       7         2   1         1     3.3
       7         2   1         2     4.8
       7         2   4         1     6.2
       7         2   4         2     6.4
       7         2   7         1    12.9
       7         2   7         2    13.1
       8         2   2         1     0.0
       8         2   4         1     0.0
       8         2   8         1     0.0
       9         2   2         1     2.7
       9         2   2         2     3.2
       9         2   4         1     5.6
       9         2   4         2     5.4
       9         2   8         1    14.9
       9         2   8         2    14.8
      10         2   1         1     0.0
      10         2   4         1    10.7
      10         2   4         2    11.0
      10         2   7         1    13.7
      10         2   7         2    12.9
      11         2   1         1     0.0
      11         2   4         1     0.0
      11         2   7         1     0.0
      12         2   1         1     0.0
      12         2   4         1     0.0
      12         2   7         1     0.0


It can be made using this:

subject=c(1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5, 6,
6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 8, 8, 8, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10,
10, 11, 11, 11, 12, 12, 12)
treatment=c(rep(1, 20), rep(2, 31))
day=c(1, 4, 8, 8, 2, 4, 7, 7, 2, 4, 7, 2, 2, 4, 4, 6, 6, 2, 4, 7, 2, 4, 4,
7, 7, 1, 1, 4, 4, 7, 7, 2, 4, 8, 2, 2, 4, 4, 8, 8, 1, 4, 4, 7, 7, 1, 4, 7,
1, 4, 7)
replicate=c(1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 1, 2, 1, 2, 1, 2, 1, 1, 1, 1,
1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 1, 1, 1, 2, 1, 2, 1, 2, 1, 1, 2, 1, 2, 1,
1, 1, 1, 1, 1) 
outcome=c(0, 0, 14.5, 15.4, 0, 0, 12.1, 11.9, 0, 0, 0, 4.2, 5.0, 8.5,
10.0, 16.4, 18.1, 0, 0, 0, 0, 9.1, 9.7, 12.6, 10.3, 3.3, 4.8, 6.2, 6.4,
12.9, 13.1, 0,0,0, 2.7,3.2, 5.6, 5.4, 14.9, 14.8, 0, 10.7, 11.0, 13.7,
12.9, 0, 0, 0, 0, 0, 0)

data<-data.frame(cbind(subject, treatment, day, replicate, outcome))

I have two groups of subjects, each given a different treatment. The
outcome (growth) was observed post-treatment on each of three days. If
there was growth, it was measured in duplicate measurements.

There are uneven numbers of subjects in my two treatment groups. Also, the
outcome was always observed on 3 days, but the exact day of observation is
not always consistent.

I just want to know the effect of treatment on outcome.

This is the model I've run:

model <- lme(outcome ~ treatment * day, random = list(subject = pdDiag(~
day)), data = data)
summary(model)


Can any experts out there let me know if I'm doing this right? Thanks!!!