I would like to make a multinomial model with random effects, but I don't know how.
The model would look like this: native_driftertype ~treat+(1|replica)+(1|compartment/originhive)
,
with native_driftertype
a factor with 5 levels, treat
a factor with 3 levels, replica
a factor with 2 levels, compartment
a factor with 3 levels, and originhive
a factor with 24 levels.
The data looks like this:
data6 <- structure(list(origin_hive = structure(c(1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 9L,
9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 16L, 16L, 16L, 16L, 16L,
16L, 16L, 16L, 16L, 16L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L,
7L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 21L, 21L,
21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 23L, 23L, 23L, 23L, 23L,
23L, 23L, 23L, 23L, 23L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L,
6L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 14L, 14L, 14L, 14L,
14L, 14L, 14L, 14L, 14L, 14L, 19L, 19L, 19L, 19L, 19L, 19L, 19L,
19L, 19L, 19L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 13L, 13L, 13L, 13L, 13L, 13L,
13L, 13L, 13L, 13L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L, 17L,
17L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 18L, 18L,
18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 20L, 20L, 20L, 20L, 20L,
20L, 20L, 20L, 20L, 20L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L,
22L, 22L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 10L, 10L, 10L,
10L, 10L, 10L, 10L, 10L, 10L, 10L, 15L, 15L, 15L, 15L, 15L, 15L,
15L, 15L, 15L, 15L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 24L,
24L, 3L, 3L, 19L, 3L, 3L, 19L, 3L, 3L, 3L, 3L, 19L, 19L, 19L,
3L, 3L, 3L, 6L, 9L, 6L, 6L, 6L, 6L, 9L, 6L, 9L, 9L, 6L, 6L, 6L,
9L, 6L, 8L, 16L, 8L, 16L, 16L, 16L, 8L, 16L, 16L, 16L, 8L, 1L,
1L, 23L, 14L, 1L, 23L, 1L, 23L, 1L, 3L, 7L, 3L, 19L, 3L, 9L,
9L, 9L, 6L, 9L, 16L, 16L, 8L, 1L, 23L, 1L, 23L, 14L, 3L, 3L,
7L, 7L, 9L, 11L, 11L, 16L, 16L, 8L, 21L, 23L, 1L, 23L, 19L, 3L,
19L, 19L, 19L, 19L, 6L, 6L, 6L, 11L, 11L, 6L, 6L, 6L, 6L, 9L,
9L, 6L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 1L, 14L, 1L,
10L, 13L, 10L, 10L, 13L, 13L, 13L, 10L, 20L, 24L, 24L, 5L, 20L,
20L, 20L, 5L, 20L, 24L, 5L, 5L, 20L, 12L, 17L, 12L, 12L, 12L,
15L, 12L, 12L, 12L, 17L, 17L, 17L, 12L, 15L, 15L, 12L, 12L, 17L,
12L, 15L, 17L, 12L, 12L, 12L, 12L, 12L, 22L, 22L, 2L, 4L, 22L,
2L, 22L, 2L, 13L, 18L, 13L, 5L, 5L, 12L, 17L, 22L, 22L, 22L,
22L, 13L, 13L, 18L, 18L, 18L, 20L, 20L, 20L, 20L, 5L, 5L, 5L,
5L, 24L, 5L, 5L, 12L, 17L, 17L, 12L, 17L, 12L, 4L, 10L, 13L,
18L, 13L, 10L, 5L, 5L, 24L, 20L, 20L, 20L, 5L, 20L, 24L, 12L,
17L, 12L, 17L, 17L, 12L, 17L, 22L, 22L), levels = c("10C1", "10C2",
"11C1", "11UV2", "12C2", "12UV1", "13G1", "14UV1", "16C1", "1UV2",
"2G1", "2G2", "3C2", "4UV1", "4UV2", "5C1", "5C2", "6G2", "6UV1",
"7G2", "8G1", "8G2", "9G1", "9UV2"), class = "factor"), treat = structure(c(1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 3L, 1L,
1L, 3L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 1L, 1L, 1L, 3L, 1L, 3L,
3L, 3L, 3L, 1L, 3L, 1L, 1L, 3L, 3L, 3L, 1L, 3L, 3L, 1L, 3L,
1L, 1L, 1L, 3L, 1L, 1L, 1L, 3L, 1L, 1L, 2L, 3L, 1L, 2L, 1L,
2L, 1L, 1L, 2L, 1L, 3L, 1L, 1L, 1L, 1L, 3L, 1L, 1L, 1L, 3L,
1L, 2L, 1L, 2L, 3L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 3L,
2L, 2L, 1L, 2L, 3L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 2L,
3L, 3L, 3L, 3L, 1L, 1L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 3L, 1L, 3L, 1L, 3L, 3L, 1L, 1L, 1L, 3L, 2L, 3L, 3L, 1L,
2L, 2L, 2L, 1L, 2L, 3L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 2L, 3L,
2L, 2L, 2L, 1L, 1L, 1L, 2L, 3L, 3L, 2L, 2L, 1L, 2L, 3L, 1L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 3L, 2L, 1L, 2L, 1L, 1L, 2L,
1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 1L, 2L, 2L, 1L, 1L, 2L, 1L,
2L, 3L, 3L, 1L, 2L, 1L, 3L, 1L, 1L, 3L, 2L, 2L, 2L, 1L, 2L,
3L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 2L), levels = c("C",
"G", "UV"), class = "factor"), native_driftertype = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L), levels = c("native",
"Resident", "Transient", "Voyeur", "unknown"), class = "factor"),
replica = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L), levels = c("1", "2"), class = "factor"),
compartment = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 2L,
2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 2L,
1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L,
2L, 2L, 2L, 1L, 2L, 2L, 3L, 1L, 2L, 3L, 2L, 3L, 2L, 2L, 3L,
2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 3L, 2L, 3L,
1L, 2L, 2L, 3L, 3L, 2L, 3L, 3L, 2L, 2L, 1L, 3L, 3L, 2L, 3L,
1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 1L, 1L, 1L, 1L,
2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 3L,
1L, 3L, 3L, 1L, 1L, 1L, 3L, 2L, 3L, 3L, 1L, 2L, 2L, 2L, 1L,
2L, 3L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 2L, 3L, 2L, 2L, 2L, 1L,
1L, 1L, 2L, 3L, 3L, 2L, 2L, 1L, 2L, 3L, 1L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 1L, 3L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 2L,
1L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L,
1L, 1L, 1L, 3L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 3L, 3L, 1L,
2L, 1L, 3L, 1L, 1L, 3L, 2L, 2L, 2L, 1L, 2L, 3L, 2L, 1L, 2L,
1L, 1L, 2L, 1L, 2L, 2L), levels = c("12", "14", "16"), class = "factor")), row.names = c(NA, -464L
), class = "data.frame")
I tried using the brm function (Fit Bayesian Generalized (Non-)Linear Multivariate Multilevel Models) from the brms package, but when running the following model, I get the following error:
fit=brm(native_driftertype~treat+(1|replica)+(1|compartment/origin_hive), family = multinomial(), data = data6)
Error: At least 2 response categories are required.
I also tried the mclogit function with the following model, but get the following error:
mclogit(native_driftertype~treat,
random = list(~1|replica, ~1|compartment/origin_hive), data=data6)
Error in formula[[2]][[1]] : object of type 'symbol' is not subsettable