I have a dataframe that I am attempting to analyze using the lmList() function
in package lme4. I'm using this funciton to select which parameters in this
model wqarrant random effects. I have a subset of the data below. I input data
and change class of necessary items so that I have several factors and several
numeric variables. I then run lmList using id as a grouping factor, which
produces an error. This only occurs using id as grouping factor, other IV's
work fine. R says contrasts can only be applied to factors of 2 or more levels.
The entire data set contains 48 levels of id, this subset contains 3, yet the
error persists.
I'm relatively new to R and this is my first question posted. I apologize if
I've not followed the posting rules exactly, I'm trying to do so, but find
coding quite difficult.
Thank you in advance for any help.
> library(lme4)
> chm <- dput(head(chm))
structure(list(id = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("1",
"2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13",
"14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24",
"25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35",
"36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46",
"47", "48"), class = "factor"), site = structure(c(1L, 1L, 1L,
1L, 1L, 1L), .Label = c("C-H", "M"), class = "factor"), plot = structure(c(2L,
2L, 3L, 3L, 3L, 8L), .Label = c("2001", "2002", "2003", "2004",
"2005", "2006", "2007", "2008", "2009", "2010", "2011", "2012",
"2013", "2014", "2015", "2016", "2017", "2018", "2019", "2020",
"2021", "2022", "2023", "2024", "2025", "2026", "2027", "2028",
"2029", "2030", "2031", "2032", "2033", "2034", "2035", "2036",
"2037", "2038", "2039", "2040", "2041", "2042", "2043", "2044",
"2045"), class = "factor"), rx = structure(c(1L, 1L, 1L, 1L,
1L, 2L), .Label = c("1", "2", "3", "4", "5", "6"), class = "factor"),
rxg = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("1",
"6"), class = "factor"), rxl = structure(c(5L, 5L, 5L, 5L,
5L, 3L), .Label = c("C", "H", "Mc", "McH", "Mn", "MnH"), class = "factor"),
t = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("N",
"Y"), class = "factor"), w = structure(c(1L, 1L, 1L, 1L,
1L, 1L), .Label = c("N", "Y"), class = "factor"), l = c(14.55,
14.55, 13.34, 13.34, 13.34, 11.63), spp = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("ac", "rm", "ro", "sm"), class = "factor"),
inid = c(9.6, 7.4, 6, 7.1, 7.5, 5.7), inih = c(74.5, 69.5,
66.7, 75.4, 57.5, 71.5), d09 = c(9.6, 6, 5.7, 7.5, 6.9, 6
), d10 = c(13, 9.8, 8, 13, NA, 7.7), d11 = c(13.5, NA, 11,
11.8, NA, NA), d12 = c(14.2, 10.7, 10.1, 12.3, NA, 8.5),
h09 = c(96, 72, 75, 101, 58, 84), h10 = c(109, 77, 80, 113,
NA, 89), h11 = c(102, 76, 79, 115, NA, 84), h12 = c(110,
92, 91, 128, NA, 86)), .Names = c("id", "site", "plot", "rx",
"rxg", "rxl", "t", "w", "l", "spp", "inid", "inih", "d09", "d10",
"d11", "d12", "h09", "h10", "h11", "h12"), row.names = c(NA,
6L), class = "data.frame")
> chm$id = as.factor(chm$id)
> chm$spp = as.factor(chm$spp)
> chm$h12 = as.numeric(chm$h12)
> str(chm)
> ch.list <- lmList(h12~spp+t+w+l+inih|id, data=mydata)
Thanks!
Ethan
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