[R] Error: contrasts can be applied only to factors with 2 or more levels

[Rolf Turner]

In the example data that you provide, the factor "id" has only one level,
namely "1".  Your example date appears to be just the head (first 6 rows)
of your real data, so this may not be the real story.  It's hard to tell 
from
what you've said.

Also see in line below.

     cheers,

         Rolf Turner

On 17/05/13 03:05, Belair, Ethan D wrote:
> 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)

     Why on earth did you do the foregoing?  The components id and spp
     are already factors and h12 is already numeric.  Don't throw bits 
of code
     around mindlessly.  Understand what you are doing and why you are
     doing it.  To quote from fortune(184) "The underlying assumption 
[of R] is
     that the useR is thinking about the analysis while doing it."
>> str(chm)
>> ch.list <- lmList(h12~spp+t+w+l+inih|id, data=mydata)

     WTF is "mydata"?  Did you mean "data=chm"?