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

Thu, 16 May 2013 17:16:10 -0700 


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"?

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