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

Thu May 16 21:21:56 CEST 2013

Hi,
The example dataset only shows 1 level for ID.
chm
  id site plot rx rxg rxl t w     l spp inid inih d09  d10  d11  d12 h09 h10
1  1  C-H 2002  1   1  Mn N N 14.55  ac  9.6 74.5 9.6 13.0 13.5 14.2  96 109
2  1  C-H 2002  1   1  Mn N N 14.55  ac  7.4 69.5 6.0  9.8   NA 10.7  72  77
3  1  C-H 2003  1   1  Mn N N 13.34  ac  6.0 66.7 5.7  8.0 11.0 10.1  75  80
4  1  C-H 2003  1   1  Mn N N 13.34  ac  7.1 75.4 7.5 13.0 11.8 12.3 101 113
5  1  C-H 2003  1   1  Mn N N 13.34  ac  7.5 57.5 6.9   NA   NA   NA  58  NA
6  1  C-H 2008  2   1  Mc N N 11.63  ac  5.7 71.5 6.0  7.7   NA  8.5  84  89
  h11 h12
1 102 110
2  76  92
3  79  91
4 115 128
5  NA  NA
6  84  86

Using another dataset:
data(warpbreaks)
warpbreaks2<- warpbreaks
warpbreaks2$id<-rep(1:6,9)
warpbreaks2$id<- factor(warpbreaks2$id)
set.seed(45)
 warpbreaks2$inih<- rnorm(54,70)
 str(warpbreaks2)
#'data.frame':    54 obs. of  5 variables:
# $ breaks : num  26 30 54 25 70 52 51 26 67 18 ...
# $ wool   : Factor w/ 2 levels "A","B": 1 1 1 1 1 1 1 1 1 1 ...
# $ tension: Factor w/ 3 levels "L","M","H": 1 1 1 1 1 1 1 1 1 2 ...
# $ id     : Factor w/ 6 levels "1","2","3","4",..: 1 2 3 4 5 6 1 2 3 4 ...
# $ inih   : num  70.3 69.3 69.6 69.3 69.1 ...
library(lme4)
lmList(breaks~wool+tension+ inih|id,data=warpbreaks2)
#Call: lmList(formula = breaks ~ wool + tension + inih | id, data = warpbreaks2) 
#Coefficients:
#  (Intercept)      woolB   tensionM   tensionH      inih
#1   -170.9470  -6.634896  -7.214566  -9.376711  2.930854
#2    247.7175   5.363119  -1.958410 -10.652740 -3.183826
#3   -304.1479 -13.483864 -28.437529 -26.656611  5.120942
#4   -641.4617  -5.273322  -9.876885 -16.222166  9.670360
#5    476.4729  -6.296008 -10.416367 -16.337461 -6.256378
#6    335.3178 -14.219225 -17.714808 -13.488733 -4.054001
#Degrees of freedom: 54 total; 24 residual
#Residual standard error: 12.52028

warpbreaks3<- warpbreaks2
 warpbreaks3$id<- as.numeric(as.character(warpbreaks3$id))
 lmList(breaks~wool+tension+ inih|id,data=warpbreaks3)
#Call: lmList(formula = breaks ~ wool + tension + inih | id, data = warpbreaks3) 
#Coefficients:
#  (Intercept)      woolB   tensionM   tensionH      inih
#1   -170.9470  -6.634896  -7.214566  -9.376711  2.930854
#2    247.7175   5.363119  -1.958410 -10.652740 -3.183826
#3   -304.1479 -13.483864 -28.437529 -26.656611  5.120942
#4   -641.4617  -5.273322  -9.876885 -16.222166  9.670360
#5    476.4729  -6.296008 -10.416367 -16.337461 -6.256378
#6    335.3178 -14.219225 -17.714808 -13.488733 -4.054001
#
#Degrees of freedom: 54 total; 24 residual
#Residual standard error: 12.52028

A.K.

----- Original Message -----
From: "Belair, Ethan D" <ebelair at purdue.edu>
To: "r-help at R-project.org" <r-help at r-project.org>
Cc: 
Sent: Thursday, May 16, 2013 11:05 AM
Subject: [R] Error: contrasts can be applied only to factors with 2 or more
 levels

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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