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" <ebel...@purdue.edu>
To: "r-help@R-project.org" <r-help@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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
