Belair, Ethan D
2013-May-16 15:05 UTC
[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 [[alternative HTML version deleted]]
John Kane
2013-May-16 16:33 UTC
[R] Error: contrasts can be applied only to factors with 2 or more levels
Beautiful first question. 333 ch.list <- lmList(h12~spp+t+w+l+inih|id, data=mydata) Should that not be data= chm John Kane Kingston ON Canada> -----Original Message----- > From: ebelair at purdue.edu > Sent: Thu, 16 May 2013 15:05:35 +0000 > To: r-help at r-project.org > 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 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.____________________________________________________________ FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on your desktop!
arun
2013-May-16 19:21 UTC
[R] Error: contrasts can be applied only to factors with 2 or more levels
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 ??? [[alternative HTML version deleted]] ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Rolf Turner
2013-May-17 00:13 UTC
[R] Error: contrasts can be applied only to factors with 2 or more levels
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"?