Naming a random effect in lmer

-----Original Message-----
From: r-help-bounces at r-project.org 
[mailto:r-help-bounces at r-project.org] On Behalf Of spencerg
Sent: Friday, May 22, 2009 3:01 PM
To: Leigh Ann Starcevich
Cc: r-help at r-project.org
Subject: Re: [R] Naming a random effect in lmer

[ ... elided statistical advice ... ]
If you and your advisor still feel that what you are doing 
makes sense, 
I suggest you first get the source code via "svn checkout 
svn://svn.r-forge.r-project.org/svnroot/lme4" (or by downloading 
"lme4_0.999375-30.tar.gz" from 
"http://cran.fhcrc.org/web/packages/lme4/index.html"), then 
walk through 
the code line by line using the "debug" function (or "browser" or the 
"debug" package). From this, you will likely see either (a) 
how you can 
do what you want differently to achieve the same result or (b) how to 
modify the code so it does what you want.

Hope this helps.
Spencer


Leigh Ann Starcevich wrote:

Here is a test data set and code. I am including the data set after 
the code and discussion to make reading easier. Apologies 

for the size 

of the data set, but my problem occurs when there are a lot of Z 
variables. Thanks for your time.

# Enter data below

# Sample code
library(lme4)
mb<- length(unique(testsamp$WYear))

# Create the formula for the set of identically distributed random 
effects
Zs<- paste("Z",2:(mb-1)),sep="")
Trendformula <-as.formula(paste("LogY ~ WYear + 

(1+WYear|Site) + (1|", 

randommodel=paste(paste(Zs,collapse="+"), ")")))

fittest<-lmer(Trendformula, data = testsamp)
summary(fittest)

# Here I get an error because the name of the random effect is too 
long to print
# in the random effects output (I think).
# The error message is: Error in names(bars) <- unlist(lapply(bars, 
function(x)
# deparse(x[[3]]))) : 'names' attribute [3] must be the 

same length as 

the vector [2]

# However, when fewer Z variables are used in the random portion of 
the model,
# there is no error.
# Using only Z2 + ... + Z9 for the random intercept

Zs2<- paste("Z",2:9,sep="")
Trendformula2 <-as.formula(paste("LogY ~ WYear + (1+WYear|Site) + 
(1|", randommodel=paste(paste(Zs2,collapse="+"), ")")))
fittest2<-lmer(Trendformula2, data = testsamp)
summary(fittest2)


# Is there a way to either name the set of iid random effects 
something else or
# to define a random variable that could be used in the 

model to create a

# random intercept?

# I have had some success in lme, but it would be helpful for my 
simulation if I
# could conduct this analysis with lmer. My model in lme is 

not correctly

# estimating one of the variance components (random Site intercept).
# I am using:

detach(package:lme4)
library(nlme)
random.model.lme 

<-as.formula(paste("~-1+",paste(paste("Z",2:(mb-1),sep=""),col
lapse="+"))) 

n<-dim(testsamp)[1]
testsampgroup <- rep(1,n)
testsamp.lme <-cbind(testsamp,testsampgroup)
testgroupSamp<- groupedData(LogY ~ WYearCen|testsampgroup, 

inner= ~Site,

data= data.frame(testsamp.lme))

fittest3<-lme(LogY ~ WYearCen, random= 
pdBlocked(list(pdIdent(~-1+WYearCen:as.factor(Site)), 
pdIdent(~-1+as.factor(Site)), pdIdent(random.model.lme))),data= 
testgroupSamp)
summary(fittest3)
VarCorr(fittest3)


# Data

testsamp <-
structure(list(Year = c(2008, 2008, 2008, 2008, 2008, 2008, 2008,
2009, 2009, 2009, 2009, 2009, 2009, 2009, 2010, 2010, 2010, 2010,
2010, 2010, 2010, 2011, 2011, 2011, 2011, 2011, 2011, 2011, 2012,
2012, 2012, 2012, 2012, 2012, 2012, 2013, 2013, 2013, 2013, 2013,
2013, 2013, 2014, 2014, 2014, 2014, 2014, 2014, 2014, 2015, 2015,
2015, 2015, 2015, 2015, 2015, 2016, 2016, 2016, 2016, 2016, 2016,
2016, 2017, 2017, 2017, 2017, 2017, 2017, 2017, 2018, 2018, 2018,
2018, 2018, 2018, 2018, 2019, 2019, 2019, 2019, 2019, 2019, 2019,
2020, 2020, 2020, 2020, 2020, 2020, 2020, 2021, 2021, 2021, 2021,
2021, 2021, 2021, 2022, 2022, 2022, 2022, 2022, 2022, 2022),
WYear = c(0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 2, 2,
2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4,
5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7,
7, 7, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10,
10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12,
12, 12, 12, 13, 13, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14,
14, 14), Site = c(4, 18, 26, 40, 67, 75, 94, 4, 18, 26, 40,
67, 75, 94, 4, 18, 26, 40, 67, 75, 94, 4, 18, 26, 40, 67,
75, 94, 4, 18, 26, 40, 67, 75, 94, 4, 18, 26, 40, 67, 75,
94, 4, 18, 26, 40, 67, 75, 94, 4, 18, 26, 40, 67, 75, 94,
4, 18, 26, 40, 67, 75, 94, 4, 18, 26, 40, 67, 75, 94, 4,
18, 26, 40, 67, 75, 94, 4, 18, 26, 40, 67, 75, 94, 4, 18,
26, 40, 67, 75, 94, 4, 18, 26, 40, 67, 75, 94, 4, 18, 26,
40, 67, 75, 94), LogY = c(0.848648866298552, 0.809143925760456,
0.734173952725014, 1.46749967704437, 0.716106254860468, 
0.843871512951468,
1.09120092433378, 0.800893809796851, 0.996674977596997, 
0.917613604481207,
1.71928772722884, 0.797853604855215, 0.922298691760041, 
0.964654422529188,
0.782903180421921, 1.13457969553106, 1.21628917384868, 

2.03084776647495,

0.872954085910578, 1.02192794559856, 0.746307251774509, 
0.439812203188778,
1.11164109549224, 1.18414357836729, 2.00157711459358, 

0.66577753155877,

0.856374433428581, 0.343862060001402, 0.278505653147057,
1.20632152691478, 1.32289150679746, 2.19814430598707, 

0.538363941164496,

0.820038163290321, 0.070054765524828, 0.0479738684639024,
1.29137364087568, 1.52436357249377, 2.32150525025777, 

0.595507040392793,

0.851417610550757, -0.115908144193410, 0.0118306018140099,
1.39448009350962, 1.71677754106603, 2.59146662837284, 

0.595750060671620,

0.855387479311679, -0.430729785591898, 0.0178423104900579,
1.60964246000316, 1.99184029256509, 2.86865842252168, 

0.695124899993409,

0.96175860396451, -0.600991172113926, -0.174420349224615,
1.73794158380868, 2.06718359946362, 3.04502112974038, 

0.730730638403177,

0.961110819398807, -0.856693722990918, -0.549458074126028,
1.52302453916110, 2.05923417821491, 2.95885487422314, 

0.302432275785407,

0.718537282886428, -1.41807557701934, -0.474811468779057,
1.88486023048201, 2.47921637905194, 3.31076232685622, 

0.600331824659821,

0.997014319132077, -1.36760375228162, -0.491828047247449,
2.09353379020743, 2.74721582678157, 3.58818112810645, 

0.65742631492698,

1.06027358323846, -1.58298244571648, -0.934472752299038,
1.83456803880667, 2.62936515021684, 3.56971226362308, 

0.389323036788794,

0.748060984171013, -2.13928096660883, -1.26100797232926,
1.83430218924218, 2.65380472944419, 3.62529901196750, 

0.271765247781891,

0.639379726021376, -2.50138714617066, -1.36434864536697,
1.95417376162485, 2.84537426171405, 3.76029816545047, 

0.171262422338166,

0.63595411426061, -2.72648123827278), Y = c(2.33648781083889,
2.24598443402562, 2.08375999711081, 4.33837423214822, 

2.04644932501053,

2.32535220351989, 2.97784809630864, 2.22753102803039, 

2.70925849019601,

2.50330936997246, 5.5805521729813, 2.22076916113014, 

2.51506510968675,

2.62388074570782, 2.18781467519546, 3.10986617752641, 

3.37464176115807,

7.62054406285807, 2.39397241834575, 2.77854648986394, 

2.10919688492552,

1.55241565242538, 3.03934215461328, 3.26788693363161, 

7.40071868133414,

1.94600301201132, 2.35460841009671, 1.41038407371191, 

1.32115407405314,

3.34117160999488, 3.75426116973332, 9.0082813655785, 

1.71320166935217,

2.27058648893032, 1.07256691933604, 1.04914323924183, 

3.63778012876121,

4.59222002395514, 10.1910027761430, 1.81395045797806, 

2.34296591199978,

0.89055702237416, 1.01190086017652, 4.03287730840125, 

5.56656151506009,

13.3493357676049, 1.81439133829339, 2.35228566604212, 

0.650034535742804,

1.01800243542715, 5.00102284245171, 7.32900887997844, 

17.6133726381587,

2.00395935282089, 2.61629345414488, 0.548267938797843, 

0.839943753736141,

5.68562798048777, 7.90253504257589, 21.0104751440743, 

2.07659729526341,

2.61459920843830, 0.424563488824068, 0.577262559146385, 

4.58607500338397,

7.83996349588931, 19.2758857986172, 1.35314603256567, 

2.05143035272921,

0.242179624775457, 0.622002312266844, 6.58543393476032, 

11.9319106582846,

27.4060098478603, 1.82272352466727, 2.71017801013783, 

0.254716592899401,

0.611507507191544, 8.11353609874542, 15.5991406590765, 

36.1682306843681,

1.92981919064962, 2.8871607600197, 0.20536170381795, 

0.392792910103641,

6.26242843503692, 13.8649649375266, 35.5063752059022, 

1.47598127057995,

2.11289909722918, 0.117739471204143, 0.283368255138982, 

6.26076379244682,

14.2079935097071, 37.5359451785784, 1.31227890476568, 

1.89530490631499,

0.0819712136688162, 0.2555470735606, 7.0580849532232, 

17.2079977586343,

42.961233624846, 1.18680215155599, 1.88882343537745, 

0.065449185044807

), Z2 = c(0.47227027821606, 0.47227027821606, 0.47227027821606,
0.47227027821606, 0.47227027821606, 0.47227027821606, 

0.47227027821606,

0.269868730409177, 0.269868730409177, 0.269868730409177,
0.269868730409177, 0.269868730409177, 0.269868730409177,
0.269868730409177, 0.0986058822648916, 0.0986058822648916,
0.0986058822648916, 0.0986058822648916, 0.0986058822648916,
0.0986058822648916, 0.0986058822648916, -0.0415182662167964,
-0.0415182662167964, -0.0415182662167964, -0.0415182662167964,
-0.0415182662167964, -0.0415182662167964, -0.0415182662167964,
-0.150503715035887, -0.150503715035887, -0.150503715035887,
-0.150503715035887, -0.150503715035887, -0.150503715035887,
-0.150503715035887, -0.228350464192381, -0.228350464192381,
-0.228350464192381, -0.228350464192381, -0.228350464192381,
-0.228350464192381, -0.228350464192381, -0.275058513686277,
-0.275058513686277, -0.275058513686277, -0.275058513686277,
-0.275058513686277, -0.275058513686277, -0.275058513686277,
-0.290627863517575, -0.290627863517575, -0.290627863517575,
-0.290627863517575, -0.290627863517575, -0.290627863517575,
-0.290627863517575, -0.275058513686277, -0.275058513686277,
-0.275058513686277, -0.275058513686277, -0.275058513686277,
-0.275058513686277, -0.275058513686277, -0.228350464192381,
-0.228350464192381, -0.228350464192381, -0.228350464192381,
-0.228350464192381, -0.228350464192381, -0.228350464192381,
-0.150503715035887, -0.150503715035887, -0.150503715035887,
-0.150503715035887, -0.150503715035887, -0.150503715035887,
-0.150503715035887, -0.0415182662167965, -0.0415182662167965,
-0.0415182662167965, -0.0415182662167965, -0.0415182662167965,
-0.0415182662167965, -0.0415182662167965, 0.0986058822648916,
0.0986058822648916, 0.0986058822648916, 0.0986058822648916,
0.0986058822648916, 0.0986058822648916, 0.0986058822648916,
0.269868730409177, 0.269868730409177, 0.269868730409177,
0.269868730409177, 0.269868730409177, 0.269868730409177,
0.269868730409177, 0.47227027821606, 0.47227027821606, 

0.47227027821606,

0.47227027821606, 0.47227027821606, 0.47227027821606, 

0.47227027821606

), Z3 = c(-0.456256435177108, -0.456256435177108, 

-0.456256435177108,

-0.456256435177108, -0.456256435177108, -0.456256435177108,
-0.456256435177108, -0.0651794907395872, -0.0651794907395872,
-0.0651794907395872, -0.0651794907395872, -0.0651794907395872,
-0.0651794907395872, -0.0651794907395872, 0.175483244298888,
0.175483244298888, 0.175483244298888, 0.175483244298888,
0.175483244298888, 0.175483244298888, 0.175483244298888,
0.290800804838157, 0.290800804838157, 0.290800804838157,
0.290800804838157, 0.290800804838157, 0.290800804838157,
0.290800804838157, 0.305842225778062, 0.305842225778062,
0.305842225778062, 0.305842225778062, 0.305842225778062,
0.305842225778062, 0.305842225778062, 0.245676542018443,
0.245676542018443, 0.245676542018443, 0.245676542018443,
0.245676542018443, 0.245676542018443, 0.245676542018443,
0.135372788459142, 0.135372788459142, 0.135372788459142,
0.135372788459142, 0.135372788459142, 0.135372788459142,
0.135372788459142, 4.80758108354045e-17, 4.80758108354045e-17,
4.80758108354045e-17, 4.80758108354045e-17, 4.80758108354045e-17,
4.80758108354045e-17, 4.80758108354045e-17, -0.135372788459142,
-0.135372788459142, -0.135372788459142, -0.135372788459142,
-0.135372788459142, -0.135372788459142, -0.135372788459142,
-0.245676542018443, -0.245676542018443, -0.245676542018443,
-0.245676542018443, -0.245676542018443, -0.245676542018443,
-0.245676542018443, -0.305842225778062, -0.305842225778062,
-0.305842225778062, -0.305842225778062, -0.305842225778062,
-0.305842225778062, -0.305842225778062, -0.290800804838157,
-0.290800804838157, -0.290800804838157, -0.290800804838157,
-0.290800804838157, -0.290800804838157, -0.290800804838157,
-0.175483244298888, -0.175483244298888, -0.175483244298888,
-0.175483244298888, -0.175483244298888, -0.175483244298888,
-0.175483244298888, 0.0651794907395869, 0.0651794907395869,
0.0651794907395869, 0.0651794907395869, 0.0651794907395869,
0.0651794907395869, 0.0651794907395869, 0.456256435177108,
0.456256435177108, 0.456256435177108, 0.456256435177108,
0.456256435177108, 0.456256435177108, 0.456256435177108),
Z4 = c(0.393641410895141, 0.393641410895141, 0.393641410895141,
0.393641410895141, 0.393641410895141, 0.393641410895141,
0.393641410895141, -0.168703461812203, -0.168703461812203,
-0.168703461812203, -0.168703461812203, -0.168703461812203,
-0.168703461812203, -0.168703461812203, -0.341732653414463,
-0.341732653414463, -0.341732653414463, -0.341732653414463,
-0.341732653414463, -0.341732653414463, -0.341732653414463,
-0.276846706563615, -0.276846706563615, -0.276846706563615,
-0.276846706563615, -0.276846706563615, -0.276846706563615,
-0.276846706563615, -0.0979187925203697, -0.0979187925203697,
-0.0979187925203697, -0.0979187925203697, -0.0979187925203697,
-0.0979187925203697, -0.0979187925203697, 0.0987052888458345,
0.0987052888458345, 0.0987052888458345, 0.0987052888458345,
0.0987052888458345, 0.0987052888458345, 0.0987052888458345,
0.244207109056825, 0.244207109056825, 0.244207109056825,
0.244207109056825, 0.244207109056825, 0.244207109056825,
0.244207109056825, 0.297295611025701, 0.297295611025701,
0.297295611025701, 0.297295611025701, 0.297295611025701,
0.297295611025701, 0.297295611025701, 0.244207109056826,
0.244207109056826, 0.244207109056826, 0.244207109056826,
0.244207109056826, 0.244207109056826, 0.244207109056826,
0.0987052888458344, 0.0987052888458344, 0.0987052888458344,
0.0987052888458344, 0.0987052888458344, 0.0987052888458344,
0.0987052888458344, -0.0979187925203697, -0.0979187925203697,
-0.0979187925203697, -0.0979187925203697, -0.0979187925203697,
-0.0979187925203697, -0.0979187925203697, -0.276846706563615,
-0.276846706563615, -0.276846706563615, -0.276846706563615,
-0.276846706563615, -0.276846706563615, -0.276846706563615,
-0.341732653414463, -0.341732653414463, -0.341732653414463,
-0.341732653414463, -0.341732653414463, -0.341732653414463,
-0.341732653414463, -0.168703461812203, -0.168703461812203,
-0.168703461812203, -0.168703461812203, -0.168703461812203,
-0.168703461812203, -0.168703461812203, 0.393641410895141,
0.393641410895141, 0.393641410895141, 0.393641410895141,
0.393641410895141, 0.393641410895141, 0.393641410895141),
Z5 = c(-0.307723646230283, -0.307723646230283, -0.307723646230283,
-0.307723646230283, -0.307723646230283, -0.307723646230283,
-0.307723646230283, 0.351684167120324, 0.351684167120324,
0.351684167120324, 0.351684167120324, 0.351684167120324,
0.351684167120324, 0.351684167120324, 0.300960489170276,
0.300960489170276, 0.300960489170276, 0.300960489170276,
0.300960489170276, 0.300960489170276, 0.300960489170276,
0.0135263141200131, 0.0135263141200131, 0.0135263141200131,
0.0135263141200131, 0.0135263141200131, 0.0135263141200131,
0.0135263141200131, -0.230869588730213, -0.230869588730213,
-0.230869588730213, -0.230869588730213, -0.230869588730213,
-0.230869588730213, -0.230869588730213, -0.307416230000283,
-0.307416230000283, -0.307416230000283, -0.307416230000283,
-0.307416230000283, -0.307416230000283, -0.307416230000283,
-0.207505955250191, -0.207505955250191, -0.207505955250191,
-0.207505955250191, -0.207505955250191, -0.207505955250191,
-0.207505955250191, 2.73029795708800e-17, 2.73029795708800e-17,
2.73029795708800e-17, 2.73029795708800e-17, 2.73029795708800e-17,
2.73029795708800e-17, 2.73029795708800e-17, 0.207505955250191,
0.207505955250191, 0.207505955250191, 0.207505955250191,
0.207505955250191, 0.207505955250191, 0.207505955250191,
0.307416230000283, 0.307416230000283, 0.307416230000283,
0.307416230000283, 0.307416230000283, 0.307416230000283,
0.307416230000283, 0.230869588730212, 0.230869588730212,
0.230869588730212, 0.230869588730212, 0.230869588730212,
0.230869588730212, 0.230869588730212, -0.0135263141200123,
-0.0135263141200123, -0.0135263141200123, -0.0135263141200123,
-0.0135263141200123, -0.0135263141200123, -0.0135263141200123,
-0.300960489170277, -0.300960489170277, -0.300960489170277,
-0.300960489170277, -0.300960489170277, -0.300960489170277,
-0.300960489170277, -0.351684167120323, -0.351684167120323,
-0.351684167120323, -0.351684167120323, -0.351684167120323,
-0.351684167120323, -0.351684167120323, 0.307723646230283,
0.307723646230283, 0.307723646230283, 0.307723646230283,
0.307723646230283, 0.307723646230283, 0.307723646230283),
Z6 = c(0.219001863703187, 0.219001863703187, 0.219001863703187,
0.219001863703187, 0.219001863703187, 0.219001863703187,
0.219001863703187, -0.438003727406375, -0.438003727406375,
-0.438003727406375, -0.438003727406375, -0.438003727406375,
-0.438003727406375, -0.438003727406375, -0.084231486039687,
-0.084231486039687, -0.084231486039687, -0.084231486039687,
-0.084231486039687, -0.084231486039687, -0.084231486039687,
0.269540755326999, 0.269540755326999, 0.269540755326999,
0.269540755326999, 0.269540755326999, 0.269540755326999,
0.269540755326999, 0.301701868178519, 0.301701868178519,
0.301701868178519, 0.301701868178519, 0.301701868178519,
0.301701868178519, 0.301701868178519, 0.076574078217897,
0.076574078217897, 0.076574078217897, 0.076574078217897,
0.076574078217897, 0.076574078217897, 0.076574078217897,
-0.191435195544744, -0.191435195544744, -0.191435195544744,
-0.191435195544744, -0.191435195544744, -0.191435195544744,
-0.191435195544744, -0.306296312871592, -0.306296312871592,
-0.306296312871592, -0.306296312871592, -0.306296312871592,
-0.306296312871592, -0.306296312871592, -0.191435195544745,
-0.191435195544745, -0.191435195544745, -0.191435195544745,
-0.191435195544745, -0.191435195544745, -0.191435195544745,
0.0765740782178983, 0.0765740782178983, 0.0765740782178983,
0.0765740782178983, 0.0765740782178983, 0.0765740782178983,
0.0765740782178983, 0.301701868178517, 0.301701868178517,
0.301701868178517, 0.301701868178517, 0.301701868178517,
0.301701868178517, 0.301701868178517, 0.269540755327, 

0.269540755327,

0.269540755327, 0.269540755327, 0.269540755327, 0.269540755327,
0.269540755327, -0.0842314860396875, -0.0842314860396875,
-0.0842314860396875, -0.0842314860396875, -0.0842314860396875,
-0.0842314860396875, -0.0842314860396875, -0.438003727406375,
-0.438003727406375, -0.438003727406375, -0.438003727406375,
-0.438003727406375, -0.438003727406375, -0.438003727406375,
0.219001863703188, 0.219001863703188, 0.219001863703188,
0.219001863703188, 0.219001863703188, 0.219001863703188,
0.219001863703188), Z7 = c(-0.141858517577507, -0.141858517577507,
-0.141858517577507, -0.141858517577507, -0.141858517577507,
-0.141858517577507, -0.141858517577507, 0.42557555273252,
0.42557555273252, 0.42557555273252, 0.42557555273252, 

0.42557555273252,

0.42557555273252, 0.42557555273252, -0.185507292216737, 
-0.185507292216737,
-0.185507292216737, -0.185507292216737, -0.185507292216737,
-0.185507292216737, -0.185507292216737, -0.338278003454058,
-0.338278003454058, -0.338278003454058, -0.338278003454058,
-0.338278003454058, -0.338278003454058, -0.338278003454058,
-0.0327365809794237, -0.0327365809794237, -0.0327365809794237,
-0.0327365809794237, -0.0327365809794237, -0.0327365809794237,
-0.0327365809794237, 0.272804841495205, 0.272804841495205,
0.272804841495205, 0.272804841495205, 0.272804841495205,
0.272804841495205, 0.272804841495205, 0.272804841495207,
0.272804841495207, 0.272804841495207, 0.272804841495207,
0.272804841495207, 0.272804841495207, 0.272804841495207,
4.25663509926017e-16, 4.25663509926017e-16, 4.25663509926017e-16,
4.25663509926017e-16, 4.25663509926017e-16, 4.25663509926017e-16,
4.25663509926017e-16, -0.272804841495207, -0.272804841495207,
-0.272804841495207, -0.272804841495207, -0.272804841495207,
-0.272804841495207, -0.272804841495207, -0.272804841495206,
-0.272804841495206, -0.272804841495206, -0.272804841495206,
-0.272804841495206, -0.272804841495206, -0.272804841495206,
0.0327365809794244, 0.0327365809794244, 0.0327365809794244,
0.0327365809794244, 0.0327365809794244, 0.0327365809794244,
0.0327365809794244, 0.338278003454055, 0.338278003454055,
0.338278003454055, 0.338278003454055, 0.338278003454055,
0.338278003454055, 0.338278003454055, 0.185507292216741,
0.185507292216741, 0.185507292216741, 0.185507292216741,
0.185507292216741, 0.185507292216741, 0.185507292216741,
-0.425575552732522, -0.425575552732522, -0.425575552732522,
-0.425575552732522, -0.425575552732522, -0.425575552732522,
-0.425575552732522, 0.141858517577507, 0.141858517577507,
0.141858517577507, 0.141858517577507, 0.141858517577507,
0.141858517577507, 0.141858517577507), Z8 = c(0.083314261738317,
0.083314261738317, 0.083314261738317, 0.083314261738317,
0.083314261738317, 0.083314261738317, 0.083314261738317,
-0.345159084344455, -0.345159084344455, -0.345159084344455,
-0.345159084344455, -0.345159084344455, -0.345159084344455,
-0.345159084344455, 0.379949655180232, 0.379949655180232,
0.379949655180232, 0.379949655180232, 0.379949655180232,
0.379949655180232, 0.379949655180232, 0.143739990032049,
0.143739990032049, 0.143739990032049, 0.143739990032049,
0.143739990032049, 0.143739990032049, 0.143739990032049,
-0.284733356050736, -0.284733356050736, -0.284733356050736,
-0.284733356050736, -0.284733356050736, -0.284733356050736,
-0.284733356050736, -0.251773867890516, -0.251773867890516,
-0.251773867890516, -0.251773867890516, -0.251773867890516,
-0.251773867890516, -0.251773867890516, 0.114442667222960,
0.114442667222960, 0.114442667222960, 0.114442667222960,
0.114442667222960, 0.114442667222960, 0.114442667222960,
0.320439468224296, 0.320439468224296, 0.320439468224296,
0.320439468224296, 0.320439468224296, 0.320439468224296,
0.320439468224296, 0.114442667222965, 0.114442667222965,
0.114442667222965, 0.114442667222965, 0.114442667222965,
0.114442667222965, 0.114442667222965, -0.251773867890520,
-0.251773867890520, -0.251773867890520, -0.251773867890520,
-0.251773867890520, -0.251773867890520, -0.251773867890520,
-0.284733356050731, -0.284733356050731, -0.284733356050731,
-0.284733356050731, -0.284733356050731, -0.284733356050731,
-0.284733356050731, 0.143739990032042, 0.143739990032042,
0.143739990032042, 0.143739990032042, 0.143739990032042,
0.143739990032042, 0.143739990032042, 0.379949655180234,
0.379949655180234, 0.379949655180234, 0.379949655180234,
0.379949655180234, 0.379949655180234, 0.379949655180234,
-0.345159084344455, -0.345159084344455, -0.345159084344455,
-0.345159084344455, -0.345159084344455, -0.345159084344455,
-0.345159084344455, 0.0833142617383167, 0.0833142617383167,
0.0833142617383167, 0.0833142617383167, 0.0833142617383167,
0.0833142617383167, 0.0833142617383167), Z9 = c(-0.0440394305225472,
-0.0440394305225472, -0.0440394305225472, -0.0440394305225472,
-0.0440394305225472, -0.0440394305225472, -0.0440394305225472,
0.239071194265257, 0.239071194265257, 0.239071194265257,
0.239071194265257, 0.239071194265257, 0.239071194265257,
0.239071194265257, -0.436038757151818, -0.436038757151818,
-0.436038757151818, -0.436038757151818, -0.436038757151818,
-0.436038757151818, -0.436038757151818, 0.16647872637096,
0.16647872637096, 0.16647872637096, 0.16647872637096, 

0.16647872637096,

0.16647872637096, 0.16647872637096, 0.318922908948979, 

0.318922908948979,

0.318922908948979, 0.318922908948979, 0.318922908948979,
0.318922908948979, 0.318922908948979, -0.120987446490507,
-0.120987446490507, -0.120987446490507, -0.120987446490507,
-0.120987446490507, -0.120987446490507, -0.120987446490507,
-0.326666105524386, -0.326666105524386, -0.326666105524386,
-0.326666105524386, -0.326666105524386, -0.326666105524386,
-0.326666105524386, 1.6560876488147e-15, 1.6560876488147e-15,
1.6560876488147e-15, 1.6560876488147e-15, 1.6560876488147e-15,
1.6560876488147e-15, 1.6560876488147e-15, 0.326666105524385,
0.326666105524385, 0.326666105524385, 0.326666105524385,
0.326666105524385, 0.326666105524385, 0.326666105524385,
0.120987446490508, 0.120987446490508, 0.120987446490508,
0.120987446490508, 0.120987446490508, 0.120987446490508,
0.120987446490508, -0.318922908948989, -0.318922908948989,
-0.318922908948989, -0.318922908948989, -0.318922908948989,
-0.318922908948989, -0.318922908948989, -0.166478726370943,
-0.166478726370943, -0.166478726370943, -0.166478726370943,
-0.166478726370943, -0.166478726370943, -0.166478726370943,
0.436038757151805, 0.436038757151805, 0.436038757151805,
0.436038757151805, 0.436038757151805, 0.436038757151805,
0.436038757151805, -0.239071194265252, -0.239071194265252,
-0.239071194265252, -0.239071194265252, -0.239071194265252,
-0.239071194265252, -0.239071194265252, 0.0440394305225465,
0.0440394305225465, 0.0440394305225465, 0.0440394305225465,
0.0440394305225465, 0.0440394305225465, 0.0440394305225465
), Z10 = c(0.0207056819701757, 0.0207056819701757, 

0.0207056819701757,

0.0207056819701757, 0.0207056819701757, 0.0207056819701757,
0.0207056819701757, -0.141981819224062, -0.141981819224062,
-0.141981819224062, -0.141981819224062, -0.141981819224062,
-0.141981819224062, -0.141981819224062, 0.371109530696229,
0.371109530696229, 0.371109530696229, 0.371109530696229,
0.371109530696229, 0.371109530696229, 0.371109530696229,
-0.392270282599825, -0.392270282599825, -0.392270282599825,
-0.392270282599825, -0.392270282599825, -0.392270282599825,
-0.392270282599825, -0.0361780597061064, -0.0361780597061064,
-0.0361780597061064, -0.0361780597061064, -0.0361780597061064,
-0.0361780597061064, -0.0361780597061064, 0.356774827793781,
0.356774827793781, 0.356774827793781, 0.356774827793781,
0.356774827793781, 0.356774827793781, 0.356774827793781,
-0.0061434441010547, -0.0061434441010547, -0.0061434441010547,
-0.0061434441010547, -0.0061434441010547, -0.0061434441010547,
-0.0061434441010547, -0.344032869658285, -0.344032869658285,
-0.344032869658285, -0.344032869658285, -0.344032869658285,
-0.344032869658285, -0.344032869658285, -0.00614344410104096,
-0.00614344410104096, -0.00614344410104096, -0.00614344410104096,
-0.00614344410104096, -0.00614344410104096, -0.00614344410104096,
0.356774827793798, 0.356774827793798, 0.356774827793798,
0.356774827793798, 0.356774827793798, 0.356774827793798,
0.356774827793798, -0.0361780597061478, -0.0361780597061478,
-0.0361780597061478, -0.0361780597061478, -0.0361780597061478,
-0.0361780597061478, -0.0361780597061478, -0.392270282599797,
-0.392270282599797, -0.392270282599797, -0.392270282599797,
-0.392270282599797, -0.392270282599797, -0.392270282599797,
0.371109530696221, 0.371109530696221, 0.371109530696221,
0.371109530696221, 0.371109530696221, 0.371109530696221,
0.371109530696221, -0.141981819224062, -0.141981819224062,
-0.141981819224062, -0.141981819224062, -0.141981819224062,
-0.141981819224062, -0.141981819224062, 0.0207056819701758,
0.0207056819701758, 0.0207056819701758, 0.0207056819701758,
0.0207056819701758, 0.0207056819701758, 0.0207056819701758
), Z11 = c(-0.00849937774690609, -0.00849937774690609, 
-0.00849937774690609,
-0.00849937774690609, -0.00849937774690609, -0.00849937774690609,
-0.00849937774690609, 0.0716376124382085, 0.0716376124382085,
0.0716376124382085, 0.0716376124382085, 0.0716376124382085,
0.0716376124382085, 0.0716376124382085, -0.248910348302249,
-0.248910348302249, -0.248910348302249, -0.248910348302249,
-0.248910348302249, -0.248910348302249, -0.248910348302249,
0.43225406827121, 0.43225406827121, 0.43225406827121, 

0.43225406827121,

0.43225406827121, 0.43225406827121, 0.43225406827121, 

-0.307191795709549,

-0.307191795709549, -0.307191795709549, -0.307191795709549,
-0.307191795709549, -0.307191795709549, -0.307191795709549,
-0.146917815339487, -0.146917815339487, -0.146917815339487,
-0.146917815339487, -0.146917815339487, -0.146917815339487,
-0.146917815339487, 0.360616455833108, 0.360616455833108,
0.360616455833108, 0.360616455833108, 0.360616455833108,
0.360616455833108, 0.360616455833108, 2.37442501121216e-14,
2.37442501121216e-14, 2.37442501121216e-14, 2.37442501121216e-14,
2.37442501121216e-14, 2.37442501121216e-14, 2.37442501121216e-14,
-0.360616455833123, -0.360616455833123, -0.360616455833123,
-0.360616455833123, -0.360616455833123, -0.360616455833123,
-0.360616455833123, 0.146917815339424, 0.146917815339424,
0.146917815339424, 0.146917815339424, 0.146917815339424,
0.146917815339424, 0.146917815339424, 0.307191795709669,
0.307191795709669, 0.307191795709669, 0.307191795709669,
0.307191795709669, 0.307191795709669, 0.307191795709669,
-0.432254068271316, -0.432254068271316, -0.432254068271316,
-0.432254068271316, -0.432254068271316, -0.432254068271316,
-0.432254068271316, 0.248910348302301, 0.248910348302301,
0.248910348302301, 0.248910348302301, 0.248910348302301,
0.248910348302301, 0.248910348302301, -0.0716376124382226,
-0.0716376124382226, -0.0716376124382226, -0.0716376124382226,
-0.0716376124382226, -0.0716376124382226, -0.0716376124382226,
0.00849937774690764, 0.00849937774690764, 0.00849937774690764,
0.00849937774690764, 0.00849937774690764, 0.00849937774690764,
0.00849937774690764), Z12 = c(0.00295373795124409, 

0.00295373795124409,

0.00295373795124409, 0.00295373795124409, 0.00295373795124409,
0.00295373795124409, 0.00295373795124409, -0.0299593420769036,
-0.0299593420769036, -0.0299593420769036, -0.0299593420769036,
-0.0299593420769036, -0.0299593420769036, -0.0299593420769036,
0.132074282677049, 0.132074282677049, 0.132074282677049,
0.132074282677049, 0.132074282677049, 0.132074282677049,
0.132074282677049, -0.323223324378965, -0.323223324378965,
-0.323223324378965, -0.323223324378965, -0.323223324378965,
-0.323223324378965, -0.323223324378965, 0.450234056282428,
0.450234056282428, 0.450234056282428, 0.450234056282428,
0.450234056282428, 0.450234056282428, 0.450234056282428,
-0.27385370433672, -0.27385370433672, -0.27385370433672,
-0.27385370433672, -0.27385370433672, -0.27385370433672,
-0.27385370433672, -0.15317241090017, -0.15317241090017,
-0.15317241090017, -0.15317241090017, -0.15317241090017,
-0.15317241090017, -0.15317241090017, 0.389893409563986,
0.389893409563986, 0.389893409563986, 0.389893409563986,
0.389893409563986, 0.389893409563986, 0.389893409563986,
-0.153172410899934, -0.153172410899934, -0.153172410899934,
-0.153172410899934, -0.153172410899934, -0.153172410899934,
-0.153172410899934, -0.273853704336934, -0.273853704336934,
-0.273853704336934, -0.273853704336934, -0.273853704336934,
-0.273853704336934, -0.273853704336934, 0.450234056282481,
0.450234056282481, 0.450234056282481, 0.450234056282481,
0.450234056282481, 0.450234056282481, 0.450234056282481,
-0.323223324378928, -0.323223324378928, -0.323223324378928,
-0.323223324378928, -0.323223324378928, -0.323223324378928,
-0.323223324378928, 0.132074282677017, 0.132074282677017,
0.132074282677017, 0.132074282677017, 0.132074282677017,
0.132074282677017, 0.132074282677017, -0.0299593420768935,
-0.0299593420768935, -0.0299593420768935, -0.0299593420768935,
-0.0299593420768935, -0.0299593420768935, -0.0299593420768935,
0.00295373795124293, 0.00295373795124293, 0.00295373795124293,
0.00295373795124293, 0.00295373795124293, 0.00295373795124293,
0.00295373795124293), Z13 = c(-0.000820388989417742, 
-0.000820388989417742,
-0.000820388989417742, -0.000820388989417742, -0.000820388989417742,
-0.000820388989417742, -0.000820388989417742, 0.00984466787301128,
0.00984466787301128, 0.00984466787301128, 0.00984466787301128,
0.00984466787301128, 0.00984466787301128, 0.00984466787301128,
-0.0533252843121323, -0.0533252843121323, -0.0533252843121323,
-0.0533252843121323, -0.0533252843121323, -0.0533252843121323,
-0.0533252843121323, 0.170640909798784, 0.170640909798784,
0.170640909798784, 0.170640909798784, 0.170640909798784,
0.170640909798784, 0.170640909798784, -0.351946876459913,
-0.351946876459913, -0.351946876459913, -0.351946876459913,
-0.351946876459913, -0.351946876459913, -0.351946876459913,
0.469262501946444, 0.469262501946444, 0.469262501946444,
0.469262501946444, 0.469262501946444, 0.469262501946444,
0.469262501946444, -0.351946876459763, -0.351946876459763,
-0.351946876459763, -0.351946876459763, -0.351946876459763,
-0.351946876459763, -0.351946876459763, 1.30897668096353e-14,
1.30897668096353e-14, 1.30897668096353e-14, 1.30897668096353e-14,
1.30897668096353e-14, 1.30897668096353e-14, 1.30897668096353e-14,
0.351946876459646, 0.351946876459646, 0.351946876459646,
0.351946876459646, 0.351946876459646, 0.351946876459646,
0.351946876459646, -0.469262501946203, -0.469262501946203,
-0.469262501946203, -0.469262501946203, -0.469262501946203,
-0.469262501946203, -0.469262501946203, 0.351946876459683,
0.351946876459683, 0.351946876459683, 0.351946876459683,
0.351946876459683, 0.351946876459683, 0.351946876459683,
-0.170640909798657, -0.170640909798657, -0.170640909798657,
-0.170640909798657, -0.170640909798657, -0.170640909798657,
-0.170640909798657, 0.0533252843120879, 0.0533252843120879,
0.0533252843120879, 0.0533252843120879, 0.0533252843120879,
0.0533252843120879, 0.0533252843120879, -0.009844667873002,
-0.009844667873002, -0.009844667873002, -0.009844667873002,
-0.009844667873002, -0.009844667873002, -0.009844667873002,
0.000820388989416903, 0.000820388989416903, 0.000820388989416903,
0.000820388989416903, 0.000820388989416903, 0.000820388989416903,
0.000820388989416903), Z14 = c(0.000157883934625923, 
0.000157883934625923,
0.000157883934625923, 0.000157883934625923, 0.000157883934625923,
0.000157883934625923, 0.000157883934625923, -0.00221037508476475,
-0.00221037508476475, -0.00221037508476475, -0.00221037508476475,
-0.00221037508476475, -0.00221037508476475, -0.00221037508476475,
0.0143674380509829, 0.0143674380509829, 0.0143674380509829,
0.0143674380509829, 0.0143674380509829, 0.0143674380509829,
0.0143674380509829, -0.0574697522039801, -0.0574697522039801,
-0.0574697522039801, -0.0574697522039801, -0.0574697522039801,
-0.0574697522039801, -0.0574697522039801, 0.158041818561072,
0.158041818561072, 0.158041818561072, 0.158041818561072,
0.158041818561072, 0.158041818561072, 0.158041818561072,
-0.316083637122359, -0.316083637122359, -0.316083637122359,
-0.316083637122359, -0.316083637122359, -0.316083637122359,
-0.316083637122359, 0.474125455683776, 0.474125455683776,
0.474125455683776, 0.474125455683776, 0.474125455683776,
0.474125455683776, 0.474125455683776, -0.541857663638757,
-0.541857663638757, -0.541857663638757, -0.541857663638757,
-0.541857663638757, -0.541857663638757, -0.541857663638757,
0.474125455683927, 0.474125455683927, 0.474125455683927,
0.474125455683927, 0.474125455683927, 0.474125455683927,
0.474125455683927, -0.316083637122536, -0.316083637122536,
-0.316083637122536, -0.316083637122536, -0.316083637122536,
-0.316083637122536, -0.316083637122536, 0.158041818561182,
0.158041818561182, 0.158041818561182, 0.158041818561182,
0.158041818561182, 0.158041818561182, 0.158041818561182,
-0.0574697522040225, -0.0574697522040225, -0.0574697522040225,
-0.0574697522040225, -0.0574697522040225, -0.0574697522040225,
-0.0574697522040225, 0.0143674380509932, 0.0143674380509932,
0.0143674380509932, 0.0143674380509932, 0.0143674380509932,
0.0143674380509932, 0.0143674380509932, -0.00221037508476627,
-0.00221037508476627, -0.00221037508476627, -0.00221037508476627,
-0.00221037508476627, -0.00221037508476627, -0.00221037508476627,
0.00015788393462604, 0.00015788393462604, 0.00015788393462604,
0.00015788393462604, 0.00015788393462604, 0.00015788393462604,
0.00015788393462604), WYearCen = c(-7, -7, -7, -7, -7, -7,
-7, -6, -6, -6, -6, -6, -6, -6, -5, -5, -5, -5, -5, -5, -5,
-4, -4, -4, -4, -4, -4, -4, -3, -3, -3, -3, -3, -3, -3, -2,
-2, -2, -2, -2, -2, -2, -1, -1, -1, -1, -1, -1, -1, 0, 0,
0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2,
3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5,
5, 5, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7)), .Names = c("Year",
"WYear", "Site", "LogY", "Y", "Z2", "Z3", "Z4", "Z5", "Z6", "Z7",
"Z8", "Z9", "Z10", "Z11", "Z12", "Z13", "Z14", "WYearCen"), 

row.names 

= c(4L,
18L, 26L, 40L, 67L, 75L, 94L, 104L, 118L, 126L, 140L, 167L, 175L,
194L, 204L, 218L, 226L, 240L, 267L, 275L, 294L, 304L, 318L, 326L,
340L, 367L, 375L, 394L, 404L, 418L, 426L, 440L, 467L, 475L, 494L,
504L, 518L, 526L, 540L, 567L, 575L, 594L, 604L, 618L, 626L, 640L,
667L, 675L, 694L, 704L, 718L, 726L, 740L, 767L, 775L, 794L, 804L,
818L, 826L, 840L, 867L, 875L, 894L, 904L, 918L, 926L, 940L, 967L,
975L, 994L, 1004L, 1018L, 1026L, 1040L, 1067L, 1075L, 1094L,
1104L, 1118L, 1126L, 1140L, 1167L, 1175L, 1194L, 1204L, 1218L,
1226L, 1240L, 1267L, 1275L, 1294L, 1304L, 1318L, 1326L, 1340L,
1367L, 1375L, 1394L, 1404L, 1418L, 1426L, 1440L, 1467L, 1475L,
1494L), class = "data.frame")






At 11:17 AM 5/22/2009 -0700, spencerg wrote:

The first exaample on the "lmer" help page uses a formula 

"Reaction ~ 

Days + (Days|Subject)". Here, "Subject" is the name of a column in 
the data.frame "sleepstudy", with levels "308", "309", ... .

Does this answer your question? If no, please provide commented, 
minimal, self-contained, reproducible code, as requested in the 
posting guide "http://www.R-project.org/posting-guide.html". Your 
example is not "self-contained, reproducible".

Hope this helps. Spencer


Leigh Ann Starcevich wrote:

Dear guRus:

I am using lmer for a mixed model that includes a random 

intercept 

for a set of effects that have the same distribution, Normal(0, 
sig2b). This set of effects is of variable size, so I am using an 
as.formula statement to create the formula for lmer. For 

example, if 

the set of random effects has dimension 8, then the lmer call is:

Zs<- paste("Z",1:mb,sep="")
Trendformula <-as.formula(paste("LogY ~ WYear + (1+WYear|Site) + 
(1|", paste(paste(Zs,collapse="+"), ")")))
fit2.4a<-lmer(Trendformula, data = testsamp)

which, for mb=8, expands to:

fit1<-lmer(LogY ~ WYear + (1 | Site) + (1 | Year) + (1 | 

Z1+ Z2 + Z3 

+ Z4 + Z5 + Z6 + Z7 + Z8), data = testsamp)


I have no problems with this. However, if the set of 

random effects 

has a dimension of 30, then the lmer call is:

fit2<-lmer(LogY ~ WYear + (1 | Site) + (1 | Year) + (1 | 

Z1+Z2 + Z3 

+ Z4 + Z5 + Z6 + Z7 + Z8 + Z9 + Z10 + Z11 + Z12 + Z13 + 

Z14 + Z15 + 

Z16 + Z17 + Z18 + Z19 + Z20 + Z21 + Z22 + Z23 + Z24 + Z25 + Z26 + 
Z27 + Z28 + Z29+ Z30), data = testsamp)

In this case, I get an error because the name "Z1+Z2 + Z3 

+ Z4 + Z5 

+ Z6 + Z7 + Z8 + Z9 + Z10 + Z11 + Z12 + Z13 + Z14 + Z15 + 

Z16 + Z17 

+ Z18 + Z19 + Z20 + Z21 + Z22 + Z23 + Z24 + Z25 + Z26 + 

Z27 + Z28 + 

Z29+ Z30" is too long to print in the output. Is there any way to 
name the random effect in lmer so that the shorter (and more 
descriptive) name may be used and the error avoided? Or 

is there a 

way to combine these into a single variable prior to the lmer 
function call? In SAS, I am able to parameterize these as 

a Toeplitz 

structure with bandwidth 1.

Thanks for any help.

Leigh Ann Starcevich
Doctoral student
Oregon State University
Corvallis, Oregon
[[alternative HTML version deleted]]