Naming a random effect in lmer
Hi Bill,
I'm about to take a look at this. If I understand the issue, very
long expressions for what I call the "grouping factor" of a random
effects term (the expressions on the right hand side of the vertical
bar) are encountering problems with deparse. I should have realized
that, any time one uses deparse, disaster looms.
I can tell you the reason that the collection of random-effects terms
is being named is partly for the printed form and partly so that terms
with the same grouping factor can be associated.
I guess my simplistic solution to the problem would be to precompute
these sums and give them names, if it is the sum like
Z2 + Z3 + Z4 + Z5 + Z6 + Z7 + Z8 + Z9
that is important, why not evaluate the sum
testGroupSamp <- within(testGroupSamp, Z29 <- Z2 + Z3 + Z4 + Z5 + Z6 +
Z7 + Z8 + Z9)
and use Z29 as the grouping factor.
Even the use of variables with names like Z1, Z2, ... and the use of
expressions like paste("Z", 2:9, sep = "") is not idiomatic R/S code.
It's an SPSS/SASism. (You know I never realized before how close the
word "SASism", meaning a construction that is natural in SAS, is to
"Sadism".) Why not create a matrix Z and evaluate these sums as
matrix/vector products?
Zs2<- paste("Z",2:9,sep="")
On Fri, May 22, 2009 at 5:30 PM, William Dunlap <wdunlap at tibco.com> wrote:
-----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.
The coding error is right in the error message: ?Error in names(bars) <- unlist(lapply(bars, function(x) deparse(x[[3]]))) and I suspect that traceback() would tell you that came from a call to lmerFactorList. That code implicitly assumes that deparse() will produce a scalar character vector, but it doesn't if the input expression is complicated enough. Changing the ? ?deparse(x[[3]]) to ? ?deparse(x[[3]])[1] or ? ?paste(collapse=" ", deparse(x[[3]])[1]) would fix it. ?The first truncates the name and the second my make a very long name. There is at least one other use of that idiom in the lme4 code and your dataset and analysis may require that all of them be fixed.
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,
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0.66577753155877,
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0.538363941164496,
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0.600331824659821,
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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,
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2.10919688492552,
1.55241565242538, 3.03934215461328, 3.26788693363161,
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3.63778012876121,
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2.34296591199978,
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17.6133726381587,
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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,
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1.47598127057995,
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6.26076379244682,
14.2079935097071, 37.5359451785784, 1.31227890476568,
1.89530490631499,
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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,
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0.47227027821606,
0.47227027821606, 0.47227027821606, 0.47227027821606,
0.47227027821606
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0.450234056282428, 0.450234056282428, 0.450234056282428,
0.450234056282428, 0.450234056282428, 0.450234056282428,
-0.27385370433672, -0.27385370433672, -0.27385370433672,
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-0.15317241090017, -0.15317241090017, -0.15317241090017,
-0.15317241090017, -0.15317241090017, 0.389893409563986,
0.389893409563986, 0.389893409563986, 0.389893409563986,
0.389893409563986, 0.389893409563986, 0.389893409563986,
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-0.153172410899934, -0.153172410899934, -0.153172410899934,
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-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,
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-0.323223324378928, 0.132074282677017, 0.132074282677017,
0.132074282677017, 0.132074282677017, 0.132074282677017,
0.132074282677017, 0.132074282677017, -0.0299593420768935,
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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,
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0.351946876459683, 0.351946876459683, 0.351946876459683,
-0.170640909798657, -0.170640909798657, -0.170640909798657,
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-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,
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0.0143674380509829, 0.0143674380509829, 0.0143674380509829,
0.0143674380509829, 0.0143674380509829, 0.0143674380509829,
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-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,
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0.158041818561182, 0.158041818561182, 0.158041818561182,
0.158041818561182, 0.158041818561182, 0.158041818561182,
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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]]
______________________________________________ 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.
______________________________________________ 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.
______________________________________________ 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.