I am having trouble modifying the lmer code to make the change that William Dunlap suggested, and I believe that this is because the environment is locked.
I tried: 1. Revising the lmerFactorList function in a word processor and copying/pasting into lmer, but this did not work because the environment is locked. 2. Setting the environment and modifying the functionality of the lmerFactorList function as recommended in this post (https://stat.ethz.ch/pipermail/r-devel/2006-July/038547.html), but the unmodified lmerFactorList function was still used in the lmer call and the same error was generated. 3. Creating a new version of the lme4 package for my modified function with the makecdfenv package, but I do not know how to create a CDF file, feel that I am well beyond my programming expertise, and hope there is a more simple resolution to this issue. Thanks for any help -- las Leigh Ann Starcevich Doctoral student Oregon State University Corvallis, Oregon At 03:30 PM 5/22/2009 -0700, William Dunlap wrote: > > -----Original Message----- > > From: r-help-boun...@r-project.org > > [mailto:r-help-boun...@r-project.org] On Behalf Of spencerg > > Sent: Friday, May 22, 2009 3:01 PM > > To: Leigh Ann Starcevich > > Cc: r-help@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, > > > 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, 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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, > > > 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> -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]] > > >>> > > >>> ______________________________________________ > > >>> R-help@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@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. > > [[alternative HTML version deleted]] ______________________________________________ R-help@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.
