Thank you very much, First, sorry for posting on wrong mailing list, I did not know that there exists a special one for lmer. Yes, there are collinearities in the data. Still, I would like to have the variables in one model to compare explained variability. Is there some option, or it is simply impossible? Thank you, Anna
On 07.11.2013 16:03, bbolker [via R] wrote: > a_lampei <anna.lampei-bucharova <at> uni-tuebingen.de> writes: > > > > > Dear all, > > I have a problem with interactions in lmer. I have 2 factors (garden > and > > gebiet) which interact, plus one other variable (home), > > dataframe arr. When > > I put: > > / > > lmer (biomass ~ home + garden:gebiet + ( 1|Block), data = arr)/ > > > > it writes: > > /Error in lme4::lFormula(formula = biomass ~ home + garden:gebiet > > + (1 | : > > rank of X = 28 < ncol(X) = 30/ > > > > In the lmer help I found out that if not all combination of > > the interaction > > are realized, lmer has problems and one should do new variable using > > "interaction", which I did: > > / > > arr$agg <- interaction (arr$gebiet, arr$garden, drop = TRUE)/ > > > > when I fit the interaction term now: > > / > > lmer (biomass ~ home + agg+ ( 1|Block), data = arr)/ > > > > The error does not change: > > / > > Error in lme4::lFormula(formula = biomass ~ home + agg + (1 | > Block), : > > rank of X = 28 < ncol(X) = 29/ > > > > No NAs are in the given variables in the dataset. > > > > Interestingly it works when I put only given interaction like > > > > /lmer (biomass ~ agg + ( 1|Block), data = arr)/ > > > > Even following models work: > > /lmer (biomass ~ gebiet*garden + ( 1|Block), data = arr) > > lmer (biomass ~ garden + garden:gebiet +( 1|Block), data = arr)/ > > > > But if I add the interaction term in th enew formate of > > the new fariable, it > > reports again the same error. > > > > /lmer (biomass ~ garden + agg +( 1|Block), data = arr)/ > > > > If I put any other variable from the very same dataframe > > (not only variable > > "home"), the error is reported again. > > > > I do not understand it, the new variable is just another > > factor now, or? And > > it is in the same dataframe, it has the same length. > > > > Does anyone have any idea? > > > > Thanks a lot, Anna > > > > This probably belongs on r-sig-mixed-models. > > Presumably 'home' is still correlated with one of the > columns of 'garden:gebiet'. > > Here's an example of how you can use svd() to find out which > of your columns are collinear: > > set.seed(101) > d <- data.frame(x=runif(100),y=1:100,z=2:101) > m <- model.matrix(~x+y+z,data=d) > s <- svd(m) > zapsmall(s$d) > ## [1] 828.8452 6.6989 2.6735 0.0000 > ## this tells us there is one collinear component > zapsmall(s$v) > ## [,1] [,2] [,3] [,4] > ## [1,] -0.0105005 -0.7187260 0.3872847 0.5773503 > ## [2,] -0.0054954 -0.4742947 -0.8803490 0.0000000 > ## [3,] -0.7017874 0.3692117 -0.1945349 0.5773503 > ## [4,] -0.7122879 -0.3495142 0.1927498 -0.5773503 > ## this tells us that the first (intercept), third (y), > ## and fourth (z) column of the model matrix are > ## involved in the collinear term, i.e. > ## 1+y-z is zero > > ______________________________________________ > [hidden email] </user/SendEmail.jtp?type=node&node=4679965&i=0> > 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. > > > ------------------------------------------------------------------------ > If you reply to this email, your message will be added to the > discussion below: > http://r.789695.n4.nabble.com/problem-with-interaction-in-lmer-even-after-creating-an-interaction-variable-tp4679951p4679965.html > > > To unsubscribe from problem with interaction in lmer even after > creating an "interaction variable", click here > <http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=4679951&code=YW5uYS5sYW1wZWktYnVjaGFyb3ZhQHVuaS10dWViaW5nZW4uZGV8NDY3OTk1MXwyMjkyNTIzNjM=>. > NAML > <http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> > > -- View this message in context: http://r.789695.n4.nabble.com/problem-with-interaction-in-lmer-even-after-creating-an-interaction-variable-tp4679951p4680022.html Sent from the R help mailing list archive at Nabble.com. [[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.
