Dear Joris, When you call rma() with the (default) argument "intercept=TRUE", then the intercept is added to the X matrix (a column of 1s is added). So, if you use:
fac <- c(1,1,2,3,3,4,4,5,5,5) X <- model.matrix(~factor(fac))[,2:5] and then: rma(ai, bi, ci, di, mods=X, data=testdata, measure="OR") the final X matrix has 1s in the first column (the intercept), and then the 4 dummies to code levels 2, 3, 4, and 5 in the other columns (with level 1 being the "reference" level, which is not included in the X matrix). So, if you want to test the factor, use: rma(ai, bi, ci, di, mods=X, data=testdata, measure="OR", btt=2:5) Or, you can use: fac <- c(1,1,2,3,3,4,4,5,5,5) X <- model.matrix(~factor(fac)) rma(ai, bi, ci, di, mods=X, intercept=FALSE, data=testdata, measure="OR", btt=2:5) which should give you the same results. I hope this helps! Best, -- Wolfgang Viechtbauer http://www.wvbauer.com/ Department of Methodology and Statistics Tel: +31 (0)43 388-2277 School for Public Health and Primary Care Office Location: Maastricht University, P.O. Box 616 Room B2.01 (second floor) 6200 MD Maastricht, The Netherlands Debyeplein 1 (Randwyck) ----Original Message---- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Joris Meys Sent: Monday, January 04, 2010 11:54 To: R mailing list Subject: [R] metafor: using mixed models > Dear all, > > I'm currently applying a mixed model approach to meta analysis using > the package metafor. I use the "model.matrix()" function to create > dummy variables. The option btt gives me the combined test for the > dummies. Problem is, I don't know which indices I have to use, and > can't really figure it out from the help file and the examples. I use > following code : > > X <- model.matrix(~factor, data=testdata)[,2:5] # to exclude the > intercept. Otherwise I get singular issues in the rma model > > rma(ai, bi, ci, di, mods=X, data=testdata,btt=c(2:5),measure="OR") > > Now I'm not sure whether btt reads the model intercept of rma as > index 1, or the first dummy as index 1. So I'm not sure if I should > use : > > rma(ai, bi, ci, di, mods=X, data=testdata,btt=c(1:4),measure="OR") > > from the examples in the help files, I should use the first option. > But there I see no option used to exclude an intercept from the model > matrix. All help greatly appreciated. Thank you in advance Joris > > > -- > Joris FA Meys > Statistical Consultant > > Ghent University > Faculty of Bioscience Engineering > Department of Applied mathematics, biometrics and process control > > Coupure Links 653 > B-9000 Gent > > tel : 09/ 264 59 87 > joris.m...@ugent.be > ------------------------------- > Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php > > [[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.
