Thanks, I suspected it would be something simple. Best wishes John On 09/08/2012 14:42, Viechtbauer Wolfgang (STAT)-2 [via R] wrote: > There is a simple explanation: > > 1) The command: > > factor(ftype) > > does not actually turn 'ftype' permanently into a factor, since you > are not re-assigning it back to the object 'ftype'. You have to use: > > ftype <- factor(ftype) > > 2) If you want to use the formula interface for specifying moderators, > you have to use mods = ~ <formula>, so in other words: > > rma(KL, VL, mods = ~ ftype) > > after you have made 'ftype' a factor (see 1). > > Or you can simply use: > > rma(KL, VL, mods = ~ factor(ftype)) > > which does the conversion of 'ftype' into a factor within the model > formula. > > Best, > > Wolfgang > > -- > Wolfgang Viechtbauer, Ph.D., Statistician > Department of Psychiatry and Psychology > School for Mental Health and Neuroscience > Faculty of Health, Medicine, and Life Sciences > Maastricht University, P.O. Box 616 (VIJV1) > 6200 MD Maastricht, The Netherlands > +31 (43) 388-4170 | http://www.wvbauer.com > > > -----Original Message----- > > From: [hidden email] > </user/SendEmail.jtp?type=node&node=4639763&i=0> [mailto:[hidden > email] </user/SendEmail.jtp?type=node&node=4639763&i=1>] > > On Behalf Of John Hodgson > > Sent: Thursday, August 09, 2012 12:56 > > To: [hidden email] </user/SendEmail.jtp?type=node&node=4639763&i=2> > > Subject: [R] Factor moderators in metafor > > > > I'm puzzled by the behaviour of factors in rma models, see example and > > comments below. I'm sure there's a simple explanation but can't see > it... > > > > Thanks for any input > > > > John Hodgson > > > > > > ------------------------------------- code/selected output > --------------- > > -- > > > > > > library(metafor) > > > > ## Set up data (from Lenters et al A Meta-analysis of Asbestos and > > Lung > > Cancer... > > ## Environmental Health Perspectives ⢠volume 119 | number 11 | > > November > > 2011) > > > > KL = c(0.02905, 0.06929, -0.1523, 1.6441, 0.1215, 0.3975, 1.0566, > 0.1257, > > 0.2277, 0.06791, 0.08164, 0.2526, 0.07577, 0.03266, 0.1141, 0.1836, > > 1.8276, > > 0.4149, 15.4974) > > SE = c(0.006633, 0.09335, 0.08909, 0.4297, 0.07858, 0.1753, 0.3679, > > 0.1837, > > 0.2172, 0.2775, 0.4201, 0.1976, 0.7688, 0.06507, 0.06239, 0.09061, > 0.9509, > > 0.2181, 7.331) > > > > VL = SE*SE > > > > amph = c(0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0) > > mix = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1) > > ftype = c(0, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2) > > > > > > factor(amph) > > factor(ftype) > > factor(mix) > > > > ## Fit ftype... > > > > > rma(KL,VL,mods=ftype) > > > > > > Mixed-Effects Model (k = 19; tau^2 estimator: REML) > > > > tau^2 (estimate of residual amount of heterogeneity): 0.0111 (SE = > 0.0095) > > tau (sqrt of the estimate of residual heterogeneity): 0.1054 > > > > Test for Residual Heterogeneity: > > QE(df = 17) = 43.0937, p-val = 0.0005 > > > > Test of Moderators (coefficient(s) 2): > > QM(df = 1) = 1.1069, p-val = 0.2928 > > > > Model Results: > > > > estimate se zval pval ci.lb ci.ub > > intrcpt 0.0811 0.0606 1.3380 0.1809 -0.0377 0.2000 > > mods 0.0473 0.0449 1.0521 0.2928 -0.0408 0.1353 > > > > > > Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 > > â â 1 > > > > > > ## why only one df for the 2-level factor? > > ## in other words, why isn't the above model the same as the > > following... > > > > > > > > > > > > > > > > rma(KL,VL,mods=cbind(amph,mix)) > > > > Mixed-Effects Model (k = 19; tau^2 estimator: REML) > > > > tau^2 (estimate of residual amount of heterogeneity): 0.0030 (SE = > 0.0046) > > tau (sqrt of the estimate of residual heterogeneity): 0.0549 > > > > Test for Residual Heterogeneity: > > QE(df = 16) = 37.5762, p-val = 0.0017 > > > > Test of Moderators (coefficient(s) 2,3): > > QM(df = 2) = 6.9220, p-val = 0.0314 > > > > Model Results: > > > > estimate se zval pval ci.lb ci.ub > > intrcpt 0.0380 0.0402 0.9448 0.3447 -0.0408 0.1169 > > amph 0.2879 0.1163 2.4754 0.0133 0.0599 0.5158 * > > mix 0.0888 0.0625 1.4199 0.1556 -0.0338 0.2114 > > > > --- > > Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 > > â â 1 > ______________________________________________ > [hidden email] </user/SendEmail.jtp?type=node&node=4639763&i=3> > 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/Factor-moderators-in-metafor-tp4639745p4639763.html > > > To unsubscribe from Factor moderators in metafor, click here > <http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=4639745&code=am9obkBmb3JtYnkucGx1cy5jb218NDYzOTc0NXwtMTEzNDA5Nzc0Mw==>. > 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/Factor-moderators-in-metafor-tp4639745p4639772.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.
