Dear all, I am trying to fit a model with crossed random effects using lme. In this experiment, I have been measuring oxygen consumption (mlmin) in bird nestlings, originating from three different treatments (treat), in a respirometer with 7 different channels (ch). I have also measured body mass (mass) for these birds.
id nest treat year mlmin mass ch hack 1EP51711 17 H 2008 1.401719138 10.7 4 2008:17 1EP51709 17 H 2008 1.257163112 9.7 5 2008:17 1EP51716 17 H 2008 1.050170714 10.2 6 2008:17 1EP51712 17 H 2008 1.330495314 9.6 7 2008:17 1EP51791 687 M 2008 1.07625708 9.7 3 2008:687 1EP51772 823 H 2008 1.336820232 10.2 4 2008:823 1EP51778 613 L 2008 1.300814516 10.7 5 2008:613 1EP52336 207 M 2008 1.071775936 10.7 3 2008:207 1EP52403 808 H 2008 1.142389688 10.3 5 2008:808 1ER17603 838 M 2009 0.984225217 9.6 3 2009:838 1ER17607 838 M 2009 1.045058894 9.3 4 2009:838 1ER17600 247 L 2009 1.047603048 9.2 5 2009:247 1ER17299 247 L 2009 0.974569658 9.2 6 2009:247 1ER17292 617 H 2009 1.271260094 10.5 7 2009:617 1ER17206 7009 M 2009 1.074791644 10.7 2 2009:7009 1ER17221 730 H 2009 1.423266177 10.2 4 2009:730 1ER17275 863 L 2009 1.433076022 10.7 4 2009:863 1ER17277 863 L 2009 1.165236024 9.7 5 2009:863 1ER17283 863 L 2009 1.139311895 10.4 6 2009:863 1ER17280 863 L 2009 1.056161196 10.4 7 2009:863 CK59991 690 H 2010 0.994878996 9.5 2 2010:690 CK59806 161 M 2010 1.070052025 9.7 6 2010:161 CK59859 545 M 2010 1.456680579 9.9 4 2010:545 CK59862 545 M 2010 1.350698793 9.9 5 2010:545 CK59871 223 L 2010 0.830582186 8.3 6 2010:223 CK59868 223 L 2010 0.776241825 8 7 2010:223 CL77343 365 M 2010 1.352454484 10.3 4 2010:365 CL77338 365 M 2010 1.327691628 9.6 5 2010:365 CL77356 191 H 2010 1.212796979 11.3 1 2010:191 CL77361 191 H 2010 0.882307732 11.4 2 2010:191 CL77355 191 H 2010 1.137097586 10.9 3 2010:191 I want to include both nesting attempt (hack) and respirometer channel (ch) as random factors in a model trying to explain variation in oxygen consumption. From Pinheiro & Bates (2000), I've gathered that this model could be fit making use of pdBlocked and pdIdent, so I've tried fitting the below model: m1.bmr<-with(bmred.df,lme(mlmin~treat*year+massout,random=pdBlocked(list(pdIdent(~hack-1),pdIdent(~ch-1))) )) However, my model fails with the following error message: Error in getGroups.data.frame(dataMix, groups) : Invalid formula for groups I would much appreciate any input on this! Kind regards, Andreas Nord Sweden -- View this message in context: http://r.789695.n4.nabble.com/Crossed-random-effects-in-lme-tp3000101p3000101.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ 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.
