I think this is much better posted on r-sig-mixed-models rather than r-help.
-- Bert On Sun, Jul 7, 2013 at 1:14 PM, Stefan Th. Gries <stgr...@gmail.com> wrote: > Hi all > > I have a hopefully not too stupid question about multi-level / > mixed-effects modeling. I was trying to test a strategy from Crawley's > 2013 R Book on a data set with the following structure: > > - dependent variable: CONSTRUCTION (a factor with 2 levels) > - independent fixed effect: LENGTH (an integer in the interval [1, 61]) > - random effects with the following hierarchical structure: MODE > > REGISTER > SUBREGISTER > FILE. Specifically: > > MODE: S > REGISTER: monolog > SUBREGISTER: scripted > SUBREGISTER: unscripted > REGISTER: dialog > SUBREGISTER: private > SUBREGISTER: public > REGISTER: mix > SUBREGISTER: broadcast > MODE: W > REGISTER: printed > SUBREGISTER: academic > SUBREGISTER: creative > SUBREGISTER: instructional > SUBREGISTER: nonacademic > SUBREGISTER: persuasive > SUBREGISTER: reportage > REGISTER: nonprinted > SUBREGISTER: letters > SUBREGISTER: nonprofessional > > with various levels of FILE in each level of SUBREGISTER. Here's the > head of the relevant data frame (best viewed with a non-proportional > font): > > CASE MODE REGISTER SUBREGISTER FILE CONSTRUCTION LENGTH > 1 1 W printed reportage W2C-002 V_P_DO 11 > 2 2 W printed nonacademic W2B-035 V_P_DO 8 > 3 3 W nonprinted nonprofessional W1A-014 V_P_DO 8 > 4 4 W printed reportage W2C-005 V_P_DO 6 > 5 5 S dialog private S1A-073 V_DO_P 2 > 6 6 S dialog private S1A-073 V_DO_P 2 > > And here's the unique-types distribution of FILE in the design: > tapply(FILE, list(SUBREGISTER, REGISTER, MODE), function (qwe) > length(unique(qwe))) > > , , S > dialog mix monolog nonprinted printed > academic . . . . . > broadcast . 20 . . . > creative . . . . . > instructional . . . . . > letters . . . . . > nonacademic . . . . . > nonprofessional . . . . . > persuasive . . . . . > private 96 . . . . > public 77 . . . . > reportage . . . . . > scripted . . 25 . . > unscripted . . 66 . . > > , , W > dialog mix monolog nonprinted printed > academic . . . . 26 > broadcast . . . . . > creative . . . . 20 > instructional . . . . 19 > letters . . . 28 . > nonacademic . . . . 37 > nonprofessional . . . 17 . > persuasive . . . . 9 > private . . . . . > public . . . . . > reportage . . . . 20 > scripted . . . . . > unscripted . . . . . > > # I would usually have done this (using lme4) > model.1.tog <- lmer(CONSTRUCTION ~ LENGTH + > (1|MODE/REGISTER/SUBREGISTER), family=binomial) > > # but Crawley (2013:692ff.) suggests this: > LEVEL2 <- MODE:REGISTER > LEVEL3 <- MODE:REGISTER:SUBREGISTER > model.1.sep <- lmer(CONSTRUCTION ~ LENGTH + (1|MODE) + (1|LEVEL2) + > (1|LEVEL3), family=binomial) > > The results are the same for fixed and random effects, ok, but what I > don't understand in this case is why the random adjustments to > intercepts at the highest level of hierarchical organization (MODE) > are 0: > > ranef(model.1.sep) > $LEVEL3 > (Intercept) > S:dialog:private -0.9482442 > S:dialog:public 0.1216021 > [...] > > $LEVEL2 > (Intercept) > S:dialog -0.4746389 > [...] > > $MODE > (Intercept) > S 0 > W 0 > > I am guessing that's got something to do with the fact that what the > random adjustments to intercepts at the level of MODE would do is > already taken care of by the random adjustments to intercepts on the > lower levels of the hierarchical organization of the data - but when I > run the code from Crawley on his data (a linear mixed-effects model, > not a generalized linear mixed-effects model as mine), the highest > hierarchical level of organization does not return 0 as random > adjustment. What am I missing? > > Thanks for any input you may have! > STG > > ______________________________________________ > 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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm ______________________________________________ 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.
