I failed to c.c. the list. And it should be r-sig-mixed-models list. Bert ---------- Forwarded message ---------- From: "Bert Gunter" <bgunter.4...@gmail.com> Date: Jul 7, 2016 2:06 PM Subject: Re: [R] lmer causes R session to terminate To: "David Kikuchi" <dwkiku...@gmail.com> Cc:
Off the top, I would guess that you'd need 10 or more times the data to get > meaningful estimates of the variance components, and heaven knows what > sorts of rank deficient matrices imbalance in the data may be producing. > But post on the r-mixed-models list to get an authoritative answer, which > this ain't. > > Cheers, > Bert > On Jul 7, 2016 10:55 AM, "David Kikuchi" <dwkiku...@gmail.com> wrote: > >> Hi, >> >> I am working with a large dataset of neotropical birds, and am trying to >> partition the variance in log(body mass) within different taxonomic >> levels. >> To better explain what I mean, the taxonomic levels are species, genus, >> family, and order. Species are within genera, genera are within famillies, >> and famlies are within orders. >> >> Sample data look like this: >> >> mass species genus family order.2 >> 377.0000 Geranospiza caerulescens Geranospiza Accipitridae >> Accipitriformes >> 213.1667 Harpagus bidentatus Harpagus Accipitridae >> Accipitriformes >> 500.0000 Leptodon cayanensis Leptodon Accipitridae >> Accipitriformes >> 1750.0000 Penelope albipennis Penelope Cracidae >> Galliformes >> 278.0000 Leucopternis semiplumbeus Leucopternis Accipitridae >> Accipitriformes >> 66.2500 Notharchus pectoralis Notharchus Bucconidae >> Galibuliformes >> 213.1667 Harpagus bidentatus Harpagus Accipitridae >> Accipitriformes >> 31.0000 Gymnopithys leucaspis Gymnopithys Thamnophilidae >> Passeriformes >> 31.0000 Gymnopithys leucaspis Gymnopithys Thamnophilidae >> Passeriformes >> >> >> I want to know how much variability in log(mass) there is at the species >> level, genus level, family level, and order level. >> >> The code that I have been using to do this looks like: >> >> bm.full <- lmer(log(mass) ~ 1 + (1|order.2/family/genus/species)) >> >> however, it crashes R every time, whether I run it on my laptop with 4 gb >> RAM or a desktop with 8 gb RAM. If I remove any of the taxonomic levels, >> though, it does run and produces reasonable output on either machine. >> There >> are 1943 observations (different studies occassionaly give different >> masses >> for the same species), 791 species, 381 genera, 60 families, and 21 >> orders. >> If I am able to modestly increase RAM, e.g. to 16 GB, is it likely that R >> will be able to handle the model, or is there such a dramatic increase in >> the computation required with four nested groups that it simply won't be >> possible? >> >> Thank you for your advice, >> >> David >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> 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. >> > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
