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Dear Ian, Maybe not - but I also have problems when I code it as a fixed factor - see my other message... Cheers, Tom -----Original Message----- From: ian m s white [mailto:i.m.s.white at ed.ac.uk] Sent...

Dear all, Would any of you happen to have any further ideas on how to accomplish profiling intraclass correlations calculated from a lme4 glmer object? So far I just profiled the random effect variances (see below, keeping the total variance...

Hi Thierry, I now tried library(devtools) install_github("lme4",user="lme4") # latest development version library(lme4) library(multcomp) library(gtools) library(car) data=read.csv("http://www.kuleuven.be/bio/ento/temp/test_data_sexratio.csv",header=T,stringsAsFactors...

Dear all, For vector-based output, PDF export of R graphs works well, but unfortunately Office on Windows provide poor support for PDF and importing & exporting to other formats using Inkscape can be buggy. Enhanced metafile export in turn does...

Hi Thierry, Many thanks for your comments - fitting group (colony) as a fixed factor is no problem, see code below. But would you know by any chance how I should profile the total variance, or calculate a profiled Vtot on...

Dear all, I would appreciate any feedback on the following experimental setup and especially regarding a referee comment that suggested we were using inflated degrees of freedom and that our experiment suffered from pseudoreplication. So my question is whether the...

Dear all, Further to my previous message it appears that there might be a problem with the case where you set use.u=T (to also simulate random effects) in bootMer. This appears to be the case judging from the...

Dear Henrik, Many thanks for this fast response! The other error I mentioned apparently was due to me having afex_0.6-77 installed, or loading it after lme4 (I think that masked lme4's refit), with afex_0.5...

Hi Thierry, Ha, are you sure - can't I use it to model possible overdispersion in this case? Cheers, Tom -----Original Message----- From: ONKELINX, Thierry [mailto:Thierry.ONKELINX at inbo.be] Sent: 20 January 2014 15:41 To: Tom Wenseleers...

Hi Thierry, Many thanks for that - that's exactly what I needed! Cheers, Tom -----Original Message----- From: ONKELINX, Thierry [mailto:Thierry.ONKELINX at inbo.be] Sent: 20 January 2014 09:24 To: Tom Wenseleers; r-sig-mixed-models at r...

Dear Ben, Many thanks for your message - after some experimentation I did indeed confirm that the correct specification in lmer was the one you mentioned, i.e. the correct code to get almost identical output as in SAS/glimmix was...

Dear Sarah, The effect package I believe would give confidence intervals as if they would be calculated from the SE on the Wald statistics, so this is not totally ideal. Would the lsmeans package perhaps work better for you? That...

Dear all, Just to ask a bit of advice about the correct way to specify a nested binomial GLM, in the context of estimating variance components / intraclass correlations to infer heritabilities of a behavioural trait. The behavioural trait is a...

Dear all, I was just trying to use parametric bootstrapping to calculate significance levels in a Poisson mixed model using afex/pbkrtest. Using the data in attachment and the code data_alates=read.csv("alates_raw_FINAL3.csv", header=TRUE...

Hi Jarrod, In the meantime I think I found what I was doing wrong - I should have included all the control bees that we genotyped and which did not eat any eggs as well in the dataset, specifying they ate...

Hi Brian, Thanks for your message. Just to clarify - I've seen this problem on Windows both under Windows 8.1 and Windows 10, and the RStudio people were also aware of the problem (it's also a known problem...

Hi Jake, Many thanks for your advice! And yes realised the model would never quite get to 0% or 100% - that's why I had been trying putting in an intercept, as in data$baseline=qlogis(c(0.001,0...

Dear all, Given that the Intel MKL multithreaded BLAS is now free (https://software.intel.com/en-us/mkl/choose-download, released under the very permissive Intel Simplified Software License, https://software.intel.com/en-us/license/intel-simplified-software...

Hi Jarrod, Well the structure of the datafile is such that each row of the datafile contains the proportion of the eggs eaten in each trial by each individual bee (that belongs to a particular patriline, ie there would be...

Hi Jarrod, Well the structure of the datafile is such that each row of the datafile contains the proportion of the eggs eaten in each trial by each individual bee (that belongs to a particular patriline, ie there would be...