glmer

1. Binomial GLMM residual pattern

I am trying to complete a binomial GLMM but I don't think that the residuals look right when I compare them to the years. Is this too much of a pattern in the residuals? My model looks like this: binary response ~ carbon + I(carbon^3) + nitrogen + class + (1|Year). In my model, carbon and...
2. Confidence intervals from glmer models

Hi! When reading this, please keep in mind I'm pretty bad with statistics so please bear with me. So, I'm trying to analyse data from an ecotoxicological experiment. I have fish that were exposed to a substance during development and want to look at behavioural effects in the adult fish. I have...
3. Two way repeated measures with zeros, non integer values, and non-normal distribution

I would really appreciate some help with a few models I am trying to run. Essentially my data looks at how often a subject was visited depending on treatment and subject type across two years. The data looks like this: Year | Subject | SubjectType | Treatment | BlockNum | NumberOfVisits |...
4. Have I correctly specified my model in glmer ?

The following multilevel logistic model with one explanatory variable at level 1 (individual level) and one explanatory variable at level 2 (group level) : \text{logit}(p_{ij})=\pi_{0j}+\pi_{1j}x_{ij}\ldots (1) \pi_{0j}=\gamma_{00}+\gamma_{01}z_j+u_{0j}\ldots (2)...
5. How to compute the residual standard deviation from glmer() function in R?

I want to extract standard deviation of residual from glmer() function in R . So I wrote : lmer_obj = glmer(Y ~ X1 + X2 + (1|Subj), data = D, family = binomial) sigma(lmer_obj) I noticed that the last command sigma(lmer_obj) returns always "1" irrespective of data ...
6. How to compute the residual standard deviation from glmer() function in R?

I want to extract standard deviation of residual from glmer() function in R . So I wrote : lmer_obj = glmer(Y ~ X1 + X2 + (1|Subj), data = D, family = binomial) sigma(lmer_obj) I noticed that the last command sigma(lmer_obj) returns always "1" irrespective of data ...
7. Use of scale () function and conflicting standardized values for fixed effects

Hi, I'm currently using the scale() function in a glmer model (see below) and I'm having some inconsistencies between my standardized coefficient estimates from SAS and those in R. In SAS, the STDCOEF option in a generalized linear mixed model reports solutions for fixed effects in terms of the...
8. setting covariates in glmer (fixed factors vs covariates)

Hi everybody, i am a complete beginner in R, so please forgive me if I ask a stupid question. I ran an experiment on the effect of slowed speech (speech.rate; three speech rates) on syntactic structures (OS.SO.sentencetype; with a subject-first and an object-first (OS) structure) to see if...
9. Trouble with random factors glmm

Hi. I am doing a behavioural ecology study on juvinile brown trout and want to perform a glmm (glmer, package lme4) to analyse the effect of activity, size and treatment on survival. The variables i am using and are: response-survival (dead or alive), fixed effects- size (continuous), activity...
10. M

Identifying Fixed Effects from glmer

I've created a model using glmer and I'm trying to understand my output. In the past it has given me sensible effect names, but this time it seems arbitrary and I need to be certain which order the effects are in. I'm hoping somebody here can give some guidance. Some code: #reshape data...
11. Problem with mixed effects model with binary data

Hi guys, I have a question about logit mixed effects model. I tried to use lmer to fit a model with binary dependent variable (Yes or No), a categorical fixed predictor with 3 levels, and two random effects. However, it turned out that one level of the fixed resulted in only positive outcomes...