Generalized Linear Mixed (effects) Models are typically used for modeling non-independent non-normal data (eg, longitudinal binary data).

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Usage of rma.glmm() for random effect single group study

Below are first few rows of my data that need to be analysed. I would need to understand the relation between number of years and survival rate. My statistical teacher advised on using rma.glmm() ...
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27 views

What GLM family and link function for “proportion of time”?

A simple question to which I don't seem to find the answer anywhere. I have a response variable duration of time spent doing A of individuals tested for ...
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104 views
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Likelihood and estimates for mixed effects Logistic regression

First let's simulate some data for a logistic regression with fixed and random parts: ...
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1answer
26 views

correct use of Negative Binomial with a Geometric distribution in a mixed model (glmmPQL)

I am trying to fit a NB GLMM with a gemoetric distribution. I have come across very little information on this form of regression. And would like some pointers/reasurance. some literature is ...
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18 views

How to specify binomial glmm with random and correlation in R?

I am working on developing a model with a binomial response variable. My data consist of GPS points from tracked animals. The data set is large and contains 15,000 observations from 40 individuals. I ...
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2answers
20 views

GLMM for SNA and non-independency data

I contact you because my case is particular and I don’t know much about GLMM. I have data of social networks (network metrics) of a nonhuman primate species. These data are by nature non independent ...
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1answer
36 views

Taking a random factor into account while measuring a proportion a low N

I need to be neat in measuring the success rate of a treatment. It is anyway pretty high. But as it is all about ecology, multpliying experiments is difficult. I have treated $N = 20$ individuals, ...
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29 views

lmmlasso does not work for p>n

I am using the following example from the R manual: ...
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33 views

Model diagnostics for a glmmPQL in R mixed-effects model

Several texts (both online and published books) have been reviewed prior to asking this. What diagnostics are accepted as best practise for a generalised linear mixed-effects model fitted in R using ...
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33 views

Compare LMM GLMM (generalised linear mixed model, negative binomial) by numerical measure (AIC BIC, cross validation, R² squared) for model validation

How to compare results of generalized linear mixed model (GLMM, negative binomial) with a log transformed linear mixed model (multilevel, hierarchical) . I have a data set (counts), which is nested. ...
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47 views

R² (squared) from a generalized linear mixed-effects models (GLMM) using a negative binomial distribution

I try to compute the marginal and conditional R² for a GLMM using a negative binomial distribution by following the procedure recommended by Nakagawa & Schielzeth (2013) . Unfortunately, the ...
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27 views

How to use the Huber/White estimator of covariances in a generalized linear mixed model (glmmPQL) in R?

An analysis was implemented in SPSS 22 that uses the "Generalized Linear Mixed Models" feature of the program. Now I am looking for a way to port this to R. I use the glmmPQL() function of the MASS ...
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17 views

Specifying a glmm for panel data

I'm trying to predict counts based on variables sampled on a monthly basis as well as a few that are not related to time. In several places I've read that the MCMCglmm package in R would be ...
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25 views

differences between different notations in mixed effects model

I have never been so confused in my life. Could anyone please tell me what is the difference between the following mixed effects models: ...
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25 views

glm or glmm model with unequal variance

I am applying a GLM model with binomial family: glm(response ~ Treatment, family = binomial, data=dat) The only explaratory variable treatment is a categorical ...
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1answer
69 views

Linear mixed effect models with two independent variables

I am estimating a random intercept and a random slope model using the following R code. My dependent and independent variable are both continuous. ...
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38 views

R-squared for linear mixed effects model [duplicate]

I ran linear mixed effects model in R. model<-lmer(yld ~ rain + (1+rain|state),data=data,REML=FALSE) Is there any way I can generate an R-squared for the ...
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39 views

Elastic net package for mixed effects models?

I know about glmmLasso but would prefer to use elastic net. I wonder if there are any glmm analogues of glmnet out there, or if ...
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1answer
47 views

Measuring goodness of fit for mixed logistic regression model - inconsistent results from R squared and AUC

I am trying to assess the goodness-of-fit or accuracy of 6 generalised linear models. I first assessed this using AUC (calculated from function auc1 described here), and got results ranging from 0.65 ...
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57 views

Is this longitudinal data too complicated for GLMM or GEE?

After writing this post, I've realized that I am running around in circles, chasing my tail. Any help approaching this problem would be greatly appreciated, as I think I just need to bounce ideas ...
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1answer
61 views

Testing significance of a random effect glmmADMB model

Below is the output from a model of novel object test scores fit with the nbinom1 (quasi-Poisson) option in glmmADMB. I used ...
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23 views

How to account for multiple & varying amounts of observations per factor level & still retain info? As a random effect in GLMM or take the mean?

I would appreciate any help! Specifically I would like to know which option is best. Question Does Var2 influence Var1 in relation to the factor(Ind), and does Var3 & Var4 also have some effect. ...
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155 views

Q: plot glmm fixed and random effects (glmer in package lme4) using ggplot2

I am trying to visualize the results from a glmm that I ran with the lme4 package. ...
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1answer
69 views

Significance of the overall model GLMM using lme4

Maybe it's a basic question, but I'm learning about GLMM using the lme4 package. I'm confused about the way that I can know the significance the overall model using glmer. First, the random model is: ...
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1answer
195 views

Coefficients from glmer in R

In a mixed effect model where the intercept is random effect and the slope is fixed effect (see the code below), I understand the output of summary(glmer(...)). But ...
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35 views

Should I use a beta-binomial or binomial glmm?

I have several data sets on wildlife disease incidence. One of the issues with my dependent variable is that it represents only current infection status, therefore 0 (no disease) can represent either ...
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38 views

Calculating random effects from a glmerMod object (r package lme4)

Using the lme4 package, how does ranef() calculate (or extract) estimates of random effects from a ...
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55 views

GLMM and two slopes

My outcome variable is binomial, and I have 11 independent variables and a time variable. The time variable has different slopes, so I fixed it to time-before and ...
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43 views

Quantifying variable importance for GLMM using hierarchical partitioning (in R)

I am interested in quantifying variable importance for a binomial logistic mixed-model regression. My model has 5 fixed effects, and 3 random effects (2 nested). I am doing model selection and ...
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25 views

How to compare pairs of coefficients within a glmm with binomial error

I have a generalised linear mixed model with 34 explanatory variables (over 130,000 observations for each). 10 of these variables are different unprotected habitat types, and another 10 are the same ...
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1answer
18 views

How to compare the magnitude of a response among two groups?

I performed generalized linear mixed models to test the effects of a treatment on two different groups (I performed a model for each group). Now I would like to test which of the groups is most ...
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1answer
79 views

Interactions between random effects

I'm considering a mixed-effects model to try to understand factors that influence the number of ticks sampled on wild rodents. My data is nested so that I have one tick count per rodent, multiple ...
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74 views

Lme4 Error Help: “maxstephalfit…pwrssUpdate”

I am using a mixed model to assess the effects of various treatments on bee behavior (e.g., avoidance frequency - total avoidances per total visits; feeding frequency, and mating frequency). Bee ...
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1answer
71 views
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56 views

Should I be using a GLMM?

I'm looking at the influence of pollen type on whether a flower sets fruit (i.e., yes or no = 1 or 0). Then looking at number of seeds per fruit (1-6 possible). I was told I should use lmer, however ...
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Methods for analysing effects of percentage mortality on population data with zero/low abundances

I want to analyse the effects of percentage mortality from two sources (a predator and a disease) on the population abundance of a host measured at 12 sites for 8 years, with the main aim being to ...
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1answer
62 views

code needed for p values in GLMM

I need to get p values for the fixed effects in the following GLMM's I ran. Does anyone know of code that I can run that will give me the p values I need? At the moment the output from the ANOVA only ...
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116 views

Reading the output from a GLMM run in R

I am a complete novice and dummy when it comes to statistics so I apologise in advance... I have been asked to report the results of my GLMMs (I ran two) in a table. This table must state: effect, ...
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130 views

How to handle underdispersion in GLMM (binomial outcome variable)

I'm working on the following model in R: ...
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56 views

plot effects on glmer

I done a GLMM with the function glmer form lme4, the variable paternity is binomial (yes or no)(model<-glmer(paternity~factor1, factor 2 ....,family=binomial). My model run correctly, but after I ...
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49 views

Including a nested factor as random effect in a GLMM

Good afternoon, I'd like to ask for advice on including a nested factor as a random effect in a GLMM. I've read other threads in this forum, but still am not able to answer my question. Any help is ...
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17 views

Does GLMM or LMM already give us planned contrasts?

I use GLMM and LMM to find significant factors for my data. And could I ask if the results from these two models already give me planned contrasts? Or do I need to run them separately?
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1answer
99 views

Binomial GLMM: Model validation & ceiling effect

My data has a binary response acc(correct/incorrect), one continuous predictor score, three categorical predictors (...
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1answer
34 views

GLMM: Many models?

I use R to run GLMM models in my study. Then in my situation, I have 10 independent variables and one of them has 3 categories. Then, when I run the GLMM, it usually uses one category as baseline, so ...
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34 views

Prediction Model for the number of defects

I work at a software company, and we are trying to build a statistical model to predict the defect density (the number of defects that exist in a certain software release that is delivered to a ...
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1answer
343 views

Binomial GLMM with categorical predictors: p-values?

My data has a binary response (correct/incorrect), one continuous predictor score, three categorical predictors (race, ...
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0answers
111 views

Binomial mixed model with categorical predictors: model selection and getting p-values [closed]

My data has a binary response (correct/incorrect), one continuous predictor (with NaNs) and several categorical predictors. I want to add a random intercept for a ...
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77 views

Logistic regression with binary inputs

Is logistic regression an appropriate classifier when the input data are binary? Say we are conducting an experiment where the subject is presented with blue and green circles of varying shades, and ...
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34 views

How to assess whether IQ predicts emotional experiment more at time 1 or time 2 controlling for covariates?

I have the following data set of a two-wave longitudinal study in educational psychology. A group of 400 people did some questionnaire on IQ, personality and two different emotional states (sadness ...
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1answer
36 views

Generalized linear mixed model: what is base dependent variable?

I have run Generalized linear mixed model with glmer in lme4. I use R version 3.0.1. My dependent variable is binary (correct or wrong). And this is my results: ...