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

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Confidence intervals for odds ratio in GLMM with interactions

I have the following output from a GLMM The model is $$ \log\left(\dfrac{p_{i}}{1 - p_{i}}\right) = \beta_0 + \beta_1 \texttt{type}_i + \beta_2\texttt{treat}_i + \beta_3(\texttt{type}\times\texttt{...
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10 views

Sample size calculation GLMM

I have a problem with the calculation of sample size of my study. Design: each participant will value 4 health states, including one 'baseline' state and 3 new states of interest. The sequence of the ...
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1answer
30 views

Interpreting dispersion parameters of poisson GLMM with count data

I am working with count data and trying to understand if my model fit is acceptable for this poisson Generalized Linear Mixed Model: Richness.glmer<-glmer(Richness ~ Unit.type + plot.type + (1|NFI....
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19 views

Interpretation of GLMM output

I have an output ("summary()") of a GLMM ("lme4::glmer()") but I am not quite sure how to interpretate the estimate values of the fixed effects. My response variable is binary and all independent ...
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1answer
17 views

Variance structure with GLMMPQL

I want to know the influence of different climate variables on the abundance of berries. I have an average number of berries per plot and a number of plot per site (unbalanced design) for a number of ...
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25 views

Random effects for multiple social partners

I am a behavioral scientist attempting to estimate the degree to which animal subjects in my dataset exhibit consistent individual differences ('personality') in their social behavior. The dataset ...
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11 views

GLMM- Is it possible to limit variable combinations?

Let's assume I want to see all possible variable's combinations of a GLMM but I don't want to consider two variables at the same time in a model. How do I do that? For instance, I want to consider 3 ...
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2answers
344 views

Should I use Poisson distribution for non-integer, count-like data?

It's my first question here, I hope I'll ask it correctly. I am trying to find out how to analyse non-integer, count data (yes!). I am looking at the effect of a given treatment on habitat suitability ...
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23 views

likelihood ratio test (mixed model, nlme in R) not significant, but big R²?

I am carrying out linear mixed models with only one factor as predictor. I start with a likelihood ratio test (LRT) to see if adding the factor (to the null model consisting of the random effect ...
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2answers
80 views

GLMM- relationship between AICc weight and random effects?

I am developing GLMM's in order to assess habitat selection (using GLMMs' coeficients to construct Resource selection functions). I have (telemetry) data from 5 study areas, and each area has a ...
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27 views

Parametric bootstrap testing for random effect in GLMM

I am trying to learn GLMM using R. From what I have understood parametric bootstrap is a robust method to know the significance of fixed as well as random effects ...
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17 views

Fitting GLMM (lme4 in r) to uneven data and excluding strong effect

I'm stucked with my analysis and kindly ask for hints. I have to say that i'm not really a "mathematical mind" and new in mixed models. I'm dealing with strongly unevenly distributed data along the ...
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27 views

Defining “p” value for glmm randomisation psuedo-p value

I am currently using a Bayesian approach to glmm (MCMCglmm in R) to estimate regression coefficients (see here where I ask whether randomisation of fixed effects is ...
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2answers
53 views

GLMM: relationship between AIC, R squared and overdispersion?

First of all, I am a beginner in statistics, and I have been reading some questions and comments here regarding this matter but I am still a bit lost. My problem: I am constructing GLMM's in order to ...
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19 views

How to add a random effects term to a generalized poisson regression model?

I want to add random effects terms to a generalized poisson regression model. I know this will involve approximation of the loglikelihood (laplace or Gaussian quadratures). Please, i need some more ...
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13 views

What is the importance of overdispersion in GLMM?

I am constructing several GLMMs and someone suggested me to estimate the overdispersion (using overdisp.glmer {RVAideMemoire}). Why is this important, and which consequences exist when ignored? And ...
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6 views

GLMM with correlated explanatory variables

I am using prediction from GLMM to explore how two variables ($X_1$ and $X_2$) affect a response variable ($Y$). In my data these two variables are negatively correlated ($r_{X_1,X_2} = -0.24$). ...
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18 views

Using randomisation of fixed effects for a psuedo-p in mcmc glmm

I'm running generalized linear mixed models in R using the function MCMCglmm(), and with summary this generates p (pMCMC) values. However, pMCMC is, by the authors ...
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2answers
24 views

How to select automatically the best GLMM?

I have a set of 14 variables and I want to construct GLMM's. I want to include at first each variable and then add all the others, one at the time. This will require a lot of combinations of ...
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1answer
19 views

Multivariate/interaction prediction from glmm

Previously I have asked how to calculate the predicted response for groups (split by two categorical variables) given a single continuous fixed effect, in a glmm. Now I would like to take it one step ...
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6 views

prediction of Random Effect (BLUP) in unique model framework

Basic question: Is there any method that could predict the random effect in different model framework than GLMM(generalized linear mixed model)? while I was reading ...
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3answers
226 views

Can I test for correlation between variables before standardize them?

What I want to do is to construct GLMM's to evaluate resource selection, and I have a set of variables (some representing distances and others representing % of land cover). Can I test for ...
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27 views

Which assumptions do I need to check for a GLMM with a binary response (and how?)

I am modeling binomial responses using Generalized Linear Mixed Models with a nested random effect (not of interest, simply a control: year nested within location) and both categorical, count, and ...
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13 views

Question regarding variables transformation for GLMM's

I have a response variable (binary:1/0) and a set of explanatory variables, with different units: some have values in %, others in meters (distances, altitude and differences between elevation pixels),...
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12 views

Odds ratio in multivariate GLM

How to calculate odds ratio in multivariate GLM? I selected parameter estimation in option but the outcome didn't show EXP(B).
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18 views

LRT for a Linear Mixed Model

I want to compare the likelihoods for a model with population structure (a mixed effect represented by a variance-covariance matrix) to one without population structure (represented by an identity ...
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42 views

Question about application of GLMM with Poisson

I'm working on revising stats for a manuscript involving male reproductive success of deer. We measured three variables (body size, ...
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32 views

How do I report the results of likelihood ratio test from glmmADMB?

I want to test if an interaction is significant. My data are strongly overdispersed and contain repeated measures so I have a negative binomial GLMM model in ...
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13 views

What error distribution can I use for GLMM with continuous data but not normal due to too many 0s?

I am having problems with building a generalised linear model with random effects. I am modelling how a sensitivity ratio between various taxa and cyanobacteria (logSR) is effected by the taxa and ...
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16 views

Nested GLMMs: which are my random factors?

I am analyzing the number of seed capsules between different genotypes (A,B and C) I have 4 replicates for each genotype and in each of these replicates, I have 8 plants. Here is an example of the ...
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1answer
36 views

Random slopes for interactions without random slopes for main effects?

I have a GLMM with the following form: m1 <- glmer(Y ~ A*B + (A*B|Subject), data, family=binomial(logit)) where A and <...
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34 views

Beta binomial GLMM dispersion statistic issue

I am analyzing proportion data with GLMM in which the number of occurrence a behaviour of interest has been displayed and has not been displayed are concatenated and fitted as a single response ...
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18 views

How to apply multiple random (clustered) factors in HGLM package? And how to solve Cholmod error: wrong dimensions? [closed]

I'm working on alien reptiles on Mediterranean Islands. The idea is to assess which variables are influencing/favouring reptiles introductions, which reptiles are being introduced and which island are ...
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59 views

Variance Partition Coefficient and R²GLMM(c)

After computation of one model many times with GLMM (the DV has 3 values / I compute the model for the 3 values and for 26 different cohorts separately) the results at first were no surprise: In the ...
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Using variables measured at different scales in a binomial GLMM with successes and failures

I have seed and seedling abundance data for several plant species. I am trying to model the effect of my treatment on how many seeds successfully transition into seedlings (seed-to-seedling ...
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2answers
96 views

Key scientific publications reporting non-normal GLMMs in marine biology

I developed Poisson and Binomial GLMMs following the steps described in the excellent book from Zuur et al. (2009) Mixed Effects Models and Extensions in Ecology with R and I'm now ready to include my ...
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1answer
63 views

Using DIC to test which data should be used - different sample sizes

I have a glmm model $y \sim b_1 * b_2 * b_3 + random$ where $b_i$ are the fixed effects. I am using DIC to compare models and select the best fitting model. I also have some options in setting up ...
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1answer
33 views

Using DIC for model selection: (in)valid comparisons

Imagine I have the following 7 glmm models where $b_1$ through $b_3$ are fixed effects. $M_1 = y \sim b_1 \times b_2 \times b_3$ $M_2 = y \sim b_2 \times b_3$ $M_3 = y \sim b_1 \times b_3$ $M_4 = ...
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1answer
24 views

Is there a limit proportion of 0 and 1 to fit binary data using glm (link “logit”)

In relation with my other question here where I observe a strange behavior of the residuals after fitting binary data using glm/glmer, I now wonder: Are there boundaries on the proportion of 0 (or 1) ...
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41 views

Residuals with glm / glmer don't have null mean

I am trying to fit accuracy data (taking values 0 or 1) using glmer and I am puzzled to observe that the residuals of the model don't have a null mean. Wasn't this the whole point of the optimization.....
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1answer
35 views

Time as random effect or fixed effect in glmmADMB

I have a longitudinal dataset where patients have a measurement with a date, currently coded as time from end of treatment (days). Now, I want to build a model. Roughly, a zero inflated Poisson model ...
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1answer
57 views

Prediction using fixed effects in glmm

I have the following generalized linear mixed effects model (mcmcglmm in R) with data based on this paper. Sex is a two level factor (M or F), ...
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49 views

How to improve the fit of a zero-inflated, negative binomial glmmADMB model

I have been trying to fit count data that is zero-inflated and overdispersed using generalized linear mixed models. My research led me to the glmmadmb function in the glmmADMB package. I am fitting ...
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1answer
52 views

Conflicting results between GLMM and Post-hoc lsmeans

I'm studying the effect of pH and cross-types on mortality of fish. Treatment is categorical (2 levels: control and low pH) and cross-types is also categorical (4 levels: parents wild male x wild ...
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1answer
39 views

Binomial glmer with data between 0-1, not count data, not normal proportion

I have a special case of a binomial glmer and I can't figure out how to properly model it. I have a random factor (1|Species) to account for differences in species....
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7 views

Long-tailed random effect posterior distribution from unbalanced design

I am using MCMCGLMM to estimate the effect of some factors on a trait. The model is constructed with $Y \backsim B*S$ to find an interaction effect of factor B (...
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20 views

Formal formula for GLMM given glmer syntax

I'm looking for help writing the formal formula for a binomial mixed model with three crossed random intercepts, one numeric fixed effect, a logit link function, and a log-transformed offset term. ...
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Multivariate regression, non-normal response variable

I am attempting to run multivariate regression model with interactions terms to understand the combined effect for categorical variables and 2 other continuous variables. My response variable is ...
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56 views

How to validate a Poisson GLMM model?

I’m using the glmer function from the lme4 package in R to model species richness adjacent ...
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18 views

Test of significance for glmer

I would like to test the effect of a treatment ("crop") on species richness. I would rather use a glm for richness as it is a kind of count data. Besides, I have a nested sampling design (5 values ...