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Questions tagged [glmm]

75 questions
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glmer.nb. I get different results when I run the same variable together with other predictors and by itself

I'm running a glmer.nb with land cover as my predictors, it is the proportion of each land cover. When i run some variables together i get a significant result but when I run them individually, the results aren't the same not even close! How should…
user21422926
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"object 'merPredDb' not found" error in ggpredict

I am trying to plot the predicted data with ggpredict() and having an error "Error in object@pp$b(1) : object 'merPredDb' not found": glmmdata3.17_predict <- ggpredict(glmmdata3.17, terms="days_cnt2[all]",type = "re") Error in object@pp$b(1) :…
KMatsuda
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ziformula specification for zero-inflated binomial using glmmTMB

I am looking for some clarification on specifying ziformula= in the glmmTMB package. I understand if you have zero-inflation then ziformula=~1 if inflation is independent or any predictors (or alternatively you can specify which terms) BUT can you…
Emma Neigel
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Problems dividing multilevel data into folds for cross validation using the perry package

I am trying to assess the performance of a generlaized linear mixed model I have built using behavior and performance data from dairy cows. The data has a nested structure (cows within farms) which I have tried to reflect in the model. I would like…
ILo
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Understanding random effects in glmm

I am trying to write a model for skewed count data, with repeat measures on the same ID at 15 timepoints over a 40 day period. I did an experiment with three factors at two levels, and these are included as fixed effects with interaction. For the…
kirchoffs
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convergence & large eigenvalues/ scaling issues in R trying to run glmer with continuous and factor variables

Help! I have a nested mixed effects model I am trying to run with site and plot ("plotID") as my random effects. Multiple plots fall within sites (9 plots per site) so site is assigned as a shared number between all 9 plots within that site, i.e.…
Emma Neigel
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How to calculate lsmeans from a glm model with family=binomial?

I would like to calculate adjusted means from a glm model with family = binomial. This is my script: data$Phenotype<- as.factor(data$Phenotype) data$Batch<- as.factor(data$Batch) data$Tray<- as.factor(data$Tray) data$Genotype<-…
user21260341
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Singularity in LMM with simple nested random effects

I have a simple experimental design. Each experiment consists of 6 treatments organized in 6 blocks with each treatment replicated once per block. The whole experiment was repeated 6 times. The outcome variable is an insect count for each subject.…
Pharcyde
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Building General Linear Mixed Model in R

I am trying to build a glmm in R but constantly get error messages (I am a complete beginner). I have conducted an experiment with Camera traps in which I tested, if they react to a target, that I pulled in front of them, so my response variable is…
saimensis
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How to manually set the dispersion parameters for truncated negative binomial distribution in glmmTMB?

I am using glmmTMB to run a glmm with a zero-truncated error distribution. I would like to manually set the dispersion parameter in my model and found a webpage that suggests that this is possible. However, there are no examples of how to actually…
JWaterton
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plot_models() panel size and/or label spacing issue

plot_models() function from library(sjPlot) does not seem to allow label offsets apart from spacing which make vertical adjustments. Please advise on how to prevent label cutoffs vertically and horizontally. Here is the model list object. Herewith…
Rion Lerm
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Linear Mixed Model (LMM) with statsmodels library (syntax suggestion)

I have a dataset that I tried that I want to analyised with Linear Mixed Effect (LMM). The Fixed effect is a binary classification (H and L), and the Block effect is Region (A, B and C). In other words, I wanted so see if Test1 and Test2 predict…
jsmgl
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Problems with GLMM models, with an error message - 'failed to converge' - have tried to scale and center

This is the code I'm using which has the error message fails to converge Q1glmm3<-lmer(log10.stock ~ log10.GDP +(log10.GDP|Area) + (Year|Area), data=LOG10.STOCK.VS.GDP.GLMM) Warning messages: 1: In checkConv(attr(opt, "derivs"), opt$par, ctrl =…
TLG1
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PiecewiseSEM - Error in cbind(ret, isSig(ret[, 5])) : object 'ret' not found

I'm trying to run a path analysis using the piecewiseSEM package. When I try to run summary or coefs(), I get this error: Error in cbind(ret, isSig(ret[, 5])) : object 'ret' not found or: Error in cbind(ret, isSig(ret[, 5])) : object 'ret' not…
Rayane Rodrigues
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What do these iteration warnings in ordinal::CLMM mean and how do I handle them?

I'm fitting a cumulative link mixed model (CLMM in the 'ordinal' package) to try and explain variance in negative experiences, coded on a 1 to 5 ordinal scale (1=absent, 5=very high) from a speech sample (N=618). My fixed effects are the time period…
E. Perkins
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