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Questions tagged [glmmtmb]

R package to fit linear and generalized linear mixed models with various extensions, including zero-inflation.

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non-positive-definite Hessian matrix/non-convergence problem with glmmTMB

I've got a dataset that has temperature (21c or 29c), inoculation (mock (m),single inoculations (c or r), or coinoculation (rc)), and age group (y or o). I am trying to model the interactive effects ...
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GLMM for not so gaussian data

I am having an issue with GLMM and hope you could advice me. So basically I have data from microscopy experiment of three independent groups (variable: subfolder) nested within 4 experimental ...
Julius Bogomolovas's user avatar
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Fitting random slope for a subject-level predictor

In a nutshell, I am trying to understand whether it makes sense to include random slopes for group-level (or subject-level) predictors in a mixed effects model? Some Background: I am fitting a mixed ...
Stephanie Rivest's user avatar
3 votes
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Including random effect reduces model fit

I am fitting a zero-inflated negative binomial GLMM to model counts. Fixed effects are all categorical except Effort_sq which are non-zero values. The experiment is performed several times within a ...
Alessandra Bielli's user avatar
2 votes
1 answer
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When to include random-effects in zero-inflation model component?

Is it appropriate to specify random-effects (RE) in zero-inflation (ZI) component of the model? My intuition is that whatever RE is appropriate for main component should be appropriate for ZI ...
Suhas Bharadwaj's user avatar
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Is it appropriate to calculate odds ratios from random effects glmm output?

Is it appropriate to calculate odds ratios from random effects glmm output? about the data: grown (binary): whether flower grows over a certain height (TRUE/FALSE)...
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Difference between zero-inflated model and zero-altered model

Could someone explain what assumptions I am making (perhaps implicitly) when I specify family = nbinom2() versus ...
Suhas Bharadwaj's user avatar
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How to tweak my glmmTMB model to address several items? i.e. covariates, reference levels, random factors, and zero-inflation model

I recently ran a Zero-inflated negative binomial mixed model (ZINB hereafter) using the glmmTMB function from the glmmTMB ...
bribina's user avatar
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Next steps - variable can't be a fixed and random effect?

I have been trying to run a binomial GLMM on the proportion of emerged seedlings across locations (categorical variable) and over the monitoring period (continous variable). We obtained and planted ...
TruthSeeker4's user avatar
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41 views

Beta-binomial relationship between dispersion and correlation parameters

Context: I have created a beta-binomial model using glmmTMB() from the glmmTMB package and I am now trying to simulate a beta-...
Reid's user avatar
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glmmTMB ZINB model non-convergence

I am looking for help with fitting a ZINB model with mixed-effects. The model which I intend to fit contains a random-intercept (three variables/terms denoting the nested, hierarchical group structure)...
Suhas Bharadwaj's user avatar
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Addressing Heteroscedasticity in Mixed Effects Models with glmmTMB and DHARMa in R [duplicate]

I am analyzing ecological data in R, where I aim to understand the impact of urbanization on species trends. My response variable is the coefficient of species trends (estimate), and my main predictor ...
Pau Colom Montojo's user avatar
3 votes
1 answer
162 views

Addressing Heteroscedasticity in Mixed Effects Models with glmmTMB and DHARMa in R

I am analyzing ecological data in R, where I aim to understand the impact of urbanization on species trends. My response variable is the coefficient of species trends (...
Pau Colom Montojo's user avatar
1 vote
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What are the assumptions of beta-binomial models, and how do I test for them in r?

I want to model the effects of dispersal distance (disp) and reproductive rate (rep) on colonization rate, quantified as the ...
JessKL's user avatar
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How to deal with under-dispersion in negative binomial GLMM?

I have some animal species. I am interested in seeing what is the relationship between the area they occupy (my response variable, p, which is a count of cells) and ...
LT17's user avatar
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Non-transformed Log scale response variable in LMM - which distribution to use?

I am currently modelling tea bag index results across different forest "treatments" to infer differences, effect sizes and influence of covariates. One element of these results and a ...
Eco_Analysis's user avatar
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glmmTMB for non-regression ecological count data?

Study design: I am analyzing ecological count data for fish in a pre-existing database with observations of fish species abundances(zero_filled). Each species were recorded at a site twice a month of ...
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Interpreting output from sum constrast model

I have a question following the great response @DaveArmstrong answered in this topic about sum contrast coding. To first introduce my problem, have a model to account for species richness which is: <...
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How to account for relative frequency in a generalized linear mixed model?

I have a dataset of scan sampling done on animals in intervals of 20 minutes. Each observation, an animal is categorized by category 1 (A, B, C, D, or E) and by category 2 (1, 2, 3, or 4). I am trying ...
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1 vote
1 answer
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How do I prioritise model diagnostics while considering model selection and parameter uncertainty?

I have fitted a generalized linear mixed model using glmmTMB on the data (110 observations, balanced data) collected from an observational study to understand the ...
medium-dimensional's user avatar
2 votes
1 answer
61 views

How to model predicted proportion data without weights

Research Question I am trying to determine if maternal nest-site choice influences offspring sex ratio in a species where nest temperature determines sex. Data I have temperature traces from real nest ...
Claud's user avatar
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Setting random effect and nested random effect correctly in glmmTMB model

I have been having trouble fitting my data of seedsets of flowers. I have gathered data from seven flowering species in four different elevations. Not all the species appear in every elevation and the ...
Dominik Anyz's user avatar
1 vote
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Power analysis compatible with package glmmTMB

I am trying to conduct a power analysis on the following model: NativeAntModel <- glmmTMB(NativeAnts~ Treatment + Month + (1|Site), data = NativeAntData, family = t_family) Background on the data: ...
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Is the GLM a good fit or should I use a non-parametric test?

I have been having trouble interpreting my data of seedsets of flowers. I have gathered data from seven flowering species in four different elevations. Not all the species appear in every elevation ...
Dominik Anyz's user avatar
1 vote
1 answer
69 views

Analyzing compositional data (sum of proportions = 1) using mixed models with explanatory variables for each proportion

I aim to investigate how the relative abundance of species across communities is associated with the functional traits of each species. For each location ($>250$), I have compositional data that ...
Ruben's user avatar
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Help needed fitting a general latent variable model in glmmTMB

as Ben Bolker suggested here I should ask this question in this forum! I am trying to fit a GLVM similar to the one presented in this vignette: https://cran.r-project.org/web/packages/glmmTMB/...
Max M's user avatar
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Fitting a glmmTMB mode with pre-defined coefficients

I'm working on an analysis in which I conducted multimodel inference and model averaging using glmmTMB, which I used for the ordered beta distribution and I would like to stick with. I dredged the ...
corrinak's user avatar
4 votes
1 answer
235 views

R: Parameterization differences betwen MASS::glm.nb and glmmTMB "nbinom2"

I'd like opinions on two differing GLM outputs in RStudio. I model count data (dung pellets) over 21 sites, using quadrats counted as an area offset. I started with a GLM Poisson regression for the ...
JeremieT's user avatar
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56 views

Calculate the average marginal effect (AME) in the multilevel regression with glmmTMB package

I am writing this message because I want to calculate the average marginal effects (AME) in order to be able to interpret an interaction resulting from a multilevel regression. However, I am finding ...
Jules's user avatar
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Multilevel model: Contradictory results between multilevel model with interactions and segmented model

I am working on a research paper exploring the differential effect (or interaction) of financialization on the housing conditions of the population according to tenure status. For this purpose, I ...
Jules's user avatar
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Residuals assumptions in glmm not verified! Help

I am trying out GLMMs models to test whether two categorical variables (species and sex) and their interaction (sex + species + sex*species= fixed factors) influence certain acoustic parameters (...
Alice 's user avatar
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Can a covariate also be a random effect in glmmTMB model with ar1 [closed]

I have data consisting of catches of insects at weekly intervals over 2 years, repeated with the same methods at the same location 3 decades later. My main question is, have numbers (total and for ...
IMH's user avatar
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1 answer
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LMM for Repeated Measures tree ring chronology

Having my first go at R and stats. I sampled and analyzed tree rings for different measures (width, density, etc.). There are 3 treatments, 3 plot per treatment, and 5 trees per plot. The ring time ...
mink's user avatar
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4 votes
1 answer
350 views

glmmTMB truncated models with zero inflation

everyone. I am fitting a glmm model using the R library glmmTMB for predicting a count response variable with excess-zeros and overdispersion (...
Javier's user avatar
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Back-transform binomial and betabinomial to counts with emmeans

My first outcome is a bounded count (range = 0-5, not zero-inflated, not overdispersed), so I specified a model using a successes-failures matrix and a binomial distribution: ...
bcarothers's user avatar
2 votes
1 answer
336 views

How to interpret odds ratios by emmeans for glmmTMB-beta

I fit this mixed model with beta for the response variable: photochemical efficiency or Fv/Fm and the predictor variables are categorical: ...
Franelibethgalvez's user avatar
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100 views

Extract some modeled values from glmmTMB object

I modelled some dummy data in glmmTMB package in R: ...
LT17's user avatar
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27 views

glmmTMB profile argument, what does it do?

I tried running analysis using glmmTMB with profile=TRUE and the model that previously wasn't converging, now converging, anyone knows what assumptions does this parameter "profile" takes ...
user395714's user avatar
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1 answer
93 views

obtaining a goodness of fit indices for an analysis with tweedie distribution

I performed an analysis specifying a dependent variable with a tweedie distribution using the glmmTMB package in R. I got several fit indices, specifically: AIC, BIC, Logliklihood. What is the most ...
Lior's user avatar
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Significance in ZINB GLMM disappears when par1 * par 2 is used instead of par1 : par2 in R [duplicate]

I am working with a zero-inflated negative binomial model in R, using the glmmTMB package. My main goal is to investigate if there is a significant difference in the amount of times a grassland field ...
Barbara Perez de Araújo's user avatar
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0 answers
17 views

Dyadic reciprocity for binary outcome in asymmetric block design

I am trying to estimate dyadic reciprocity in a binary outcome collected with asymmetric block design (speed-dating where each person indicates whether or not they are interested in a second date with ...
Avi Kluger's user avatar
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1 answer
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Specify a correlation between two cross-classified random variables in a mixed-effect model

I posted this question in a different version on R-sig-mixed-models and received no reply. I am trying my luck here. I am trying to emulate an ANOVA-based approach to analyzing round-robin data with a ...
Avi Kluger's user avatar
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0 answers
61 views

How do I move forward to find a better model fit, help interpreting DHARMa residuals

I am trying to test if there is an effect on number of individuals depending on the proportion of a certain land use type and its management. But I don't find a model with a good fit. There seems to ...
Vevey's user avatar
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1 vote
0 answers
79 views

GLMM optimised with CG gives empty warning, diagnose() finds no problem

I am running the following code for a ZINB GLMM, using the glmmTMB package in R: ...
Barbara Perez de Araújo's user avatar
1 vote
1 answer
61 views

How to specify random slopes when random effects are nested or crossed

I'm trying to run a model which has 3 random effects. Its data on an animal species and the random effects are 'group', 'mother' and 'individual'. Individual should be nested within mother, and then ...
JJRich91's user avatar
1 vote
1 answer
35 views

Is this GLM approach appropriate for binary data and determining difference between 8 groups?

I have been given a dataset to analyze looking at some herbicide treatments for invasive trees in three states with 3 sites in state 1, 2 sites in state 2, and 1 site in state 3. We hope to answer ...
E10's user avatar
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Why would a model indicate overdispersion without random effects but underdispersion with random effects? (and how to handle)

Overview: In my model building process, I fit both GLMs and GLMMs. I noticed that the GLMs suggested overdispersion in the data, while the GLMMs suggested underdispersion. How can I make sense of this,...
Reid's user avatar
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0 answers
37 views

Binomial model with glmmTMB library [duplicate]

I proposed the following binomial model, with the glmmTMB library, because I want to evaluate if there are differences between the proportions of infection by a given parasite for different ...
Elisa Helman's user avatar
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0 answers
28 views

How can I best formulate my glmm if i want to test within individuals and within context for these individuals?

I am a beginner in using glmm, I have a question about which structure to test "within individual and within context". I have collected vocal data on 12 different individuals (animals) in a &...
AN93's user avatar
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161 views

How to deal with overdispersion with glmmTMB for generalized linear models

I'll try to make it as brief as possible. I'm trying to fit a glm to echolocation clicks count data using the glmmTMB function. I started with a Poisson glm and ...
Carlos Benítez Collins's user avatar

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