Questions tagged [glmmtmb]

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

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Problems with uniformity in residuals using DHARMA to check zero-inflated count glmm

very new to statistical modelling & have found lots of the existing questions and answers from this community hugely helpful. I'm running into some issues of my own now that I can't find answers ...
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27 views

Temporal autoregression in glmmTMB: what do alternative syntax forms mean?

The argument ar1() in glmmTMB accepts two different forms of syntax (that I know of, there might be others): ...
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Does pairwise correlation and multicollinearity matter in dispersion and zeroinflation model of glmmTMB?

I'm using glmmTMB to calculate beta-binomial GLMMs with nested and crossed random intercepts. I have overdispersed, zero-inflated data (assessed with Dharma). I use continuous terms in the very ...
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29 views

Varying dispersion parameter (=dispformula) in glmmTMB in R to account for heteroscedasticity that originates from one predictor

I struggle with understanding the dispersion model and dispersion parameter of glmmTMB , and could not find answers anywhere. I constructed a GLMM using ...
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Infinite upper and lower CL after fitting the model (glmmtmb)

I am new in GLMM. In my dataset, There are 2 islands, 2 sites were selected (nonrandom) per each island, 6 transects randomly were located on each site, then the number of corals was counted in three ...
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45 views

Generalized Mixed Model with repeated measurements

I’ve have been working with a mixed model (glmmTMB) to analyse the abundance of snails in dependency of several categorical predictors. The data was measured twice in the same sample sites in two ...
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41 views

Validation, Interpretation and Post-hoc testing with a zero-truncated GLMM (using glmmTMB, DHARMa and emmeans)

I tried to go as far on my own as I could. But after 6 months of searching and reading, I'm still unsure if everything I did is statistically sound. Unfortunately, I neither have a statistican nor ...
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building a good (mixed) linear model for agri-ecology data [duplicate]

I encountered an problem. I cannot build a good mixed linear model. For example, ...
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16 views

Can glmmTMB be used without a random effect?

I'm curious whether glmmTMB can be used without a random effect. Both glmer, lmer, and ...
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39 views

How to handle exces zero's in a continuous (multilevel) outcome: two-part model or Tweedie distribution?

I am trying to fit a hierarchical model on a continuous outcome that has excess zero's. This is what my data looks like: The formula for both the main part as well a possible zero-part of the model ...
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21 views

Including dispersion parameter in prediction

I have already posted this question on r-sig-mixed-models mailing list but I received no response. I am fitting a ziGamma model using glmmTMB to predict the ...
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16 views

R: repeated subsampling for unbalanced design with zero-inflated count data using glmmtmb

I have count data with the number of individuals per observation of 64 different plant species. 3 - 5 observations were made of each plant species, and the number of arthropods on the plants were ...
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What is the most appropriate regression model to use to predict an outcome variable which is continuous but bound between 0 and 1?

I have a panel dataset of patients visiting the hospital multiple times and their health index (measured by variables SFPCS and SFMCS) is measured at each visit. Each patient may have different visit ...
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36 views

When to use Kenward-Roger, not standard glmmTMB

Please consider the following: ...
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23 views

How to evaluate overfitting in GLMMs usnig R

I am using glmmTMB in r to model count data. I use poison and negative binomial error distributions. If I add one more predictor to my models I end up having convergence problems. I would like to ...
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20 views

Do multiple model-fitting tests qualify as multiple comparisons?

My question: do I need to be concerned with multiple comparisons when fitting models to different (but related) sets of count data? My question expanded: I have a series of plots where we collected ...
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18 views

Combine multiple glmmTMB model objects

My question is quite similar to the one posted here, but I'm looking for further clarification. I have two identical glmmTMB model objects that were run using two different subsets of my full dataset. ...
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37 views

Handling 0s in a generalized linear model---climate data

I am using a generalized linear mixed model for analyzing climate data and incidence of a disease variable. The data follows a gamma distribution. But I am getting the following error when I am ...
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29 views

Which type to specify in ggpredict for GLMM with zero inflation and dispersion factor

Just wondering if I am using ggpredict to predict values for my response variable using the example model below, should I be using type="fe" or type="fe.zi"? And would this be the ...
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29 views

glmmTMB: random intercepts vs. spatial random field

I'm working on a modified example from a glmmTMB vignette (found here) using spatial covariance structures. I'm trying to show the difference between "standard&...
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54 views

Interpret the output of a Tweedie GLMM

I've fit the following glmm using the glmmTMB package with the tweedie(link = "log") distribution, where ...
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21 views

What would be a good next step in this GLMM analysis?

So I've got some count data over time looking at different treatment groups: My goal with this data is significance testing. I would like to show which treatments are effective in reducing counts, ...
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14 views

How to write up the results of a zero-inflation poisson model?

I am currently running a series of zero-inflation poisson mixed effects models using the glmmTMB function of the package of the same name and was curious about how you would write up the results of ...
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21 views

How to interpret the interaction of a zero-inflation model (logistic regression)

I have run a zero-inflation negative binomial mixed effects model looking at the effect of the amount of and direction of change in a particular environmental parameter (e.g. temperature) on the no of ...
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85 views

How to report and quantify the random effect in a logistic model? glmmTMB

I'm fitting a logistic regression model with mixed effects using the package glmmTMB. (Because the dataset is very large and lme4 produces out of memory errors). And I need help to interpret and ...
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105 views

Error in glmmTMB when fitting mixed model with interactions between two categorical variables

my mixed models contain several categorical variables with a lot of unique levels, so model matrix for fixed effects is ​​very sparse. I use glmmTMB package that ...
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40 views

random effect with one observation per group improves AIC drastically — explain

Now that I've posted an example (for a different purpose) at How will random effects with only 1 observation affect a generalized linear mixed model? (resulting in creating an account here, and being ...
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78 views

Selecting between a zero-inflated binomial, OLRE and beta-binomial model

I need some help in deciding which of the following models fits best the data that I have. This was a survey where participants reported proportions of successes (defined as n/m) in condition A and B. ...
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171 views

How should I deal with spatial autocorrelation in beta GLMM (glmmTMB)? (Bird diversity)

I am trying to compare certain a taxonomic diversity index (for bird communities) calculated for squares in a map grid system (a total of 34 squares) for two different years: 1998 and 2018. My ...
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18 views

Why does uncorrelated random slope and intercept not convergence, but correlated random slope and intercept does converge?

In contrast to what I expected, I am able to fit a model with a correlated random intercept and slope, but not the same model with an uncorrelated random intercept and slope term. I was under the ...
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187 views

Bootstrap confidence interval with mvrnorm - upper value equal to Inf

I am trying to predict a value and CI for two different treatments from a glmmTMB fitted model using posterior predictive simulations (mvrnorm function in the MASS package) as in the Salamander ...
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16 views

glmmTMB Kronecker direct product for crossed random effects

I am trying to replicate a model fit using SAS's Kronecker direct product covariance structure UN@AR(1) in glmmTMB. The model specification that I have currently is pretty close to SAS but something ...
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1answer
88 views

Significant dispersion test

I used DHARMa for my residual diagnostics. For two models, the dispersion test is significant even though the rest of the diagnostic output looks good. I am wondering if both my models are correct ...
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1answer
216 views

How does emmeans calculate degrees of freedom for glmmTMB?

I have a model that I'd really love to use glmmTMB for (beta distribution, mixed model, heterogeneous variance that the dispersion equation can help with). I found ...
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1answer
84 views

GLMM for unbalanced design, nested random factor or fixed factor?

The Goal Determine if the abundance of ectos differ between sites. The set up The data is percent abundance of ectomycorrhizal fungi from soil samples. There are ten soil samples per plot and there ...
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42 views

Plot correlation between random intercept and slope glmmTMB?

I am after some advice regarding how to plot the correlation between a random intercept and slope from a mixed model in glmmTBM? Below is a reproducible example. <...
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79 views

P value adjustment for pairwise comparisons of negative binomial

Question 1) Am I appropriately doing the pairwise comparisons? Question 2) Why is the Sidak method used for the emmeans? Should I instead use adjust = "none" for these? Context: I have a ...
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1answer
199 views

Mixed model with random slope but no random intercept?

I have two questions: Is it ok/when might it be ok to specify a mixed model with a random slope but no random intercept? How would one specify such a model in lme4/glmmTMB? I am working on a dateset ...
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1answer
69 views

Test for equality between two regression coefficients with an interaction term

I’d like to test for equality between two regression coefficients, one of which is an interaction term. I’ve been referencing Andrew P. Wheelers statistics blog: https://andrewpwheeler.com/2016/10/19/...
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135 views

Interpreting a zero-inflation negative binomial model

I am currently running a series of zero-inflated negative binomial models on the impact of the magnitude and direction of change in various weather parameters on a number of insect behaviours (...
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12 views

getting same AIC (or any other comparison criterion values) even after using different var-cov structures when comparing GLMM models

We are comparing models that are GLMM , in which for each one of them the fixed effects are exactly the same, but in the random effects portion, we used different variance-covariance structures (i.e ...
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83 views

Error in a zero-inflated negative binomial model?

Following DHARMa diagnostic tests revealing zero-inflation (ratioObsSim = 32.663, p < 2.2e-16) and over-dispersion ...
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55 views

Equation for a glmmTMB model with exponential spatial covariance structure

I have read description of the Spatial covariance structure with glmmTMB on this link (https://cran.r-project.org/web/packages/glmmTMB/vignettes/covstruct.html), ...
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1answer
105 views

GLMM comparison: likelihood ratio test result is in consistent with the conditional R square result

I am conducting a GLMM with a random slope effect and would like to know if this random slope effect is significant or no. To do this, i did two things, First, compare the full model with the random ...
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1answer
66 views

How can I calculate standardized weighted residuals 2 for a beta family glmm in R?

Hello and thank you for your time! I’m trying to calculate the "sweighted2" residuals for a beta family glmm with varying dispersion (aka precision parameter aka phi) fit using glmmTMB in R. ...
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1answer
213 views

glmmTMB: AR1 models fail to converge

I am trying to utilize the first-order autocorrelation [AR(1)] covariance structure abilities of the glmmTMB package (described here by Kasper Kristensen) to model experimental time series data ...
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44 views

Why do I not get confidence intervals for interactions using confint with glmmTMB (nbinom2) and REML=TRUE

I run a model where I test the effects of different parameters on the number of individuals (no_ind) in a field experiment. I would like to report the confidence intervals and use confint() which ...
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169 views

What is the best method to determine significance in a zero-inflated poisson model?

I am currently trying to run a zero inflated mixed effects model in R using the package glmmTMB following a significant test of zero-inflation (using the function testZeroInflation() in the package ...
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1answer
505 views

GLMM hurdle model for continuous data -Truncated negative binomial family in glmmTMB?

I am running a hurdle model using the glmmTMB function. My dependent variable is continuous and >= 0. I was looking for a function that would allow me to model the binary response in a logistic ...
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1answer
154 views

leverage() diagnostic test not supported for glmmTMB models in r

I am using a glmmTMB to look at the effect of numerous variables on how far individuals travel (distance). The example below is ...