Questions tagged [glmm]
Generalized Linear Mixed (effects) Models are typically used for modeling non-independent non-normal data (eg, longitudinal binary data).
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Is there a way to ask for “what changed between experiments”?
I have performed an experiment in which participants perform a task multiple times, the outcome being a binary "has succeeded or not".
Two cohorts have performed the same experiment in two conditions ...
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22 views
How to analyse temporal variation in R---vigilance of birds
I am currently doing a project for my Bachelor degree, for which I study vigilance in birds. Obviously, I have to analyse the data statistically. However, I do not know where to begin since I do not ...
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12 views
Specification of AR1 correlation structure for multilevel zero-inflated Poisson model with sparse outcome
I am trying to specify an AR1 correlation structure for a multilevel zero-inflated Poisson model using glmmTMB. A sample of the ...
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1answer
59 views
Estimating distribution parameter (lambda) from a poisson regression
I'm running a glmm model with a poisson $(Poi\sim (\lambda))$ family. Now I need the value of the $\lambda$ to make the PIT histogram. I know that $\lambda = \exp\{...
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11 views
Working with time data in GLMM in R
Over a period of two months, I have data for the time when honeybee colonies performed a mass-flight. At every hour interval, I have data for other environmental parameters like temp, hum etc. So ...
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1answer
21 views
How to treat a multi-level continuous variable?
I'm not sure what type of covariate I'm dealing with and how to treat it in a glmm.
I have many 1600-ha blocks. Within each block, I'm interested in the variable Burn Severity. There are 4 possible ...
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1answer
53 views
Is it possible to extract an equation from GLM or GLMM
Is it possible to extract an equation from a GLM or GLMM and is there any less technical information about this available? For an example of the question see code below (definitely not perfect, but it ...
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38 views
Fixed plus random effects and correction for serial correlation in GLMM with Gamma distribution
I have some problems and lack of knowledge (I find it quite complex) with constructing and plotting GLMMs. Therefore, I am sorry If the explanation is not as sufficient as it should be, and want to ...
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1answer
33 views
Non-independence in data and GLMMs
I am working with a dataset that consists of categorical variables and count data. My response variable is DPM SpeciesA (detection positive minutes of Species A, where for each hour I have a count of ...
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1answer
21 views
How to intepret coefficients for interaction of factor variables?
Is there a trick to interpreting the coefficients for a two-way interaction of factor variables? Both variables in the model have 3+ levels making this more complex than a simple binary explanation. ...
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1answer
38 views
Power Analysis for glmer using simr
I'm trying to run a power analysis based on pilot study. I'm using a glmer mixed effects model with a binomial logit link. The model's equation is:
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35 views
GLMM Likelihood ratio test in ASREML-R
I have set up a series of GLMMs to test the significance of two random effects: sire and sire/dam (dam nested within sire). In these models, my response variable is sex. Sex is specified as a binary ...
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1answer
43 views
problems with transforming proportion data in GLMM model
I'm comparing the effects of a single treatment on multiple response variables from a BACI study.
Most of my data are normally distributed, but I also have some proportion data (binomial) and count ...
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1answer
33 views
p-values near 1.000 for all tests in a glm() (count and binary data, Poisson and binomial distributions)
I want to run multiple GLM's to answer a few questions about changes in diet between species and over time.
Questions:
Does frequency of occurrence (FO) of pieces eaten differ between species or ...
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17 views
Interpretation of average marginal effect for continuous variable in GLMM
I am trying to get a correct interpretation for the average marginal effect (AME) of a continuous variable in a logistic mixed effects model.
I know similar questions have been asked and answered (...
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1answer
62 views
Does poisson penalized quasi likelihood regression use biased estimators?
A professor told me the Poisson glmmPQL (mixed-effects/hierarchical) regression gives biased estimates.
The paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3886992/ from PLOS One says that ...
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2answers
61 views
Singular fit with simplest random structure in glmer (lme4)?
I am trying to run mixed models (logistic regression) on a dataframe with the glmer function from lme4 but I always receive this message: "boundary (singular) fit: see ?isSingular"
Even if I create a ...
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2answers
84 views
Confused about meaning of subject-specific coefficients in a binomial generalised mixed-effects model
In A Comparison of Cluster-Specific and Population-Averaged Approaches for Analyzing Correlated Binary Data, Neuhas, Kalbfleisch, and Hauck state:
"With the cluster-specific approach, the probability ...
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1answer
54 views
GLMM with presence/absence dataset
I want to know if a treatment effectively reduces the abundance of a particular species in some location. For that, I trapped the animals and identified each individual captured, releasing the animals ...
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1answer
50 views
Advice for R packages for GLMM and (adaptive) Gauss Hermite quadrature [closed]
I was looking here for a R package to make an estimate on a general linear mixed effects model (Poisson family) with two random effects and (adaptive) Gaussian quadrature. I also need the full matrix ...
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1answer
26 views
GLMM in seed germination study
I have an experimental design measuring germination of a single species of tree under different treatments. The treatments include; cattle grazing and no cattle grazing and rodents and no rodents. The ...
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48 views
Binomial Logistic-Normal Updating
I've been considering how sports with binary outcomes might be modelled e.g. the probability of a tennis player winning a point on serve.
In text books the usual Bayesian approach uses the beta-...
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24 views
Can I use a residual variable (from a binary variable) as response variable in binomial glmm or glm?
I'm working on Rstudio and I have a question about residues in a binomial glm's case.
I used a glm to correct my response variable (germination (ger_b), encode 0, 1) by the light, because this ...
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2answers
145 views
Mixed-effect logistic regression with very large dataset
I am conducting linguistic research to determine whether a property of the subject (animacy) of a sentence has its effect on whether a particular kind of preposition phrase will be mentioned. I ...
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43 views
Model summary tables for GLMMtmb [closed]
What package do people use to nicely visualize glmm model summaries? I tried huxtable::huxreg as explained here, but the documentation must be out of date because huxreg does not accept glmmTMB ...
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1answer
32 views
Mean-center continuous predictors for GLMMs?
I have a dataset with a non-negative, right-skewed response variable and at least one non-negative, right-skewed predictor. Given the non-Gaussian, non-negative distribution of the predictor variable, ...
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1answer
64 views
Binomial GLMM (GLMER) with proportions in unbalanced, observational panel data: nesting issues and errors
Thanks in advance.
I am new to mixed models and having several doubts about a mixed model (lme4's glmer, binomial) with multiple levels, measuring a proportion [0,1] in three time periods.
My data ...
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31 views
Why these three models suggest such a great difference on the significance
Does someone could tell me why these three models suggest such a great difference on the significance of factors? And which one is much reasonable?
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2answers
45 views
Use Poisson or Linear Regression for Longitudinal Data?
I want to fit a regression with repeated measurements
Outcome：number of cigarettes smoked in the jth month (j=1,2,3)
The outcome variable DOES NOT follow a normal distribution. The outcome values ...
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53 views
How can I calculate Nagelkerke pseudo r2 with glmmkin object from GMMAT package in R?
I have used glmmkin function from GMMAT package to fit a logistic mixed model with the binary phenotype 'disease', one fixed variable 'PRS' and one kinship matrix 'GRM' to model the covariance ...
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46 views
How to solve autocorrelation and convergence warning in GLMM (lme4)
I’m trying to use linear mixed model (random intercept and slope) to investigate if these factors have an effect on response variable (BL in the model) over years? ...
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73 views
Approximating standardized effect-size measures, Cohen's d from glmer model
I'd like to compute the Cohen's d, of glmer model's fixed effects.
These are the steps I'm following:
Building a model
...
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1answer
21 views
Is a GLM the best option to analyze my data with R?
I would like to see which factors can better explain the success of a particular event to happen. I'm interested in 4 factors, being before, ...
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1answer
200 views
How are PQL, REML, ML, Laplace, Gauss-Hermite related to each other?
While learning about the Generalized Linear Mixed Models, I often see the above terms. Sometimes it seems to me these are separate methods of estimation of (fixed? random? both?) effects, but when I ...
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1answer
35 views
Explain the estimated residual variance in a Gamma mixed model, using glmer()
I am applying a generalized mix model, where the response has a gamma distribution, as below:
...
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22 views
Accounting for `Year` effect in glmer model predictions and model testing
I have built a series of glmm's to explore how habitat characteristics impact the abundance of the organism I study. I've trained these models on data from a given set of time (2 year span) and would ...
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25 views
How are factor level coefficient estimates combined for total Wald chi-squared?
I have been working with mixed-effects models, with both continuous and categorical variables. I am interested in the combined effect of categorical variables with > 2 levels. I ran type II ANOVA on ...
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1answer
38 views
Using the DHARMa package to test for temporal autocorrelation when time values are not unique?
I have fit a glmm using the glmer function from the lme4 package. I have found the DHARMa package very helpful for evaluating the fit of my model but am stuck as to what to do to evaluate temporal ...
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1answer
21 views
How to interpret intercept (and coefficients) in a GLMM with gaussian family and log link?
I am working with some bounded continuous data (between 1 and 10), which I think means I should be using a log link for my GLMM. In my reading for interpretation, it look like putting the effects (...
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26 views
I have performed three likelihood ratio tests on a factor in R. Do i need to adjust the p values?
I am a student doing a thesis for zoology. I am looking at how factors like season (winter/summer), fencing (inside fence/outside fence), and the interaction between season and fencing affects ...
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22 views
Gamma GLMM Dispersion, Random Effects, and CoV (lme4)
So I know that in glm(), with the Gamma family, one can get the dispersion parameter through the MASS package with gamma.dispersion() or can even look at the summary output as a quick estimate.
How ...
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1answer
18 views
Could this variable be modeled by a poisson regression?
I have a pc experiment and an ordered response variable with 8 levels (from 0 to 7). I have also a factor (different types of stimuli) to include as a predictor in the model. So in each trial, the ...
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27 views
Unusual residual artefacts in GLMM, is GAM or another model more appropriate?
I'm having trouble finding an appropriate model for my data. The data comprises behavioural observations of chimpanzees, where I instantaneously sampled their locomotor behaviours and parameters of ...
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40 views
Generalized linear (logit) mixed-effects model with the random (crossed) effects drawn from a bivariate normal distribution
I am trying to implement a generalized mixed-effects model specified as:
Dependent variable $y = \log(\frac{p}{1 - p})$ where $p$ is a quantity measured for a pair of individuals ($i$ and $j$).
$E(...
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0answers
109 views
How does random variable nesting in GAMs work (mgcv)?
Consider me very new to the world of GAMs, I am actually using it out of necessity rather than by choice but I thought it could be a chance to learn something new anyway.
Originally I had hoped to ...
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1answer
41 views
Generalised Logistic Regression with mixed effects - Binomial model creation / selection
I have a dataset with 72 individuals from 5 separate groups, with repeated measures - each individual was sampled 4 times. All data is binomial, and in most cases there are more 0s than 1s.
I have a ...
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1answer
23 views
Should modeled means in glmm be averaged on link or response scale?
I'm using emmeans to estimate means of 4 treatment levels. The response is a count with poisson distribution. The design is randomized complete block with 14 blocks, each with single replicate of all ...
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10 views
Probability theory for longitudinal data (book recommendations)
I am self-studying probability alongside my epidemiology degree to improve my understanding of statistics. So far, I have picked up Blitzstein & Wang (2019) Introduction to Probability, 2nd ed. ...
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1answer
27 views
How to interpret model results for Yes/No dependent variable
I have run a model for a data set that looks like the following:
...
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1answer
79 views
GLMM for continuous response in $[0, 1]$
I am looking into GLMMs because my linear model residuals' plot has a weird pattern (some residuals form a diagonal pattern), and a lack of normality was also confirmed with a Shapiro test. ...
