All Questions
297 questions
0
votes
1
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559
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Interpretation of binomial GLMM with interaction fitted with glmer
I have a glmer model from the R package lme4 with a binomial distribution and I was wondering whether I am interpreting the ...
- 433
0
votes
0
answers
45
views
Converting LMM to GLMM
I've fit my model using lme (in nlme, R). However, this is not normally distributed. Taking the log of the outcome variable ...
- 1
1
vote
1
answer
690
views
GLMM with ex-Gaussian distribution function (trial-level reaction time data)
I am trying to use GLMM in R to fit a mixed-effects model (three categorical predictors, one continuous predictor) to trial-level reaction times from a group of participants.
The reaction time ...
- 11
0
votes
0
answers
49
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Questions about Random Effects in GLMMs
Someone reccomended me to use GLMM instead of GLM for the data I used for the manuscript.
My data corresponds to transects in which I have counts of individuals of a species in several points along ...
- 21
0
votes
0
answers
3k
views
P values from lmer with lmerTest - why REML= TRUE?
I would like to obtain p-values from my model fit with lmer()from the lme4 package.
It looks something like this:
...
- 433
1
vote
0
answers
177
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Doubts about the use of Cross-Validation in GLMM
I've recently ask in statckoverflow about some doubts with logistic regression fitted with a GLMM and an user recommend me asking in this forum. So, here it goes.
I work with a wild population of a ...
- 11
2
votes
0
answers
192
views
Round values to fit a negative binomial using GLMMs
I am using a GLMM to model a network metric that ranges from 0 to 100 (contribution to nestedness) and trying to fit a model with four predictors and two random factors (species and site). I have 591 ...
1
vote
0
answers
881
views
Gamma GLMER Error: PIRLS step-halvings failed to reduce deviance in pwrssUpdate
I am attempting to run a GLMER with a gamma function in R.
Here is my code:
...
0
votes
1
answer
2k
views
Why am I encountering Error: Response is Constant, when using performing a GLMM using glmer?
I am trying to determine what factors best predict/explain where deer fawns are being killed by predators based on the kill site's distance to clear-cuts (which I've grouped into three different age ...
- 1
1
vote
1
answer
2k
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glmer.nb does not converge when one variable is included in the model
I encountered an issue when using glmer.nb() to model my data. First I used fitdistr to tell me which distribution fits my data.
...
- 23
4
votes
2
answers
2k
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How to solve the error of singular fit in glmm in R
I am trying to fit a GLMM for binary data of whether colonies of bees perform mass flight or not. I have time when the mass flight was performed, temperature, location of the hive and species of the ...
- 41
1
vote
1
answer
73
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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 ...
- 111
7
votes
1
answer
6k
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Specifying model in glmer() - interaction terms
I am running a generalised mixed effects model, of family logistic regression, using function glmer().
I am predicting likelihood of response (0/1) and my fixed effects to explore in my final model ...
- 83
2
votes
2
answers
5k
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 ...
6
votes
2
answers
1k
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 ...
- 2,187
4
votes
1
answer
2k
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 ...
- 633
0
votes
0
answers
252
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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-...
- 61
4
votes
2
answers
1k
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 ...
- 53
1
vote
0
answers
214
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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 ...
- 232
0
votes
1
answer
93
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 ...
0
votes
0
answers
67
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(...
8
votes
1
answer
4k
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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 ...
- 293
2
votes
1
answer
441
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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 ...
- 21
3
votes
1
answer
299
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 ...
- 646
1
vote
0
answers
69
views
Possible imbalance in binomial GLMM - weighting?
I'm attemtping to fit a binomial glmm to my data. I've been using lme4 and I'm somewhat confused about interpretting the results. I think you'll be able to answer my question pretty quickly, so ...
- 11
1
vote
1
answer
344
views
Why are my confidence intervals much larger in glmmADMB than glmer.nb?
I'm plotting 3-way interaction terms from a negative binomial models, and tested the models in two packages to check my work and as a sensitivity analysis. I used the effect function to extract the ...
- 658
0
votes
1
answer
349
views
How to interpret a GLMM
I am new to stats and have run a GLMM in R using the lme4 package. The model includes marine litter collected in KG, with fixed variables of population (all), wind direction, wave strength. Random ...
- 11
3
votes
2
answers
2k
views
Regression Modelling of Linear, Exponential, and Power Curves in R [closed]
Please note this is cross-posted: https://stackoverflow.com/questions/57982488/regression-modelling-of-linear-exponential-and-power-curves-in-r
I am trying to model reaction time (and other) data ...
0
votes
1
answer
944
views
High GLMER dispersion parameters
I am running a glmer with a random effect for count data (x) and two categorical variables (y and ...
- 31
1
vote
1
answer
208
views
translate formula from glmer to glmmPQL [closed]
I want to translate this formula from glmer() (lme4 package) to glmmPQL() (MASS package).
...
- 23
3
votes
1
answer
546
views
Understanding ANOVA to compare Mixed Model with a GzLM
I'm having a hard time understanding how can I compare a GLM with a GLMM, knowing that I probably can't compare their AIC as glmer from lme4 probably computes the maximum likelihood differently from ...
- 55
7
votes
2
answers
395
views
Don't understand why glmm random effect variance is zero. Have reviewed similar questions still dont get it
I study a colonially-nesting bird species. I am trying to perform an AICc evaluation of GLMMs for a nest site selection study. I collected data at nest sites and paired random sites. I want to ...
- 83
4
votes
2
answers
13k
views
Model is nearly unidentifiable: very large eigenvalue
I'm fitting a generalized linear mixed model using glmer() and I'm getting a warning that I don't understand:
...
- 75
1
vote
1
answer
269
views
Diagnostic plot of glmm model
I am very new to R and I have a problem with the diagnostics of my models...can anyone help me please?
I have run my model:
...
5
votes
1
answer
2k
views
p-value random effect in glmer() in lme4 package
I know that in order to test whether a random effect has a significant impact on a model it's necessary to sequentially remove one random effect at a time and check each model pair with ...
- 81
0
votes
1
answer
124
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Generalized linear mixed models, extracting effects at all time points using summary, for each group./ [closed]
A bit of lenghty title, but summarizes my problem well enough. Currently I am part of longitudinal-data classes and one of my tasks consists of extract the treatment effects of all the time points for ...
- 11
0
votes
1
answer
275
views
glmm models - predictions and results presentation
I'm working with GLMM and a binomial distribution to find the best model for my biological data.
I'm currently writing my PhD and I have some trouble to present my results. I read and learn a lot ...
- 31
2
votes
1
answer
2k
views
Linear Mixed Effects Models for Truncated Normal Distribution
I would like to analyze amplitude differences of discrete oscillations that were detected in a time-series using a thresholding method between three different conditions. The number of discrete events ...
- 31
4
votes
0
answers
3k
views
R: lme4 vs. glmmTMB for binomial GLMM
I am fitting a GLMM to test if parasite prevalence in snails (positive snails divided by total snails) differs between different sites (site_type). Sites were ...
- 299
3
votes
1
answer
2k
views
Why do I get so different estimations with glm and glmer?
I am using the glmer function (lme4 package) to get estimations in a Poisson regression model (generalized linear model).
I ...
- 633
3
votes
1
answer
1k
views
An R package for GLMM estimation with two random effects?
I am looking for an R package to make an estimate on a general linear model with two random effects.
I was used to lme4 (function...
- 633
2
votes
1
answer
1k
views
General linear mixed model in R which will fit quasi family [closed]
I am trying to run a GLMM with a quasibinomial family (my data is 0 inflated and I have a negative min x value), but am receiving this error message as quasi families cannot be used in glmer:
...
- 21
7
votes
2
answers
10k
views
R: How to fit a GLMM in nlme
I want to compare lme4 and nlme packages for my data. But I'm confused by how to use syntax in nlme. I'm working with Mixed-Effects Models in S and S-Plus (Pinheiro, Bates 2000) and the current ...
- 416
3
votes
1
answer
991
views
Which random effects to include in this GLMM?
In my study growth of plants was measured in different years on different plots (all plants were measured in all years).
The question I'd like to answer with my model is: Which factors influence ...
user45065
6
votes
1
answer
4k
views
Covariance structures in glmmTMB for temporal autocorrelation
I'm running a zero-inflated, mixed-effects negative binomial model with the glmmTMB package in R.
My current format:
...
- 61
2
votes
1
answer
6k
views
Linear mixed effects model with time series
I have been reading through the different posts here on linear mixed effects models, but am still very unsure whether I have understood the task correctly, therefor I am reaching out for help by the ...
- 21
1
vote
1
answer
1k
views
Which family to use for GLMM with 3-level categorical response variable in R?
I'm building a model with a 3-level categorical response variable and both fixed and random effects to analyze data from a survey of volunteers. My response variable ('wellbeing', self-reported) has ...
4
votes
0
answers
207
views
Mixed-effects logistic regression
I'm new to data analysis and I'm trying to perform a mixed-effect logistic regression.
My data look like this:
...
7
votes
1
answer
3k
views
Calculating confidence intervals of marginal means in linear mixed models
I'm using different R packages (effects, ggeffects, emmeans, ...
- 103
1
vote
1
answer
858
views
Can you perform a likelihood ratio test on two linear mixed effects models with different optimizers in lme4?
I ran into an error with my full (but not simple/null) model, so I had to use a different optimizer to avoid the fitting problems. Can I still do an LRT test using those models?
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