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Questions tagged [random-effects]

238 questions
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How to compare GAMs that include random effects and factors?

I am trying to make a model comparison (say, for hypothesis testing) of two GAMs (mgcv package), where both models include random effects smooth term (s(bs="re")), and the second model additionally include a factor variable. So: gm0 <- gam(y ~…
Kamil Bartoń
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How can I incorporate a categorical variable with ~200 levels in a nonlinear mixed effects model in R?

I am trying to fit a nonlinear mixed effects model with a categorical variable genotype that has around 200 levels. So this is the linear version of the model. mlinear <- lmer(WUE ~ moisture * genotype + (1|pot), data = d8) Now I'm trying to make…
Jon
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How do I get the within-group association using lme4 in r?

Setup: I'm testing if the association between pairs of individuals for a trait (BMI) changes over time. I have repeated measures, where each individual in a pair gives BMI data at 7 points in time. Below is a simplified data frame in long format…
Tom
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Changing colour of data points according to random effect using plot_model

I want to plot the regression between a response variable and one of the explanatory variables in a mixed effects model while also showing the data points. For this I am using the function plot_model(). I would also like the data points to have…
Sarah
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Random Slope model Assumptions

What are the assumptions of a random slope model? In particular I am interested in knowing the assumptions about level-1 and level-2 residuals and what are their expected theoretical distributions. My model in R is this, OUTCOME ~…
Bra
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How do I include a random effect in PERMANOVA (vegan)?

Another newbie R question; I have a few models structured similarly to this; communitymatrix ~ variable1 + variable2 + (1|Random effect) I want to run a permanova analysis and have structured it like this; result <- adonis(communitymatrix ~…
meg
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Model convergence warning with negative binomial glmer

I've read several posts about having convergence issues with glmer and I have tried a couple recommended work arounds (changing optimizer, changing model iterations, etc.) but nothing seems to resolve my convergence issue. I was wondering if someone…
Danielle
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How to determine the correct mixed effects structure in a binomial GLMM (lme4)?

Could someone help me to determine the correct random variable structure in my binomial GLMM in lme4? I will first try to explain my data as best as I can. I have binomial data of seedlings that were eaten (1) or not eaten (0), together with data of…
Slimke
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Linear mixed effects models in R - mixed advice on random effects factors with less than 5 levels

I ran an experiment where I moved subjects arm about the elbow to a reference position, returned it to a home position and then asked them to try and replicate the position, all without vision of their arm. I then measured the error in their…
Nkitchen1
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How do I deal with random effects terms specified in formula?

This is my following script: library(lme4) library(RColorBrewer) # needed for some extra colors in one of the graphs library(lmerTest)# to get p-value estimations that are not part of the standard lme4…
Liat Shechter
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Does the "subset" command in MuMIn's dredge function work with random effects?

I have the following GLMM with a random slope that I'm conducting model averaging on using MuMIn "dredge" (I don't think my dataset is relevant so I'm just including the code here): sett_global2 <- glmmTMB(sett_dens~ depth_scale + sst_six_scale +…
Conrad
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How do I specify a random slope for a specific contrast in lme4?

With the following dataset... Subj <- rep(1:10, each = 10) Item <- rep(1:10, times = 10) IV1 <- rep(1:5, times = 20) DV <- rnorm(100) library(data.table) data <- as.data.table(cbind(Subj, Item, IV1, DV)) data$Subj <- as.factor(data$Subj) data$Item…
Dave
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Random slopes Cox Proportional Hazards

I have been trying to use coxme to extract random slopes for each of the covariates in my model. library (coxme) Start <- runif(5000, 1985, 2015) Stop <- Start + runif(5000, 2, 10) S <- data.frame ( X1 <- runif(5000, 5.0, 7.5), X2 <-…
AEM
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Getting fixed effect estimates but not pvalues with glmmLasso

Hi I am trying perform a variable selection using the lasso approach, but my model includes a random effect. I have run the model without the random effect using both the cv.glmnet and optL1 functions in glmnet and penalized (and got results);…
broch
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Estimating logsitic parameters and random effects with nlme

I have managed to fit logistic curves to fit growth models for 129 fish belonging to 3 groups. Unfortunately the parameters I got were not consistent and very often the models I tried have crashed. Therefore I've simulated a data set on which I've…
Max13
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