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Questions tagged [random-effects]

238 questions
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individual random effects model with standard errors clustered on a different variable in R (R-project)

I'm currently working on some data from an experiment. Thus, I have data about some individuals who are randomly assigned to 2 different treatments. For each treatment, we ran three sessions. In each session, participants were asked to make a…
sciacallojo
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Survey Weighted Random Effects Logit Model in R

I am trying to predict a binary outcome with a model that includes a random effect using survey data. I've included a description of the sampling design below, so feel free to comment on my survey weighting approach. My primary question is how to…
mike
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"iteration limit reached" in lme4 GLMM - what does it mean?

I constructed several glmer.nb models with different combinations of random intercepts, and for one of the models (nested random intercepts, with the lowest AICc), I consistently get: "iteration limit reached", without the usual "Warning message: In…
kdarras
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How to reproduce average marginal effects from xtlogit model

I am interested in reproducing average marginal effects from a random effects logit model (run in Stata using xtlogit). I understand how to reproduce the average marginal effects from a logit model using the Delta method. For instance, in the code…
Eunice
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How to interpret Random Effects Plot from mgcv

I have a few questions regarding using a random effect in a GAM. First, how do you interpret and communicate the output graph? I have fire modeled as a random effect in this GAM because it is largely a random occurrence at my different field sites…
Alex Cooper
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How to predict gam model with random effect in R?

I am working on predicting gam model with random effect to produce 3D surface plot by plot_ly. Here is my code; x <- runif(100) y <- runif(100) z <- x^2 + y + rnorm(100) r <- rep(1,times=100) # random effect r[51:100] <- 2 # replace 1 into 2, making…
imtaiky
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How to add random and/or fixed effects into cloglog regression in R

Update question on treatment of one variable for fixed effects I am planning to run a cloglog regression in R with random and/or fixed effects to check for unobserved heterogeneity. Now i have not found anything on how to do this in R only one…
Amy
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prediction for lmer-model with nested random effects

I am currently trying to help a colleague and I simply cannot find a solution. So I am hoping that someone else might be able to help us. I have a dataset containing weight data assessed with different study designs, for different species in…
I Ho
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Fixing random slopes and random intercepts values in lme4

I'm currently trying to calculate the effect size (Cohen's f^2) of a given effect but need to run a null and partial model with the random effects pre-specified in order to do so (according to Selya et al., 2012 for dealing with continuous…
Brianna Brotherton
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Specifying level-3 random intercept in R

I am using the lmer() function (lme4 package) in R for analysing a longitudinal study in which I measured 120 subjects, 6 times. In first instance, I specified a model like this: library(lme4) model1 = lmer(DV ~ 1 + X1*X2 + (1+X1|SubjectID),…
Stef
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R2WinBugs data entry incompatible copy error for Conditional Binomial likelihood, probit link, Random Effects (Psoriasis example)

I was working on the the guide for calculating the effect size of different treatments using a NETWORK META-ANALYSIS as done in example 6.a. Here It works fine in winBugs, but I want to do the analysis in R using R2winugs so that I can automate the…
Lionel Duarte
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Standard Error of Variance Component from the output of GLMMadaptive::mixed_model

I am using the {GLMMadaptive} package to fit a mixed effect random slope model. And I need to extract the standard error of variance components from the output of GLMMadaptive::mixed_model(). And from the package documentation, it seems that I can…
shafee
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Model predictions for a nested random effects model in R?

I am trying to fit a mixed model with random effects: lmer model to the dataset df based on this example here. However, I run into an error that says invalid "times" argument. Any suggestions on how to fix it. set.seed(123) df <- data.frame(x.axis =…
RPlotter
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mgcv random effects - extracting estimates and plots

I am using mgcv to fit GAMs with random effects, e.g.: gam_fit <- gam(y ~ s(age) + s(region, bs='re'), data = my_data, method = 'REML') See Gavin Simpson's excellent post about using random effects in GAMs with…
Shira
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glmmTMB predictions error concerning random effect

I am trying to create a raster with predictions for a model, using glmmTMB. This is based on a model, and a rasterstack. I converted the rasterstack to a data frame, as I think this is a requirement for the function predict.glmmTMB to run. The…
Beardedant
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