Questions tagged [mixed-model]

Mixed (aka multilevel or hierarchical) models are linear models that include both fixed effects and random effects. They are used to model longitudinal or nested data.

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Suggest ways to represent additive fixed effects?

The dataset I'm working with has additive fixed effect where each term is significant. I want to plot the model fit with one of the factors temp here on the x-axis ...
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Anova shows a main effect but not the t-test

I run an ANOVA which indicates that a variable is significant, but running a t-test on the same variable shows no significance. Is this a consistent result ? Here are more details of what I did: My ...
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Autoregression associated with two variables in mixed effects model

I have data in each well of a 12 (3x4) -well plate. The data $x_{ijk}$ is for $i$th experiment in $j$th row and $k$th column. I suppose that each well is the most correlated with adjacent wells. For ...
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glmer warning messages with count data mixed-effects model and how to proceed with model fit

I have fitted a GLMM with the function glmer of lme4 package. My data consists of a repeated measures count variable, which I am trying to explain with a continuous variable (week) and some ...
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Centering predictors in linear mixed effects and explaining three-way interactions with continuous variables [duplicate]

I am working on a Linear Mixed Effects model. All four predictors are continuous variables. Full model: ...
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Test for interaction effect when contrasting specific timepoints in mixed-model

I'm having a mixed model (lmer in R) with 5 repeated measurements (time is categorical), and 6 groups, and several covariates. I'm mainly interested in seeing whether there is a significant difference ...
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When will a cross-level interaction increase the slope variance?

Heck et al (2012) give the following model $Y_{ij} = \gamma_{00} + \gamma_{01}\text{ses_mean}_j + \gamma_{02}\text{pro4yrc}_j + \gamma_{03}\text{public}_j + \gamma_{10}\text{ses}_{ij} + u_{0j} + \...
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Change paired t test to LMM: while the content tested before and after treatment is different

I'm new to linear mixed model. I'm not sure how to use it if the contents of pre and post test are different. It's a within-participant design, including two sessions (with treatment and without ...
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question of a Poisson random effect model

Assume a Poisson random effect model (with a random intercept) $$\log E(Y_{it}|b_i,x_i)=\beta_0+\beta_1x_i+b_i$$ $$b_i \sim N(0,\tau^2)$$ How to derive the population-averaged effect of one unit ...
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is ok to use the same variable in two hierarchies?

I have a dataset with two levels: the city level and person level, at the city level i have the categorical variable "poverty level", in my research estimating the effect of the "...
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the simpler model does not converge and is singular

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boundary (singular) fit due to many time points per ID

I'm getting the warning boundary (singular) fit: see ?isSingular with this dataset ...
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Fixed effect model selection when some candidate models have singular fits

I have an experiment on the performance of a new animal management technology. The response is a proportion and I have three continuous input variables. There is one grouping factor of interest (...
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Combining Biological Replicates

I am doing an experiment where I track the behavior of larval zebrafish of 3 genotypes during a photomotor assay. Due to constraints with our tracking system, I can only run between 24-48 fish at a ...
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When/what to standardize for model-averaging with(out) interactions

I’m using the {MuMIn} package in R to select models (dredge, get top models, average etc). My question is about whether I need to, or should, standardise my ...
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lmer anova effect sizes

I would like to compute the marginal R squared for the whole factors from an anova table. This post shows how to get the effect size for each fixed effect based on the ...
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Reconciling differences in CI calculated between SAS and R on same dataset

I have been given a brief of replicating statistical analysis which was done previously to verify results. Data being collected are body weights of male and female mice over 20 weeks, given a ...
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Can a mixed model random slope include a between-subjects factor in a repeated measures design?

I'm after some statistics help with generalised linear mixed models. I have built a model using glmer from the lmerTest package in R to fit my data with a gamma distribution. The formula is as follows:...
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Scaling a single continuous variable

I have a basic question. I know you have to scale your variables (fixed effects) when you have several continuous fixed effects, to be able to compare them. However, if I only have one continuous ...
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Using a linear mixed model with only one observation per subject per condition

I'm running a LMER (in R) on some behavioural data where I have one observation per participant per condition. However, I'm unsure whether it is the appropriate analysis. The data is in the below ...
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Understanding interaction output for mixed model

Two group (healthy(1) and sick(2)) with RMSSD measurements at three timepoints (Base(1), Bet(2), First(3)). Question is whether the groups differ at each timepoint AND if they differ in their change ...
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should I model time series data with or without variable time?

Let's say I would like to see if two types of physical tests are related. scores1 and scores2 are continuous variables and were ...
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LME Quantifying differences between and within intervention groups

I am new to mixed-effects models and trying to ensure I understand them appropriately. I am analysing the results of a 2x2 cross-over intervention study. Essentially, I have 50 subjects who completed ...
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How to fit a Dirichlet mixed effect model in R?

I have a compositional data from an arena experiment in which the duration of an animal in specific zones was denoted. The time in the arena was fixed for all individuals which makes the durations ...
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what to do with a mixed model when ranef returns only zeros?

I've asked a similar question here in CV but because I'm still unsure what my options are I've rephrased the question slightly. I have a very simple model with no random slopes: ...
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Random effect with compound symmetric covariance structure in glmmTMB

I have a dataset of abundance of a kind of rodents(AA) in 63 sites, and want to know which environmental factors can explain the rodent abundance, and because the sampling sites are basically locate ...
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Treating time as a continuous variable when analyzing a stepped wedge design

I am in the process of analyzing a stepped wedge clinical trial, examining the effect of an intervention aiming to improve rates of outcomes data collection (e.g. depression scales, quality of life ...
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How to select predictor variables for linear mixed model?

I have a linear mixed model with ~30 clinical/treatment variables and repeated outcome variables for patients. E.g. The outcome variable is Breast symptom scores, which were collected at different ...
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How to address faulty randomization in RCBD design?

I have a client who wants me to analyze data from a randomized complete block design study. A large agricultural field was divided up into 16 plots and each row of plots was set up as a block ...
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Regression with 'stacked' data

I've occasionally seen people do something like the following. Let's say we have a survey battery with k questions, for instance an evaluation of red jelly beans, an evaluation of green jelly beans, ...
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Manual variable selection in GLMM

I'm modeling my data using GLMM with 1 random factor and 10 variables that are of interest. Instead of using automatic selection, I started with the full model (including all variables except for the ...
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Can adding a Level 2 predictor impact the Level 1 variance?

Heck et al (2013) p.137 write: [O]ne approach often used is to examine the change in residual variance that occurs by adding predictors within a sequence of models. The analyst begins with the ...
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Linear mixed effects modeling with MZ and DZ twin pairs

I have a question on how to deal with following experimental setup. I have data on microbiome and metabolomics for twins that are either MZ or DZ, and thus we have only pairs in the dataset. I ...
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Do the p-values produced by lmerTest::lmer need to be adjusted for multiple comparisons?

I am running a fairly simple linear mixed model with multiple observations per patient, comparing a lab value to a reference group (healthy control). Here's some fake data: ...
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linear mixed model intrinsic aliasing

A bunch of us are studying for an upcoming actuarial exam and none of us understands item II. doesn't result in intrinsic aliasing. We've calculated the V = ZDZ' +R_1 matrix and as far as we can tell, ...
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Investigating the existence of plasticity (random intercept model vs. random slope model) in a response variable that is not normally distributed

I wanted to explore if the change in speed between day and night is similar among a set of individuals. To me, the logic way of testing this hypothesis is running a random intercept model and a random ...
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Specifying a correct model using glmmTMB while experiencing unusually large coefficients and z-statistics

I have a data set of an beetle community where I want to analyse species richness (for example). The experimental design is as follows: 4 blocks 19 plots 2 different treatments 3 samples of the ...
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generate marginal residuals of a continuous variable by using linear mixed effect model

I was going to generate the marginal residuals of a variable by using linear mixed model in R. The marginal residuals are the residuals after adjusting for the fixed effects in the linear mixed model. ...
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random effects variance meaning

I am trying to better understand the output for a multi-level mixed effects model. Specifically, I am confused on how to interpret the random-effects parameters, and the random effects variance. Is ...
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Why do fixed effects in a logistic regression model differ depending on the presence of a random slope?

If I have two linear regression models, one with a random slope and one without (but otherwise identical), the fixed effects in the two models are identical. My understanding is that this stems from ...
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R: emmeans back-transformation when using a constant value in the response formula

I am fitting a linear mixed model ...
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Understanding the dependencies between random effect values in lmers

I have two related (basic) questions. Linear Mixed Effects models (as implemented for example with the lmer package in R) are hierarchical. I assume that this comes from the assumption that random ...
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Is it normal when including an interaction effect as a fixed effect in a mixed effect model the p-value of the main effect change drastically?

I conducted a randomized crossover study in which I had two within subject factors; condition and Time. When running a repeated measures ANOVA the analysis shows significant main effect of condition ...
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2 votes
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Random Effect in twin study of both MZ and DZ twin pairs

I am a bit stuck with the use of linear mixed models and its random effects in a twin study analysis. What I have is microbiome data for twins that are from MZ twin pairs and DZ twin pairs, so no ...
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Level 3 variance increase when adding a contextual predictor?

I am conducting a multilevel regression analysis on a survey dataset that has three levels: Individuals - Country-Years- Country. I am regressing a series of time varying and time invariant ...
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which model should be used for calculate the residuals of DV in twin data

I want to use the residuals of the dependent variables as new variables for analyses. these variables are continuous mammographic density measures from twin data. so which model should I use for ...
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why the p value changes when I run a linear mixed model instead of a simple regression? and how random effects affect the output?

I ran two models, a linear regression model and a linear mixed model, I did this because I was suspecting that there were some levels or hierarchy in my data, specifically in my subjects and ...
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How to reconcile model results?

I have a logistic regression in which I am evaluating animal selection for various categorical landcover types (woody, herbaceous, bare), canopy cover (continuous variable), and vegetation density (...
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How to deal with crossed and nested factors at the same time in a linear mixed model?

I've recently started analysing the data for a project using linear mixed models but am not sure how to deal with crossed and nested factors at the same time. In my study, each participant reported ...
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Linear Mixed Model - Pupils within classes

Educational researcher wants to examine if a new teaching system improves pupils achievements in the exam. He goes to a single school, and takes 3 classes of pupils as his sample. Each pupils gets an ...
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