lmer (& siblings glmer & nlmer) are functions in the R package lme4 that fit mixed effects models (ie, models that include fixed & random effects). These models can be non-linear in the sense that the dependent variable is transformed by a non-linear function (eg, logistic or log) to accommodate ...

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Specifying Cross-Level Interactions in LMER

Please note: this post was previously posted on http://stackoverflow.com/q/26433718/4155221 and I have re-posted it here based on a suggestion in one of the comments. I am trying to figure out if ...
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9 views

Specifying Cross-Level Interactions in LMER [duplicate]

I am trying to figure out if it's okay to specify cross-level interactions in a hierarchical model with fixed effect predictor variables at both levels using the lmer function, and, if so, how to do ...
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26 views

lmer4, p-values, confidence intervals and bootstrapping

I have a mixed linear model made with lmer in R and find that my qq-plot looks rather much like the symbol of a famous superhero. My x-parameters are all factors but I have tried all transformations I ...
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22 views

Correlations of fixed effects in logit mixed model with a nested fixed effect

I am using lme4 in R to fit a logistic mixed effects model of psycholinguistic data with three categorial (binary) fixed effects and two crossed random factors (subjects; items). The critical ...
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20 views

use many lms or random effects (lmer) to estimate a bunch of slopes?

I have what is probably a very simple question, but I just need someone to verify my thinking. I have a dataset that consists of a variable (var1) measured at 3 time points for about 80 people. At ...
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42 views

F stats for post hoc test of a linear mixed effects model

I have an unbalanced linear mixed effects model with three fixed factors of various levels and one random factor for my repeated measures data (for details see here). Thanks to your help I managed to ...
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1answer
86 views

Summarizing and plotting several combined relationships with LMER

I want to see if there is a significant relationship between predictor and value. I've measured these two variables in 6 different conditions (not a full 3 x 3 design because feature1 and feature2 ...
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47 views

In which order should factors be removed when performing model simplification (lmer)?

I am a bachelor student in biology and for a project work, I have a model with a design like this (A, B & C are fixed factors, D is random and nested in C): ...
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47 views

lmer - interpreting fixed effects correlation matrix

I fitted four mixed linear models for 4 DVs, and 5 IVs in each of these models as fixed effects (there is a random effect as well). These 5 IVs are "time" (weeks from 1-12, 12 levels), and 4 measures ...
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30 views

Fitting a partially clustered/nested design using lmer

I have a study where clustering occurs in one condition but not the other. In the treatment group I have repeated measurements on individuals who are nested within families. And in the control ...
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1answer
58 views

What is the lme4::lmer equivalent of a three-way repeated measures ANOVA?

My question is based on this response which showed which lme4::lmer model corresponds to a two-way repeated measures ANOVA: ...
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202 views

How trustworthy are the confidence intervals for lmer objects through effects package?

Effects package provides a very fast and convenient way for plotting linear mixed effect model results obtained through lme4 ...
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32 views

lmer with multiply imputed data

How can I get pooled random effects for lmer after multiple imputation? I am using mice to multiple impute a dataframe. And lme4 for a mixed model with random intercept and random slope. Pooling lmer ...
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8 views

How to not only compute predicted values but also standard errors [migrated]

I am trying to generate standard errors for predicted values. I do manage to generate the predicted values, however, do not get the standard errors. Instead, I consistently get the following error ...
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36 views

Mixed and random effect model with multiple crossed random effects in lme4 vs nlme

I am trying to fit a few models as follows for my data of observations recorded from $p$ genotypes planted in $n$ locations for $m$ years. The aim is to estimate BLUPs finally. $$Y_{ijk} = \mu + G_i ...
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1answer
28 views

Correct specification of HLM in lmer

I originally learned about random effects models when taking a course on Hierarchical Linear Models, which was taught using Raudenbush and Bryk's HLM book and software, and it sort of indoctrinated me ...
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34 views

Intraclass Correlation Coefficient in mixed model with random slopes

I have the following model m_plot fitted with lme4::lmer with crossed random effects for participants (...
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35 views

Cross-classified HLM (random effects) with lmer in R

I need to run a cross-classified (partially nested / partially crossed) HLM in R using lmer. I haven't found many (any?) clear discussions on how to model this and how to set up the data (besides the ...
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48 views

Using a mixed effects regression model for between-subject design?

I have data from a between-subject experiment, where every subject was assigned to one of the two conditions, and completed varying number of trials (as much as they wanted). Number of trials is ...
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40 views

Mixed model with lmer: Variance of residuals should give the same as level 1 variance?

I expected that the variance of residuals from a mixed model computed by, for example, lmer should give the same as the residual variance from the summary output. ...
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58 views

Multiple correlated random non-nested intercepts in R

I am trying to estimate a longitudinal model in R in which there are several random intercepts that are correlated with each other, and the data are non-nested. For example, consider a simple ...
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1answer
51 views

What is the null model for a likelihood ratio test of a within-subjects factor?

Tissue samples were taken from 4 differention locations and repeatedly measured. This was done identically for 3 animals. The research question was: Are there differences in measurement between the ...
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14 views

lsmeans: how to have mean and SD from pairwise comparison? [duplicate]

In my previous question, I asked about effect size, but this question is about mean and SD from pairwise comparison generated by lsmeans. I am doing LMM starting from model comparisons. Then after ...
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Can I combine two pairwise comparisons?

I am using LMM in lmer. To find the most optimal model, I compare models of three-level with two level using ANOVA function. If it turns out that no significant difference between these two, then I ...
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1answer
58 views

Random effect significance in linear mixed model

I have performed LRT: ...
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188 views

Mixed effect linear regression model output interpretation

I just fitted the following linear mixed effects model: ...
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60 views

Specifying variable levels in multilevel repeated measures in R using lme4

I am trying to analyze a dataset in which there are three measures on patients within areal units, however I am having trouble in how I am thinking about random/fixed effects and including covariates ...
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99 views

I am confused with ranef function in R

Do the ranef and fixef functions in lmer give the random and fixed effect coefficients? If ...
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74 views

Specifying a linear mixed model in lmer with replications nested within a fully crossed design

I’m trying to specify a linear mixed model for a somewhat complicated, nested & crossed method comparison study with replicated measurements. The goal is to partition and compare variances. It’s ...
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91 views

Number of observations in groups - linear mixed effects model

I would like to fit linear mixed effects model to my dataset, but I was wondering if quantity of observations in groups matter? I have some groups with about 60 observations in each, but there are ...
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43 views

Multiple covariates for each fixed effect

I'm analyzing data from a classical intervention design. Subjects were divided into groups, undertaking different interventions. Each subject was measured using the same tests before and after the ...
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1answer
101 views

mixed effects model output

Let's say we have this: ...
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1answer
98 views

Mixed Model Analysis of Experiment Data using lmer() Function (lme4 package in R) where Levels in Stimulus Grouping Factor equal Observations

I am running a post-hoc analysis on the data collected during an experiment in which 15 unique stimuli were presented to participants. Having run a least squares regression using the lm() function in ...
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37 views

Predict random effects in a multilevel model with Empirical Bayes

In multilevel models, it is possible to predict (not estimate) the random effects by Empirical Bayes after the model parameters have been estimated. I know how to use the ...
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1answer
49 views

Why do my ANOVA tables keep returning $\chi^{2}$ values of 1?

I'm using ANOVA to test for differences between different values of the same factor for a mixed effects model which I produced. My model is: ...
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25 views

Assessing the effect of related variables using lmer in R

I am trying to run a model to describe the rate of water table drawdown in the soil. The predicted variable is rate, and I am interested in the effect of two categorical variables: (1) if the water ...
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1answer
150 views

Mixed effects modelling; what to do when model is over-specified?

I'm trying to use mixed-effects modelling to analyse some data. There are a number of variables that I need to specify within the model, two of which are between-participants (...
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38 views

Interpretation and visualization of lmer output

I am trying to correctly interpret the output of my lmer-model and I also want to visualize an interaction contained in the model based on the intercept values. My variables and levels are Training ...
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1answer
227 views

difference in results of mixed effects model in nlme and lme4 package

Can anyone please tell me why the results of random slope model is different for the same dataset when I use lme and lmer. I first fitted a random intercept model as follows using both lme as well ...
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56 views

collinearity in linear mixed effects model

I have one dependent variable (continuous data) and 4 independent data (mix of continuous and count) collected over 35 years across several states. I am using a linear mixed effect models with a ...
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1answer
88 views

Linear mixed effect models with two independent variables

I am estimating a random intercept and a random slope model using the following R code. My dependent and independent variable are both continuous. ...
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38 views

R-squared for linear mixed effects model [duplicate]

I ran linear mixed effects model in R. model<-lmer(yld ~ rain + (1+rain|state),data=data,REML=FALSE) Is there any way I can generate an R-squared for the ...
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18 views

difference between mixed effect and a simple ANCOVA

So I have collected data for 50 years of my dependent variable (continuous) data (x), independent (continuous) variable (y) across 10 locations. My null hypothesis is that the regression slopes ...
2
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1answer
58 views

Are best linear unbiased predictions (BLUPs) a good indicator of the mean value for that random effect member?

I have data on prices of houses in different districts, and would like to determine how expensive different districts are when it comes to buying a house. However, houses vary with respect to ...
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56 views

Help with lmer in the lme4 package

I am new to using linear mixed models and would greatly appreciate any help I can get. I have an equation of the form $ y = X\beta + Zu + \epsilon$ where $u$ is a random effect whose covariance ...
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35 views

Mixed modelling with lmer

I've read multiple posts on model fitting using lmer(), but I saw multiple versions of using the error term which made it confusing for me. I have a factorial ...
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20 views

How to model a multiplicative effect of a parameter

I am having difficulty in fitting a model on data. Basically, I have data about the evaluation of phenotypic property (i.e. hard) of 65 palm trees by 5 judges. As an evaluation scheme, each judge ...
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69 views

Recovery of Standard Errors of Random Effects in Lmer

I'm analysing data with a nested structure with the lmer-function of the Lme4 package in R. I'm interested in the estimation of the confidence intervals of the random effects (is the score of class1 ...
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96 views

Variance component analysis with lme4

I am beginner with lme4 and I am seeking some advice on how to carry a variance component analysis. The data come from a real-world scenario, not from a designed experiment, resulting in a complex ...
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22 views

Do I need by-item effects in my lmer model, with gain scores as DV?

I'm attempting to fit a relatively straightforward linear model in R, but am in doubt as to whether by-item effects should be included in the model. Any input would be most appreciated! Study design: ...