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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How to extract values for only one particular fixed factor from lmer object in R? [on hold]

I have following output for lmer object constructed using coxme package: ...
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51 views

Is the `weights=` option in lmer() doing what I want?

I want to predict PGA golfer performance. I'm wondering if I am correctly giving more weight to more recent results by using the weights= option in the lmer() ...
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18 views

Multilevel model to analyze limb injury data in Elite Athletes

I have a dataset of muscle activity measurements (variable name = RMS.mean) from a control group and an ACL injured group of elite ski racers. There are 11 ACL subjects and 12 controls. These ...
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34 views

How to set custom contrasts with lmer in R

I am using lmer in R to check the effect of condition (cond) on some result. Here are some made up data, where s is the subject identifier and ...
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16 views

Bootstrap pvalues: strange adjustment — pbkrtest PBmodcomp LRT

As far as I can tell, PBmodcomp is doing some straight up bootstrapping, similar to this Faraway example for lmer models mmod and rmod (maximal and reduced models): ...
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lmer with very small sample size [duplicate]

Can lmer be performed with random slopes and intercepts when n=3?
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how to model a repeated measures anova equivalent using lmer?

I am trying to compare means of reaction time scores for patients tested at time1 (pre-stimulation) and at time2 (post-stimulation). Also, within the stimulation paradigm, patients either received ...
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10 views

Two time series within one another

I took 5 observations per individual over the course of 10 minutes (continuous measure). Individuals came from different treatment groups. There is a substantial increase in my DV over the 4 hours ...
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33 views

linear mixed model on continuous, zero-trunctated data

I have a dataset with one continuous response variable (time), a 'treatment' explanatory variable and 5 other fixed factors: ...
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controlling for a fixed factor

n the model below, I am looking at the effects of language (2 levels) and cognitive control (scaled continuous factor) on picture naming latencies (DV). However, I need to do this while controlling ...
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Computing likelihood of a mixed-effect model manually

My question has to do with how to manually compute the likelihood of a mixed-effect model. I understand how to determine the likelihood of a fixed-effect model manually. For example, if I make up ...
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Which iterative algorithm lmer uses for REML estimation?

For mixed model, when we estimate variance component by restricted maximum likelihood estimation procedure, an iterative algorithm is required to solve the estimating equations for variance component. ...
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Partial effect plots for lmer

I ran a code to plot the following model: ...
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26 views

How to account for order/ repeated measures in a linear mixed model?

My data involves: 7 subjects who all received three different treatments (A, B and C), separated by one week Each subject received treatment A first, although treatments B and C were completed in a ...
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Difference in SAS's proc mixed and R's lme4 (Standard Errors/Covariance Structure)

I'm trying to replicate a model created in SAS using lme4 in R. The SAS Model im using is; ...
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Testing Fixed and Random Effect of Mixed Model

This pdf illustrates nicely how is to test the random effect of multilevel model . But I am simulating data from a two-level model and estimating the parameters of the model for various combination of ...
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30 views

Convergence Criteria in R's lmer

In this article , it is written in the Convergence and estimation bias para that : It is important to consider the minimum number of cases needed to ensure the model converges and that sample ...
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29 views

Have I correctly specified the lmer model?

a simple two-level model, with one explanatory variable at the individual level (X) and one explanatory variable at the group level (Z): ...
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33 views

Output from lmer in r

I am trying to evaluate the change in a variable si measured at different time points within individuals. Therefore using the time points (of which there are 3) as ...
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55 views

Random effects--mixed model

I have 2 study sites containing data from a species of wildlife. I am trying to evaluate resource selection use a use vs. availability analysis where used animal locations = 1 and random locations = ...
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58 views

Difference between two lmer model

Can you please explain where is the difference between the following two models : ...
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42 views

Interpretation of various output of “lmer” function in R

library(lme4) fm1 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy) The notation (Days | Subject) says to allow the ...
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Backing out fixed / random effects in lmer mixed model

Assume that I have a linear mixed model of the following form, specified using lme4: fit <- lmer(A ~ B + C + (1|D) + (1|E), data=data) I am struggling with ...
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Selection bias in multilevel modeling

I want to fit a multilevel model from a big survey in which the respondent could have no education, medium education or high education. My dependent variable is a continuous variable from the group of ...
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21 views

Repeatability estimation using a mixed model with repeated measures by four raters

I am a medical doctor and definitely not an expert in statistics, although I think I do okay and I am familiar with R. I have discussed the following issue with a statistician but I am still not sure ...
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Interpreting lme4 fixed effects using pamer.fnc from LMERConvenienceFunctions package in R

I'm fitting multi-level models in R using both lme from nlme package and lmer from ...
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23 views

Different mean squares reported for aov and lmer

I have a mixed effects model with 2 Locations 4 Blocks (nested in each location) In each Block I dug a hole and took soil samples at 10 Depths My variable of interest is nitrate concentration ...
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28 views

Need serious help preparing a GLMM and multinomial logit model in R

I am having trouble choosing appropriate statistical packages in R, in order to analyze (1) the relationship between a binary response variable and a few categorical variables which may be nested ...
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105 views

Repeated-measures linear mixed effect model

I have used a repeated-measures ANOVA in SPSS to analyse some of my data. It's the typical approach in my area, but I think it might be more appropriate to use a mixed effect model. However, I ...
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linear mixed models - fixed and random effects

I am analyzing plant Functional Diversity as function of environmental variables. The nature of my data is hierarchical, I have a variable x measured at plant scale, and another one, z, measured at ...
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237 views

Model Matrices for Mixed Effects Models

In the lmer function within lme4 in R there is a call for constructing a model matrix of ...
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Conflicting Mean Squares, lme vs. lmer

thanks in advance for the help. I've been getting different values for the mean squares (and as a result, F-values) using the base R lmversus ...
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Showing shrinkage with a plot for the interaction coefficient in a mixed-model

I am trying to illustrate shrinkage in linear mixed models in a 2x2 factorial design. I would like to show the shrinkage effect for all coefficients including the ...
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Spherical Parameterization of Variance-Covariance Matrix in Mixed-Effects Regression

I wonder if someone can please help me with a passage on the article by José Pinheiro and Douglas Bates on unconstrained matrix parametrization. I have been slowly working through it, and getting ...
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how to specify the order of repeated measure of same subject in multilevel modelling

I am trying to do multilevel modelling for finding the management of diabetes in 100s of patients using R (lmer). Each patient has multiple measurements of blood glucose which is taken in unequal ...
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67 views

3-way interaction with polynomials and 2 categorical variables in a LMER-model in r

My dataset contains the following variables: Within-Subject factor: Target After Onset Prime (4 levels) Within-Subject factor:Prime (2 levels; Categorical) Within-Subject factor:Target (2 levels; ...
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32 views

reporting mixed effects linear regression: t statistic or model comparison?

We have a one factor three level repeated measure experiment with ratio data (reaction times). We fit a mixed effects linear model using lmer (in fact lmerTest) - maximal, with subjects and items as ...
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66 views

Theta Calculation in Lmer R function for Mixed Effects Models

In mixed-effects models within the lmer R function of lme4 calculating the vector $\theta$ seems to be a key step, necessary to ...
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45 views

lmer replication

I did a study where I built a lmer model1 on data1. The dependent variable is continuous. There are 5 predictors (fixed effects), also continuous, and 2 random effects - factor and counts. Now I ...
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91 views

How to backtransform data that has been log transformed in order to report raw values for ease of interpretation?

I have run some lme4 analyses on reaction time data in R, with RT being the main outcome variable of interest, which I first log transformed due to non-normality ...
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80 views

Linear Mixed model with lmer in R. How to formulate the within subject factors?

I would like to know which of these formulas is better for answering my research questions (see below) and explain why, or maybe someone can suggest me another one. ...
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92 views

R lmer confint: theta values not the same as summary values

I've been using lmer's confint procedure to compute bootstrapped confidence intervals for random effects. I noticed that extracting the theta values using "getME" produces estimates that are slightly ...
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Non normality and nonlinearity in a generalized mixed model

My thesis is about the encroachment in Arctic regions. My experiment contained 6 plots, of each type (encroached and non-encroached) on three elevations. Elevation and type are fixed factors, plot is ...
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38 views

Specification of partially crossed longitudinal subjects in linear mixed effects model (lme4, lmer)

I am familiar with linear regression models, but I am in the process of learning about linear mixed effects models. My data consists of measurements for each month for a set of subjects over a long ...
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split-split plot design with unbalanced repeated measures in lme4 or nlme (SAS translation)

I am sorry if this answer has been answered before but most answers here (e.g. here, or here ) do not really adress my issue (or maybe I just do not see correctly how they do. I want to use a (linear) ...
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replication of findings in regression models

Let's say we have a dataset for which we constructed a multiple linear regression model and obtained a particular set of $\beta$ coefficients and their significance values. Now, we want to replicate ...
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interpretation of deviation coded data

How do I interpret the following result of a deviation coded dataset? As far as I understand, Cog are more accurate than NonCog irrespective of the language of the word (Code_IS_Langauge: 2 levels) or ...
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103 views

lmer, glmer, and r squared

Seems like I got really confused, so here I am... I'm trying to fit lmer model with a quite simple dataset - Observation.count as a dependent variable - count of observations for a student within ...