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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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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42 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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1answer
45 views

Difference between two lmer model

Can you please explain where is the difference between the following two models : ...
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7 views
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34 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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7 views

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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12 views

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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12 views

How to deal with a warning messages on lmer? [closed]

I ran a mixed model using lme4 for a logistic regression and got these warning messages. How to deal with it? Warning messages: 1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = ...
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1answer
18 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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22 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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23 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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1answer
90 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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1answer
46 views

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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1answer
216 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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11 views

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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15 views

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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32 views

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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10 views

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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56 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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29 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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1answer
58 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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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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73 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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70 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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73 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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35 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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1answer
59 views

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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15 views

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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91 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 ...
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1answer
91 views

Nested mixed effects with lme4

I am trying to analyze data from an experiment using lme4. In the experiment, subjects saw either dark or bright versions of 50 stimuli (between-subjects; fixed effect "brightness"). All subjects saw ...
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31 views

Interpreting output with deviation (sum)coding

How do I interpret main and interaction effects with deviation coding? This is the output I generated for Code_IS_Condition (3 levels), ...
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25 views

How to model a 2x2x2 within-subjects glmer with dichotomous dependent variable

I have a 2x2x2x2 within-subjects design with a dichotomous dependent variable. So far I've modeled this as follows: mod0=glmer(DV ~ fact1 * fact2 * fact3 * fact4+(1|subject), family="binomial", ...
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Using lmer for my data?

I´ve been using two-way repeated measurement anova for some time, but recently I started learning about linear mixed effect models. So I´m definitely a novice! Here´s my project outline (see the data ...
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51 views

Split Plot Design? lmer analysis

I need advice regarding the analysis of a project that I am working at the moment. Here the picture of the experiment: We have an RCBD with four blocks. Within each block there are 5 plots. Each plot ...
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29 views

lmer: How to determine the weights?

I want to do a meta-analysis with lme4, where for each study several values $(x_1,y_1),(x_2,y_2),...$ are reported. These values have a linear relationship, so I want to use a mixed model with study ...
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1answer
396 views

Prediction interval for lmer() mixed effects model in R

I want to get a prediction interval around a prediction from a lmer() model. I have found some discussion about this: ...
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1answer
64 views

Crossed & nested random effects in lmer

I'm trying to get the specification correct for a crossed and nested effect model. Suppose I want to cross Sample & ...
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17 views

Intra-individual covariance matrix in lme4

I wonder, why do not need to specify the structure of the variance covariance matrix and the lmer function library lme4, since using the lm function library nlme this is possible. Thank you.
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1answer
45 views

Mixed model adjusted for lme4

I am trying to fit a mixed model using the library lme4, and is emerging the following error. fixed-effect model matrix is rank deficient so dropping 10 columns / coefficients. In this case, I'm ...
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1answer
82 views

Mixed models: wrong random intercepts and interpretation issues

I have a dataset of individuals that participated in several races, but not all individuals did every race. Of every individual I have their average speed. My goal is to have a measure of how ...
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2answers
79 views

getting degrees of freedom from lmer

I've fit an lmer model with the following (albeit made up output): ...
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43 views

Linear mixed model with two correlated dependent variables

I'm using the swissmunicipalities dataset in the package sampling of R. I consider two correlated dependent variables, the population between 40 and 65 (Pop4065), and the population aged 65 or more ...
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2answers
101 views

When the dependent variable and random effects 'overlap' in mixed effects models

I have added a new example here for clarity, see original question below Eg. I have 10 schools in 5 countries, ten students from each school is sampled. Prediction variables: student test marks for ...
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33 views

Fitting a model

I have a problem with fitting a model in lmer. My DV is reaction time to picture naming which is a continuous variable. I have three IV which are categorical. The first factor is TMS condition: either ...
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1answer
192 views

Post-hoc testing in multcomp::glht for mixed-effects models (lme4) with interactions

I am new to CrossValidated, so if there is a better way for me to format or ask my question, please feel free to comment. I am performing post-hoc tests on a linear mixed-effects model in R (package ...
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29 views

Degrees of Freedom of Cross-Level Interactions Terms in LME/LMER models

I am currently working on a hierarchical linear model using a dataset with variables on two levels. Level 1 variables have roughly 90000 observations and level 2 variables 141 observations. ...