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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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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17 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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14 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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36 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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33 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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49 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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46 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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17 views

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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55 views

Random effect significance in linear mixed model

I have performed LRT: ...
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8 views

Problems running lmer after upgrading to R 3.1.1 [migrated]

I'm running Windows XP, and I recently upgraded to R 3.1.1 and updated all the packages. Oddly, I can't run a lmer on my own data any more. My code worked when I was using R 2.15. I also tried using ...
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130 views

Mixed effect linear regression model output interpretation

I just fitted the following linear mixed effects model: ...
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46 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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59 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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63 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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74 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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40 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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97 views

mixed effects model output

Let's say we have this: ...
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72 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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22 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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42 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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21 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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121 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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32 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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133 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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44 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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73 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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16 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 ...
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54 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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54 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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34 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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19 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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55 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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90 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: ...
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52 views

Comparing slopes in mixed-effect model

My data looks like the attached picture. The dependent variable indirectly measured physical activity. I tried to use mixed-effect model rather than RM Anova, because my actual data is imbalanced. ...
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58 views

In an experiment w/binomial responses, some subjects gave the same answer for all trials. [How] can a Mixed Effects model (R's lmer) deal with this?

I recently ran a pilot of an experiment on Amazon's Mechanical Turk. In the experiment, participants read 5 items, and answered a yes/no question about each one. A between-participants factor was ...
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25 views

How to account for multiple & varying amounts of observations per factor level & still retain info? As a random effect in GLMM or take the mean?

I would appreciate any help! Specifically I would like to know which option is best. Question Does Var2 influence Var1 in relation to the factor(Ind), and does Var3 & Var4 also have some effect. ...
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155 views

anova type III test for a GLMM

I am fitting a glmer model in the lme4 R package. I'm looking for an anova table with p-value shown therein, but I cannot find ...
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1answer
82 views

Multilevel modeling: longitudinal data with within-subjects factors

I have a data set with experimental data that I am analysing with multilevel modeling. Data are structured as follows: 24 Sessions 6 Subjects per Session 10 Rounds per Subject There was one ...
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31 views

Should I control for random effects of participant in an individual differences design?

I'm trying to analyse a survey study in which I'm interested in the way that individual differences between my participants influence how they respond to my stimuli. The stimuli are pieces of writing ...
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117 views

How to analyze interdependent interaction terms of lmer model

Assume I test a number of patients repeatedly over time to see how a certain treatment changes their skin conductance in response to a certain colour (cond) after 2 ...
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45 views

Estimated SD equal to 0 (lmer)

I'm trying to fit a mixed model of my data, but I'm getting the estimated between-subject standard deviation equal to zero. I need to estimate the between-subject standard deviation and within-subject ...
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2k views

Lmer model fails to converge

My data is described here What can cause a "Error() model is singular error" in aov when fitting a repeated measures ANOVA? I am trying to see the effect of an interaction using ...
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68 views

Differences between lsmeans and difflsmeans

I've created an lmer model. The effects of one of my treatments, "Fertilizer" varies depending on whether I use lsmeans or ...
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80 views

Linear Mixed Model for Longitudinal Data: Continuous vs. Discrete Time Parameter

I would like to conduct a power analysis for a linear mixed model with fixed effects for Treatment (two levels) and Time (four ...
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186 views

Is my dataset suitable for a mixed effects model?

I've been putting a lot of work over the last few days into bring mixed effects models to bear on some behavioural data I've collected for my thesis, but it's occurred to me that I'm not 100% sure ...
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70 views

Specification of a mixed model with nesting with lmer

I've been told my model wasn't statistically correct, but I'm not sure what I should do. What I have is basically 2 species: A and B. For each species, I have 3 replicates: 1, 2, and 3 (=6 ...
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57 views

Should I be using a GLMM?

I'm looking at the influence of pollen type on whether a flower sets fruit (i.e., yes or no = 1 or 0). Then looking at number of seeds per fruit (1-6 possible). I was told I should use lmer, however ...