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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Repeated measures mixed model using lmer in R

I’m hoping to get some guidance in specifying a mixed model using the lme4 package in R. The study is quite straightforward. It’s a repeated measures design with pre/post measurements on the ...
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16 views

lme / lmer - split-plot with Non orthogonal subdesign

I have an agricultural field experiment (testing a plant protection agent): Split plot design with: ...
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31 views

Cannot do Tukey test in multcomp

After performing series of linear mixed models in lme4 to justify which model with which level of interaction to be used, now I would like to do the Tukey's test for multiple comparison. So first, I ...
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39 views

lmer() parametric bootstrap testing for fixed effects

I am performing a parametric bootstrap to test whether I need a specific fixed effect in my model or not. I have mainly done this for exercise and I am interested if my procedure so far is correct. ...
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18 views

Two-way interaction: interpret output from LMM in lmer

I have asked a question in this topic relating interpreting two- and three-way interactions in this link: How to interpret 2-way and 3-way interaction in lmer? ...
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15 views

Interpretation of three-way interaction in an output of lmer

I am using lme4 to run a three-way interaction model. I have three independent variables: animal (rat, lion, dog), color (red, green, blue) and sex (male, female). The baselines are as follows: ...
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2answers
69 views

A good source to understand interaction in LMM?

I would like to know more about interaction in LMM using lmer. Can you recommend me any books, articles, websites?
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14 views

Do I need a planned contrast or post-hoc analysis when doing LMM in R?

I am doing a LMM in R and would like to know if I need to do a planned contrast or a post-hoc analysis. From my understanding, the LMM in R already provideds me a planned contrasts and if I have ...
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36 views

Is it worth reporting small fixed-effect $R^2$ (marginal $R^2$), large model $R^2$ (conditional $R^2$)?

In a mixed model analysis (lme4 + lmerTest for R), I want to analyse the effect of 3 predictors, say A, B and ...
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1answer
20 views

When no model comparison, should I use REML vs ML?

I'm running LMM, and I will make no comparison of models. Could I ask which one should I use between REML and ML?
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1answer
20 views

Does the first line of interaction output from lmer contain all levels of variables?

I am using LMM from lmer to interpret my data. As the system of its output is dummy, so it should mean that the number of levels is always the same in every line of output. For example, if I have ...
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30 views

How to incorporate time varying group covariates in linear mixed effects model

I have a continuous response $Y_{ij}$ after taking repeated measures in an individual $i$. Altogether I measure $Y_{ij}$ 5 times (j=1..5) under different types of subject motion: still1, still2, nod, ...
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29 views

predict() in lmer regression, but I need it only 2 categories [migrated]

I am attempting to estimate a multilevel model. My code is: ...
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43 views

Multilevel model specification for count data (with overdispersion) in R

I would like to specify a multilevel model including the following variables: DV: count data, i.e. a score value between 0 and 13 (resulting from an additive index) for each individual Individual ...
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1answer
77 views

Is it necessary to exclude all nonsignificant parameters to choose the best model?

I'm running LMM models and could I ask if I can just report the model after comparing random intercept with random intercept and slope model without excluding nonsignificant factor?
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9 views

Does GLMM or LMM already give us planned contrasts?

I use GLMM and LMM to find significant factors for my data. And could I ask if the results from these two models already give me planned contrasts? Or do I need to run them separately?
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42 views

lmer giving worse performance than lm

I am having trouble training a model for nested data about house prices. Lets say my data looks like following: ...
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43 views

LMM models with two difference reference categories yield two different results

I have run LMM models with different reference categories and this yield different results: ...
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1answer
38 views

Fitting random intercept and slope in lmer for lme4.

If I would like to fit random intercept and slope and if I write it as (color|writer) compared to (1+color|writer), are they the same?
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1answer
63 views

Notation for multilevel modeling

The formula one needs to specify for training a multilevel model (using lmer from lme4 R ...
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89 views

Meaning of a convergence warning in glmer

I am using the glmer function from the lme4 package in R, and I'm using the bobyqa optimizer ...
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1answer
63 views

Binomial count data - use glmer, lmer or just average it all?

I'm new to both mixed-effects models and R, so please excuse me if this is a bit of a silly question! I'm struggling with choosing the best method to analyse my data for a speech perception study, and ...
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19 views

Subjects:condition interaction random effect in a growth model

I'm investigating the effect of 'Condition' (3 levels: Quiet, Intelligible, Unintelligible) on pupil response over time (intercept, linear, cubic, quadratic, quartic and quintic terms). When I use ...
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29 views

Growth curve analysis on orthogonal polynomial terms

I am conducting a study which is looking at the effect of 'Condition' (Quiet, Intelligible, Unintelligible) on the pupil(eye) response over time. Upon visual inspection of my data plots, pupil ...
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28 views

ANOVA in lmerTest for in-between study with repeated measurements

I have a bit of trouble understanding how to formulate a correct formula in R using the lmerTest-library. Let’s assume there is an 2x2 in-between design with repeated measurements. Those repeated ...
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54 views

Afex does not give me all p-values of all parameters. What should I do?

I have installed the package afex with this formula: ...
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40 views

How to get p-value for fixed-effects by model comparsion?

I am doing linear mixed model using lme4. According to Winter (2013, http://www.bodowinter.com/tutorial/bw_LME_tutorial2.pdf), as the new version of R does not give p-values due to inconclusion of ...
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25 views

How do we know the LMM model has to add random slope with random intercept?

When I read the literature about random intercept, random slope, and random intercept and slope model, I usually see the graph that they have lines for each participant. I do not know how to plot such ...
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47 views

What should the appropriate model for my data look like?

My research objective is that I would like to test if some sounds in languages are similar to each other in terms of duration. In my situation, I have 4 languages with 5 sounds. The first three ...
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1answer
52 views

Why does the log-likelihood change when a variable is linearly transformed in a hierarchical model?

I ran into (what I think is) an inconsistency when running a random-intercept model (using the lmer function in the lme4 package in R). Here is what I do: I first run a model with a set of ...
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1answer
137 views

How to interpret 2-way and 3-way interaction in lmer?

I have a problem with interpreting 2-way and 3-way interactions in lmer. My DV is height which is a continuous variable. All IVs are categorical variables. The first factor is animal, either rat or ...
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38 views

“non-monotonic profile”: what should I do when getting this when running confint(lmer)?

I am new to R and I have run the lmer in lme4. In the model summary, there is no any warning message, but when I ask for ...
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30 views

Do you know any paper reporting only CI instead of p value when the analysis is from LMM in lmer4?

I'm finding articles that report only CI, instead of p value. All articles I found will report p value despite its issue is inconclusive. I would like to look at how they put the important information ...
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23 views

Can I select IV from their t value and confidence intervals in LMM in lmer?

As the issue of p value is still inconclusive and many papers point out that the confidence intervals are more informative in selecting factors in fixed effects, I would like to ask about ...
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21 views

within subjects design with condition rotated across presentation lists (staggered cross-over design?)

In my field, it is common to rotate levels of an experimental condition across different presentation lists in a within-subjects design. This is done to prevent a particular participant from seeing ...
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1answer
103 views

Dropping term for correlation between random effects in lme and interpretting summary output

I want to fit a model without a correlation term between the random effects with lme. In lmer this is fairly straighforward.... ...
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1answer
67 views

lsmeans vs. differences between lsmeans

I calculated the least-squares means and standard errors for a linear mixed model. I am attempting to plot the lsmeans and standard errors for the combinations of the two factors, but I notice a ...
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1answer
73 views

Interpreting random slopes equal to 0 using lmer in R

I have just started working with mixed models and the lme4 package and was after some advice interpreting some results. I have a data set looking at the change in nest height of birds (NAP) over time ...
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54 views

Interpreting coefficients for random effects models with extremely unbalanced data

I'm currently working with a data set that has numerous samples collected over time at different sites in a study area, and I'm interested in detecting a trend over time for that area. I know that in ...
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2answers
90 views

Use a baseline including all observations in lm()

When using factors in a linear model, I would like to retrieve the 'average' effect as baseline (intercept), rather than level 1 of all factors. Is this possible? ...
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37 views

Translating from aov to lmer or lme with three levels of nesting

I have data from a split-plot (or repeated measure) experiment with three factors: A is random, B is fixed and nested within A, and C is fixed and nested within B. I can test for the effect of B, C ...
2
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1answer
254 views

Are degrees of freedom in lmerTest::anova correct?

I am analyzing the results of a reaction time experiment in R. I ran a repeated measures ANOVA (1 within-subject factor with 2 levels and 1 between-subject factor with 2 levels). I ran a similar ...
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1answer
236 views

Likelihood ratio test - lmer R - Non-nested models

I am currently reviewing some work and have come across the following, which seems wrong to me. Two mixed models are fitted (in R) using lmer. The models are non-nested and are compared by ...
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1answer
262 views

How to fix an overdispersion in a Poisson GLMM with lmer function in R?

I want to model counts as being dependent on two nominal variables, one continuous variable (all as fixed effects) with 3rd-order interactions and one grouping variable (as random effect). However, I ...
6
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1answer
83 views

Dealing with correlating fixed effects in a linear mixed-effects analysis

My question is about the best way to estimate the effect of a predictor on a dependent variable, while accounting for several other predictors that may correlate with the predictor of interest. I'm ...
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68 views

Effect size in plotLMER.fnc

I'm working with linear mixed models. I used plotlmer.func, in the package lmerConvenienceFunctions to build a graphical ...
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1answer
48 views

Null GLMM Poisson underestimate the mean of the response variable. Is it indicative of poor fitting?

I want to test the fixed and random effects of some covariates on a discrete variable with non negative values. In exploratory analysis I fitted a null Poisson GLM and an null Poisson GLMM. However, ...
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1answer
268 views

Changing reference level for contrasts changes results in R 3.0.2/lme4 1.1-2 vs. R 2.15.0/lme4 .999999-0

I hope this is an appropriate forum to post this question. I recently upgraded my R software from 2.15.0 to 3.0.2. I also upgraded the lme4 package from .999999-0 to 1.1-2. After doing so, the results ...
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86 views

Why is there a dramatic difference between aov and lmer?

I have a mixed model and the data looks like this: ...