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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2 factor factorial model with random factors

Using lme4, how does one define a full 2-factor factorial model with both factors (and their interaction) being random? Specifically I am trying to recreate the ...
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24 views

Modeling error structure in lmer in R?

Is it possible to add a parameter to lmer model which will be modeling the error structure? Sth similar to TOEP(X) and SP(POW) from SAS???
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46 views

Mixed-effects: length of the experiment as a continuous fixed effect?

I have measurement of nitrogen uptake Nup across 4 different SITE very far from each other and in different years (e.g. ...
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16 views

Retrospective power analyis of lmer for sample size

I'm an MSc student doing an assignment where I am asked to analyze and write up a report on a dataset on environmental enrichment in zebra finches. Among other things we are being asked to do a ...
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39 views

In R package lme4, how do you force the random slopes and intercepts to be uncorrelated for an interaction term?

I have a mixed model, fit using lmer in R, that has three interaction terms (X1:X1, X1:X3, ...
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R lmer Model Diagnosis qqnorm

I fitted this lmer model: m1 <- lmer(logR ~ N_g.m.2 * Year + (1|Wh/N_g.m.2), data = CO2_Ratio) Rendering the attached qqplot. ...
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40 views

How do I contrast code for a factor where one level is the application of both of two others?

I have a factor 'Music' that has four levels: none, piano, guitar, and mixed. Subjects gave a response hearing no music, piano only, guitar only, or piano and guitar, so I want to create an lmer model ...
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16 views

Linear mixed model construction validation

I have 6 groups of fish made up of 8 individuals. Each group is tested three times under different treatments. These group level treatments are hungry , ...
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43 views

graphical representation of fixed effects from lmer

I have run a lmer model in R: ...
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1answer
137 views

How to formulate linear mixed model to find out effects of continuous variables?

I have a dataset with growth rate as a response variable (resp in the example) and temperature, food availability, and salinity as predictor variables (...
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39 views

Using lmer for random effect and nested interpreting model comparison

I'm trying to do a lmer in r. I did an experiment in which I manipulated the temperature. My dataframe contains the following factors: Site: 11 level, random Species: 2 levels, fixed Subject: 10, ...
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9 views

transforming of standardised effect size in MuMIN package

I ran the following model ...
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1answer
46 views

lmer: standardized regression coefficients

I have analyzed some data (the exact nature of which, I assume, is irrelevant for this question) using linear mixed effects models with the lmer() function from lme4. There has been at least one ...
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42 views

Fixed or Random: Hausman test plm vs LRT lmer, Which is the best approach to decide to use random effect?

I have an unbalanced panel data and would like to know which method is better for estimation if I want to capture the heterogeneity of the sample using the plm package or lme4. The sample have year ...
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204 views

R: equivalence between an aov between-within repeated measures model and an lmer mixed model

I have some trouble obtaining equivalent results between an aov between-within repeated measures model and an lmer mixed model. ...
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13 views

interpreting an interaction of two continuous variables in a mixed effects model [duplicate]

I am hoping for some guidance on how to interpret the interaction in a mixed effects model. The interaction is between two continuous variables (EarlyLanguageExposure and NeighborhoodSize). My ...
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56 views

Changing reference level/re-leveling contrasts changes results in non-convergence

I have a question regarding re-leveling in lme4 1.1-7. Experimental Design: Our experiment is an eyetracking while reading study (single sentence stimuli). We are analyzing four different ...
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1answer
68 views

Using the same variable as a fixed and random effect in Mixed Effect Models

The experiment this data comes from an experiment where two people collaborate to put objects in a specific order. The Direction has the target array on their screen, and the Matcher has a scrambled ...
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2answers
107 views

How many random effects to specify in lmer?

I ran a computer-based experiment in which there were two within-subject factors, A and B. So all participants got multiple trials in each A*B cell. There was also one between subject factor, C. I'm ...
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1answer
89 views

Interpreting a linear mixed effect model's interaction term

I am a biologist and am attempting to analyze the effects of time and location on depth. I was told I needed to use a mixed effects model to account for the random variables of Individual and tracking ...
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1answer
107 views

Specifying Cross-Level Interactions in LMER

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 ...
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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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50 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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36 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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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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1answer
112 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
99 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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1answer
55 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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60 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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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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200 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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420 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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70 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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1answer
73 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
44 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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81 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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64 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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55 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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51 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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94 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
65 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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15 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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23 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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1answer
61 views

Random effect significance in linear mixed model

I have performed LRT: ...
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376 views

Mixed effect linear regression model output interpretation

I just fitted the following linear mixed effects model: ...
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1answer
68 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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1answer
239 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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1answer
106 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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1answer
119 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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51 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 ...