# Tagged Questions

14 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 ...
19 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 ...
39 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: ...
29 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 ...
16 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 ...
41 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 ...
32 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 ...
62 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 ...
14 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 confint(lmer), R gives me this message at the buttom of the output: ...
28 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 ...
17 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 ...
17 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 ...
45 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.... ...
37 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 ...
59 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 ...
37 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 ...
33 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 ...
155 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 ...
214 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 ...
77 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 ...
52 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 ...
30 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, ...
160 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 ...
80 views

### Why is there a dramatic difference between aov and lmer?

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

### Unable to fit repeated measures in R

I've been trying to fit a repeated measures model in R using lmer but I get an error message. I've used SAS in the past and I was able to fit a somewhat similar ...
64 views

### Multivariate Mixed model in nlme

I have two correlated response variables ($y_1,y_2$) explained by the same covariate set ($x_1,x_2$), each with mean = 0. I have a random grouping factor ('group') which is heteroskedastic (\$group ...
59 views

### How do you specify a binary time-series-cross-section model in lme4?

I have a standard binary time-series–cross-section (BTSCS) model that I would like to specify as a mixed effects model using the lme4 package. I've read elsewhere that time-series–cross-section (TSCS) ...
476 views

### Checking assumptions lmer/lme mixed models in R

I ran a repeated design whereby I tested 30 males and 30 females across three different tasks. I want to understand how the behaviour of males and females is different and how that depends on the ...
87 views

### Mixed model fitted on time course data

I have some time course data which plotted looks like this: I have fitted a mixed model to my raw datapoints with R's lme4::lmer, as seen in this code. In ...
243 views

### Why can't I match lmer for family = binomial?

I'd like to match the outputs of lmer (really glmer) with a toy binomial example. I've read the vignettes and believe I understand what's going on. But apparently I do not. After getting stuck, I ...
59 views

### R linear models - category IDs as strings or ints

I am trying to fit a linear model (lme4::lmer()) to my data in R. I would like to look at a number of things, including "scrambling" of visual stimuli and ...
31 views

### Group effects where there is a single group

Suppose I have a table of subjects and measurements as follows subject measurement s1 1 s1 2 s1 3 s1 4 s1 5 s1 6 s1 7 s1 8 s1 9 s1 ...
105 views

### How to deal with collinearity in lme with categorical IV with > 2 levels

I'm analysing data from our experiment. We had participants in 4 groups, each participant was measured 4 times. We measured cortisol in saliva, so it leads us to the linear mixed models, because the ...
254 views

### What does it mean that random effects are highly correlated?

What does it mean when two random effects are highly or perfectly correlated? That is, in R when you call summary on a mixed model object, under "Random effects" "corr" is 1 or -1. ...
384 views

### What does the anova() command do with a lmer model object?

Hopefully this is a question that someone here can answer for me on the nature of decomposing sums of squares from a mixed-effects model fit with lmer (from the ...
275 views

### Have I correctly specified my model in lmer?

I have scoured lots of help sites and am still confused about how to specify more complicated nested terms in a mixed model as well. I am also confused as the use of ...
171 views

### Can I use an automated model selection approach on an lmer object?

I am attempting to use MuMIn to run a model selection analysis on a mixed model fitted using lme4. Because this model is fit ...
872 views

### Confusion over lmer and p-values

I was under the impression that the function lmer() in the lme4 package didn't produce p-values (see ...
103 views

### How to include level-2 variables in a random intercept model when fitting HLM with lme4?

I want to include 2 covariates that are group characteristics as fixed effects in predicting a variable that is at the individual level. How to include them in the lmer formula? At this point my ...
285 views

### nlme beginner question [closed]

I am trying to fit a mixed model to my data using the nlme library in R. Here's what I have: ...
1k views

### How do I get a a p-value for the output of an lme model with lme4?

My problem can be summarized very simply: I'm using a linear mixed-effects model and I am trying to get p-values using pvals.fnc(). The problem is that this function seems to have some trouble ...
254 views

### Mixed model with 1 observation per level

I'm fitting a random effects model with glmer to some business data. The aim is to analyse sales performance by distributor, taking into account regional variation. ...
57 views

### LME Relevelling Issue

I'm in the process of relevelling some factors for an LME using R and have hit an issue. I've reordered the factor levels to enable me to talk about the outcome of the model more easily in relation to ...
141 views

### Repeated measures across time, two treatment groups

I'm having difficulty modeling something… I think it's fairly simple, but I'm just not confident enough in my ability. I setup an experiment with two treatment groups, six replicates in each ...
449 views

### lme and lmer comparison

I was wondering if anyone could enlighten me on the current differences between these two functions. I found the following question: How to choose nlme or lme4 R library for mixed effects models?, but ...
95 views

### What is the difference between lmer(.. (1|groupingfactor1) +(1|1|groupingfactor2)) and lmer(..(groupingfactor1|groupingfactor2)?

I am quite new to lmer and quite confused about how to select the random effects part of the model. The data I am working on is divided into dependent and ...
2k views

### Is this an acceptable way to analyse mixed effect models with lme4 in R?

I have an unbalanced repeated measures data set to analyse, and I've read that the way most statistical packages handle this with ANOVA (i.e. type III sum of squares) is wrong. Therefore, I would like ...
207 views

### Specifying group covariates and cross level interactions in lmer

I'm new to R, and despite trying to read as much as I can about how lmer works in R, I still don't feel like I know how to correctly specify more complex models using the lmer syntax. For example, ...