Questions tagged [lme4-nlme]

Questions connected to R packages lme4 and nlme for linear, generalized linear and nonlinear mixed effects models. For general questions about mixed models use [mixed-model] tag.

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9 views

Possible imbalance in binomial GLMM - weighting?

I'm attemtping to fit a binomial glmm to my data. I've been using lme4 and I'm somewhat confused about interpretting the results. I think you'll be able to answer my question pretty quickly, so ...
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14 views

Is it possible for nlme's lme function to run a GARCH/ARCH models?

Is it possible for the function lme from R's nlme/gnls to run GARCH model? Or is nlme's <...
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12 views

Mixed-effects model in lme4 with partial correlation of treatment and cluster

I have data from a randomized experiment, which is clustered at two different levels in the following form: So the situation is a bit unbalanced: There are N = 14 clusters of level 1, which all ...
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1answer
18 views

Why are my confidence intervals much larger in glmmADMB than glmer.nb?

I'm plotting 3-way interaction terms from a negative binomial models, and tested the models in two packages to check my work and as a sensitivity analysis. I used the effect function to extract the ...
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0answers
24 views

How to use log link with lmer and glmer? [on hold]

I have two examples of the code. lmer: ...
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1answer
25 views

How to interpret a GLMM

I am new to stats and have run a GLMM in R using the lme4 package. The model includes marine litter collected in KG, with fixed variables of population (all), wind direction, wave strength. Random ...
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2answers
56 views

Regression Modelling of Linear, Exponential, and Power Curves in R [on hold]

Please note this is cross-posted: https://stackoverflow.com/questions/57982488/regression-modelling-of-linear-exponential-and-power-curves-in-r I am trying to model reaction time (and other) data ...
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1answer
38 views

jointModelBayes output

Consider the following example from a workshop by Dimitris Rizopoulos workshop. We have the following joint model: \begin{equation} \begin{aligned} y_i(t) &= m_i(t) + \epsilon_i(t) \\ &= \...
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1answer
59 views

How is nlme package in R “non-linear”? [on hold]

Why is the package nlme non-linear? Is it non-linear in the sense that gee is non-linear because of correlation structure/covariance pattern like exchangeable/AR1? So if we drew out correlated errors ...
2
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2answers
94 views

Why are emmeans package means different than regular means?

I am analyzing a dataset with missing data using the lme4 package for fitting mixed models and calculating fitted means from it using package emmeans. I have a feeling it relates to the missing data ...
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0answers
14 views

How do I denote a linear regression with AR - correlation?

We can fit linear models and add correlation coeffitients. In the example, x is the dependent variable, which was measured during a time series: ...
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1answer
33 views

Can I use “simr” package for power analyses on ANOVA models? [closed]

simr is an R package for conducting power analyses on linear mixed effects models. One might compute power for a model with: ...
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1answer
31 views

Feedback regarding my script and lme4package [closed]

I am struggling to generalize what I am reading (via textbooks, articles, tutorials) to my data - which led to my posting here! I appreciate any feedback from folks who are more versed in this stuff :)...
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1answer
38 views

Time varying covariates in longitudinal mixed effect models

I am looking for some help with my analysis of longitudinal data with time-varying covariates. I am planning to use R and the lme4 package. However, I am happy to use Stata also. I am interested in ...
1
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1answer
34 views

post hoc pairwise comparison

I have a model testing whether the modifications to my texts (fixed factor: Modified) affect several measures (for example IA_FIXATION_COUNT). The Texts used in my experiments are 8, and when i want ...
0
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1answer
44 views

Mixed models in repeated measurement with one treatment

I have an experiment that includes 8 subjects during one treatment, measuring response variable. The hypothesis is that there is some correlation between AV and lactate during the treatment. Some ...
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0answers
27 views

How to compare LME regression coefficients across models with same variables but different sample sizes/trial numbers?

I have a quite specific situation that does not seem to be covered by other, similar posts: I ran a study where a task (Task A) was periodically interrupted by a probe that asked participants what ...
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1answer
41 views

Is different sample size okey for a Repeated measure-between Subject experiment?

I have data from a between-subject experiment (Repeated measures, two conditions). Condition A has 15 participants while condition B is with 19. The difference is due to missing data. My aim is to ...
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2answers
38 views

Model specification in nlme: Random effects

My design has a total of 20 sites. 5 sites belong to each of four land covers: A, B, C and D. In each site, I have 5 sampling locations, 2 metres from each other. From each sampling location, I ...
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0answers
72 views

Should I be using a three-level or two-level MLM?

I am running the following study, and I am unsure about the best analytical approach. I have two ideas, but I'm not sure either one is correct. I am grateful for any feedback. I am conducting a study ...
1
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1answer
55 views

Residual diagnostic plot of mixed model

I am fitting a mixed-effects model with the following specification: ...
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1answer
60 views

What does Deviance mean in lmer [duplicate]

Probably a rather silly question, but I would like to have a clear explanation of what deviance in linear mixed models (using lmer) is. For instance, how do I interpret it along AIC, BIC, and LOgLik ...
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0answers
19 views

Interprete GLMM Estimates with log link

i am relatively new to this field and this is my first time using Generalized Linear Mixed-Effects Model. my response variable is Reaction Time (RT) and i have two fixed effects: prime and type. both ...
2
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0answers
22 views

Why are my DF for denominator so large? Reporting mixed model output

I've never used linear mixed effects models before, so I'm new to reporting the results. Following a paper that used the exact same procedures as mine (pre and post test of this specific task), I'm ...
3
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2answers
72 views

Explaining Fixed and Random Effects

Let's say that I am trying to predict the Sepal Length in Iris data from Sepal Width, ...
0
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1answer
37 views

How to correctly use lmer for mixed-effects model?

I have data of an experiment where subjects (ID) have to perform 10 trials of a go/no-go task. I want to study the influence of ...
0
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0answers
22 views

R: Why does gamm4 reduce the AUC compared to lme4?

Problem: I'm currently working on binary classification with R. I found that gamm4() from gamm4 package would give worse results than ...
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0answers
46 views

Can this model be implemented with lme4?

Suppose the data $y_{ijk}$ is structured with three indexes $i,j$ and $k$, and can be decomposed through a linear mixed-effects model: $y_{ijk}=a + b_i + \xi_j+ \eta_k + \gamma_{jk} + \epsilon_{ijk}$ ...
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1answer
19 views

Glmer: output of model when scaling a continuous dependent variable

I'm exploring the use of generalized linear mixed effects models with lme4's glmer function and I have a question regarding the scaling of independent (continuous) ...
2
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1answer
36 views

How to run mixed effects models with lots of 0's

I have ecological data (transects as the unit) from inside marine reserves and matched control transects that I would like to test the difference across 18 separate response variables. These are 3 ...
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0answers
88 views

Is this a random or a fixed effect?

I have a question about one of the variables in my study and whether or not it should be considered a random effect. I'm conducting a study of my school's 24 general learning outcomes (or "skills".) ...
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1answer
29 views

How can I adress problems of heteroscedasticity in mixed model analysis?

I am analizing pupil size data using mixed model analysis in R. I use lme() from package nlme. However, I am encountering serious problems of heteroscedasticity and ...
2
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0answers
23 views

Random effects for mutually inclusive grouping factors

I am trying to fit a model on a set of data (e.g. 10,000 observations with 20 explanatory variables). The observations belong to 30 groups, G1, G2, G3, ... G30, so I need to account for the grouping ...
1
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1answer
43 views

Overfitting model or issue of categorical predictors?

Is it possible to overfit a model by virtue of having too many categorical variables? I have 3 categorical variables and my dependent measure is continuous (or a ratio I guess, I'm measuring ...
2
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1answer
26 views

Regression with paired, repeated measures design

I have a large population of books. Each book is either a hardback or softback (thus hardback and softback books are paired with one another by title), and can fall into two categorical genres - ...
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0answers
23 views

what is the model for all random effects multilevel nested anova in lmer()? [closed]

Is it lmer(y ~ 1 + (1|a/b/c) or lmer(y ~(a + (1|a/b/c))? The first input gives a blank output for ANOVA and I try to get an ...
0
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1answer
30 views

Is an offset term necessary for a count model of a behavior where subjects determine trial length?

We are modeling data from a behavioral study in which subject pairs' conversations are coded for specific types of utterances (say "Type A"). Subjects decide when their trial is over and we count Type ...
1
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1answer
30 views

How to report orthogonal contrast codes?

In my linear mixed effects model, I had a significant interaction, I followed up the interaction with orthogonal contrast codes to see where the difference was. How do I report my findings, other ...
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0answers
54 views

Multiple Nested Random Effects affecting a Mixed Model

I have a quite complex psychophysiological data dependant of different nested data in a repeated measures experiment. The first nested structure comes from the data collection were there are several ...
2
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1answer
33 views

Feasibility of running mixed-effects poisson/logistic regression with correlation structure such as AR(1), Toeplitz

I'm not aware of any R package that lets me use specify the covariance pattern model such as in the package nlme and run the mixed effects poisson/logistic ...
2
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1answer
79 views

Comparing models: which model to choose?

I'm new to mixed effects modeling, so I need help understanding when it's appropriate to choose a model. So far I've been incrementally building my modeling with main effects and then adding in the ...
1
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2answers
27 views

How to estimate proportions of variance in outcome variable attributable to each individual fixed effect variable in lmer?

I am using multivariate models in lme4 to try to work out, quantify and compare the effects on a single outcome variable of a large group of fixed effects variables. Because the data are at week and ...
2
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2answers
28 views

linear mixed model - post hoc tests for categorical variables against fixed value null-hypothesis

I'm fitting an LME (with lmer in R) with one categorical variable that has many (80) different values. A fitting example for my problem would be how weight loss ...
1
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1answer
50 views

Random effect estimates for factor levels that don't exist

I am modeling the effect of race on test scores and would like to use a mixed or nested linear model to obtain estimates of the interaction between race and the school a student attends. I have ...
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2answers
38 views

Applying linear mixed model for RNA-Seq data [closed]

We have an RNA-Seq data set from mouse with three conditions in triplicates. For better understanding of the reaction, each of the animal was weighted and its urea levels were measured beforehand. We ...
1
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1answer
29 views

How to set up my partial cross classification model in lme4 [closed]

I have a dataset with 300 individuals $i$ that provided ratings on objects $o$ that are $y_{io}$. Each individual rated a random sample of 3 objects out of 20 possible objects so that I have 900 ...
2
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0answers
50 views

Nested Fixed-effects in a GLMER. Continuous variable nested in one level of a two-level categorical variable. Is it possible? [closed]

I am not asking for help in the coding unless that may resolve the issue. I am wondering if this is even possible from a statistics standpoint and if it is, how I go about resolving it, because all my ...
1
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2answers
47 views

Model simplification

I am currently looking at a linear mixed model of with the formula x ~ y * z I'm struggling with simplifying the model. When I run an ANOVA of my model it said ...
0
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1answer
31 views

High GLMER dispersion parameters

I am running a glmer with a random effect for count data (x) and two categorical variables (y and ...
1
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1answer
104 views

Do regression results change depending on whether a certain variable was manipulated within-subjects or between-subjects?

I was taught in my statistics classes that whether a variable was varied between-subjects and within-subjects made a difference in the results of significance tests. For example, with t-tests, all ...