# Tagged Questions

37 views

### Determine individual consistency from mixed model?

To investigate the difference between three tasks I tested 30 individuals on each of the three tasks and ran the linear model as follows: ...
111 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 ...
40 views

### Using REML in mixed models if random factor is small

I'm trying to fit linear mixed models to 3 different DV (so three models). I understand that REML gives less biased variance estimates. As im more interested in the fixed effects, I use ML for the ...
55 views

### How to do linear mixed effects modeling with this data?

Study Design: Below is a clinical trial in a longitudinal dataset. All subjects (n=34) attended V1 (baseline) and then they were assigned to either a ...
99 views

### GLMM model specification help gender effects + an effect that is nested only within female

Main question: "What are the contributing variates to daily movement distances?" Specifically my question today relates to: "What is the contribution related to gender, and then within female what ...
84 views

### How to fit different ARMA models by group in R?

I have $Y$ measurements per several Subjects and I'm studying impact of factor on $Y$ measurements. I've fit a lognormal mixed model with a random interaction, but I'm finding autoregressive ...
189 views

### lme: random effects for replicated growth curves

I am measuring the evolution of the brain response to a visual stimulation over time. The measures are done every seconds from 1 second to 14 seconds (each measure at time t gives a value summarizing ...
265 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 ...
70 views

### Correctly specifying temporal pseudo-replication in a mixed effects model in R/nlme

I would like to correctly specify that my data is temporally pseudo replicated in a mixed effects model in R using lme() of the ...
71 views

### Lagged term in time series with stationary errors: too good to be true?

I often have datasets where there are many animals, in several treatment groups, and each animal's body weight is measured at regular intervals over the course of its lifetime. The response of body ...
80 views

### Accounting for pretreatment differences (linear mixed effects model) using R/nlme

I have an experiment that is as follows: 4 years of data (1 year pre-treatment, 3 years during treatment) 20 plots total 5 plots of each type (Control, Treatment A, Treatment B, Treatment A+B) Each ...
136 views

### Selection of lme models using AIC & appropriate random effects & variance structure

I am using three categorical predictor variables X1, X2, X3 and one continuous dependent variable Y, and I want to treat X3 as a random effect. The simplest model I could come with: ...
87 views

### Mixed-effect modeling with paired observations & bounded response variables

I am quite new in the field of mixed-effect modeling. For a beginner like me, I guess I combine several levels of complication in my analysis: paired observations & bounded response variables. I ...
33 views

### Linear model when both dependent and independent variables have unpaired replicates

I've got a set of experiments where 3 replicate measurements are done for rat cell lines and for human cell lines under different conditions using various compounds. I am trying to predict the ...
77 views

### Nesting and grouping formula confusions using lme

I've seen a fair few of these posts already, and I feel a bit silly for posting yet another question on the topic - but I just cant seem to get my head around it. I'm very new to R and esp new to lme, ...
451 views

### lmer interpretation of correlation

I have the following output: ...
195 views

### Contrasts in mixed model

Suppose I have a data frame like this (four groups, for each n = 12): ...
539 views

### Mixed model specification with nlme in R

i'm having a hard time finding the right model for my data. The study is about the effect of a drug (more precise: the effect of the dose of a drug) and the time on the subject (rat). So i got the ...
253 views

My data: ...
541 views

### Problems with mixed model simulation

So i was just having a nice evening trying to simulate some hierarchical models by myself and estimate their parameters. First model I tried to simulate and estimate was ...
250 views

### Fit lme in R with multiple levels of grouping and with correlation structure defined for more than inner-most level of grouping?

I’m trying to model the correlation/covariance between a pair of variables measured concurrently and repeatedly on a group of subjects. Since both variables are measured responses I want to avoid ...
1k views

### LME() error - iteration limit reached

In specifying a crossed mixed effects model, I am trying to include interactions. However, I get the following error message: ...
739 views

### Using lme to analyse a complete randomized block design with repeated measures: Is my model correct?

I've got a completely randomized block design with three treatments and four replications. Biodiversity was measured in four successive years. I figured that a mixed model with repeated measures as ...
643 views

### Completely different results from lmer() and lme()

I got completely different results from lmer() and lme()! Just look at the coefficients' std.errors. Completely different in both cases. Why is that and which model is correct? ...
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### Split plot design with repeated measures in package (nlme) - model errors

Forgive me if this answer is already somewhere on this site, but after extensive searching I have found nothing to help me. Here is a brief overview of the experiment: I have 18 tanks, each of which ...
793 views

### Proper use of weights argument in linear mixed model [lme()]?

After attempting to produce a linear mixed model I was left with a great deal of heterogeneity. ...
194 views

### What to do with heterogeneity of variance when spread decreases with larger fitted values

I am trying to produce a linear mixed model the R code is as follows. lme(Average.payoff~Game+Type+Others.Type+Game:Type+Game:Others.Type+Type:Others.Type,random=~1|Subjects,method="REML", ...
163 views

### Suggestion about morphometric analysis in R using lm or lme

Maybe this is an over-the-top question but I have many doubts regarding my recent analysis about deer skull measurements and how to proceed with the analysis. This is a sample of my dataset: ...
300 views

### Specifying mixed-linear model in lme() for pre-/post-treatment design

Dear crossvalidated community! I am analyzing a data of a study in which every participant's performance in a memory task was measured twice (once under placebo, once under drug treatment in random ...
1k views

### error in getting predictions from a lme object

I am trying to get predictions for observations from a lme object. This is supposed to be quite straightforward. Yet, since I am get different types of errors for different trials, it seems to me I ...
2k views

### How to fit the model for crossed and nested design using lme function in R?

Suppose A is a fixed factor and B is a random factor. A and B are crossed. Another random factor C is nested in B. Taking into account the AB and AC interactions, how should I fit the model using lme ...
2k views

### Is there a way to specify a lme model with more than one within-subjects factor?

The data Suppose we have a dataset d with two between-subject factors (i.e., groups), group and ...
1k views

### Paired t-test as a special case of linear mixed-effect modeling (still unresolved)

We know that a paired t-test is just a special case of one-way repeated-measures (or within-subject) ANOVA as well as linear mixed-effect model, which can be demonstrated with lme() function the nlme ...
3k views

### How to perform post-hoc comparison on interaction term with mixed-effects model?

I’m working on a data set in order to evaluate the impact of drying on sediment microbial activities. The objective is to determine if the impact of drying varies among sediment types and/or depth ...
215 views

### Programming a new random effects structure in lme

I am seeking advice on programming a new random effects variance-covariance matrix/structure (pdmat) in R for use in lme()? I've checked out the lme source code (as suggested if you want to program ...
517 views

### Mixed model with repeated measures and both of two treatments with lme or lmer in R

I know just enough about lme() and lmer() to get myself by with simple models, and to get myself into trouble with more complex ...
218 views

### Fitting special variance structure in mixed model

I'm interested in fitting a linear mixed model with this special variance structure on the random effects $\mathbf{u}$: \$\begin{eqnarray*} \mathbb{V}\left(\mathbf{u}\right) & = & ...