All Questions
Tagged with lme4-nlme nested-data
123 questions
50
votes
2
answers
78k
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Mixed Effects Model with Nesting
I have data collected from an experiment organized as follows:
Two sites, each with 30 trees. 15 are treated, 15 are control at each site. From each tree, we sample three pieces of the stem, and ...
- 555
11
votes
1
answer
2k
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Minimum number of repeated measures and levels per nested random effect
I often read the guideline that a random factor should at least have 5-6 levels. However, it is not yet really clear to me if there is (i) a minimum number of levels for a nested factor within a block ...
- 1,029
7
votes
3
answers
554
views
Mixed model with nested and crossed random effects
I'm new to mixed effects models and am trying to use the lmer() function from the lme4 R package to specify a random effects ...
- 125
7
votes
1
answer
3k
views
GLMM - between, within and nested
I'm not entirely sure of fitting the model for experiment we've made. The variables and relevant description are as follows:
ID - participant ID
Trial - 60 for each participant
Memory - between ...
- 218
7
votes
1
answer
991
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Nested Anova vs Multilevel Linear Models
I am working on a problem which revolves around individual axons / nerve cells in two treatment conditions. All relevant questions are clearly on the axon level, and dependent on properties (size, ...
- 101
6
votes
1
answer
273
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Nesting terminology in mixed models
Suppose I have the following nested lmer structure:
lmer(Y ~ X1 + X2 + X1:X2 + (1 | A) + (1 | A:B), data=d)
which is the same ...
- 6,551
6
votes
1
answer
617
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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 ...
- 191
6
votes
1
answer
2k
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How do I analyze bimodal distibuted data with a linear mixed model
The experiment I am working on has the following design:
A B C D E F
B A D E F C
A B E F C D
B A F C D E
Each Letter represents a different level of the single factor called “...
6
votes
1
answer
1k
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Can a factor be regarded as both random and fixed effect?
I have a question about nested mixed effect model.
For example I have species A with different populations; these populations belong to two kinds of habitat types (with or without predators). So I ...
- 61
5
votes
2
answers
520
views
Glmer with count data, nested design and repeated measurements
Currently I try to fit a model for counted Individuals (response variable, integer numbers) in
Different types of traps (factorial explanatory variable).
I have two different Biotopes, and three ...
- 71
5
votes
1
answer
194
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is it correct to nest fixed effects within random factors?
In this post @Ben Bolker wrote in his answer that for the interaction between station and day we could write ...
- 1,629
5
votes
1
answer
209
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Interpreting nested random effects
I was playing around with some data and had hard time to understand the meaning of nested effects.
Here's an example of a dataset (selfesteem2 from package datarium)...
- 1,782
5
votes
1
answer
5k
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How to model nested fixed-factor with GLMM
I am a beginner on learning in GLMM and R, please forgive me if I am not making sense or asking something that is very basic.
I am trying to specify a nested fixed-factor in my GLMM model, but I don'...
- 53
5
votes
1
answer
3k
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Repeated-measures linear mixed effect model
I have used a repeated-measures ANOVA in SPSS to analyse some of my data. It's the typical approach in my area, but I think it might be more appropriate to use a mixed effect model. However, I ...
- 53
5
votes
1
answer
2k
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Non-linear mixed model (nlme) with nested random effect, do not know how to include nested random effect when bootstrapping
I have fitted a nonlinear model with nested random effect, and I'm trying to estimate confidence intervals on predictions by nested bootstrapping, by following this explanation. I have edited my ...
- 51
4
votes
1
answer
3k
views
Crossed fixed effects model specification including nesting and repeated measures using glmm in R
Background:
I am interested in looking at the effects that Culture, Treatment and Time have ...
4
votes
1
answer
7k
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Nested random effects in lme4 R
Background:
I have data on time to infection across multiple sites across a gradient. The design involves 2 latitudes (In and Out) with sites 1 and 2 nested within “In” and sites 3 and 4 nested within ...
4
votes
1
answer
406
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Should repeated measures be included as a nested or a crossed random effect in glmer?
I have a field experiment looking at the effect of a seed-mix treatment on moth abundance and I am struggling to define the correct random effects structure. My experiment is structured like this:
I ...
- 41
4
votes
1
answer
75
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Cross-nested random intercepts in mixed model?
First, forgive my uncertain terminology. I think I have a cross-nested effect. I want to model mortgage origination in multiple MSAs (metropolitan statistical areas) vs. race, income, type of loan, ...
- 1,291
4
votes
1
answer
60
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nesting/crossing in lme4
My question relates to the excellent answer given to this question a couple of years ago "Crossed vs nested random effects: how do they differ and how are they specified correctly in lme4?"
The answer ...
- 41
4
votes
1
answer
858
views
Mixed Effects Model with nested data
I have (in my opinion) a nested data-set, which I want to analyze with a mixed effects model (R's lme4 function). I need help with the model specification. The data-set consists of three subject ...
4
votes
1
answer
2k
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Three-level partially nested model
I am modeling change over time in group psychotherapy subjects using R and lme4.
My data have the following structure:
subject (id)
time (code 1-10 for equally spaced repeated measures)
outcome (for ...
4
votes
1
answer
2k
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Repeated measures with nested data mixed effects model
Hi everyone: I'm hoping for help analyzing nested data in R.
I measured the mass of chicks at 3 time points; chicks were in one of two treatments (P and W) and in one of two environmental conditions (...
- 101
4
votes
1
answer
886
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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, ...
- 41
4
votes
0
answers
593
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notation for the regression equation in a nested and repeated measures random effects model
I'm looking for help with regard to the notation for a regression equation in a repeated measures model with nested data, $\eqref{eq:2}$, and connecting the notation back to my model specification, <...
- 439
4
votes
0
answers
4k
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Random or fixed effects? GLM or GLMM?
I am interested in the behavioral response of floral visitors to a treatment, applied in a paired fashion within plants. That is, one stem on each plant receives the treatment, and another stem serves ...
- 805
3
votes
2
answers
191
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Nested data correction with mixed models
We have collected data from n patients, with each patient having one eye treated and the other untreated.
We would like to see if the treated eye progresses differently to the untreated eye using ...
- 201
3
votes
2
answers
481
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Covariance structure with one or more random intercepts
I need to choose a suitable covariance structure including one or more random intercepts:
If one factor B is nested in another factor ...
- 45
3
votes
1
answer
153
views
Mixed model with nesting
I am new to working with mixed models in R and am hoping someone can tell me if this syntax is correct.
m <- lmer(y ~ maturity * type + (1|run/block))
Where ...
3
votes
1
answer
57
views
Linear Mixed Models: Accounting an effect as a random intercept or slope
My goal is to test whether reaction is significantly different between tasks (a, b, and c). However, the order in which I run the tasks in my experiment may affect the reaction. But I'm not interest ...
- 31
3
votes
2
answers
434
views
How to combine random effect and nested random effect with lme
I'm doing a mixed linear model. And I have subjects who have been select in 20 schools. So I want to take this to account.
For this, I want to put a random intercept for the "SCHOOL" variable and a ...
- 51
3
votes
1
answer
53
views
Nesting in experimental desing
Suppose I have following results from my 2 experiments that contain 3 Block each and there are 4 treatments per Block (the example is R based)
...
- 121
3
votes
1
answer
544
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Setting up a mixed model or a split-plot ANOVA for an experiment with male/female fishes in replicated tanks
I am designing an experiment with juvenile fishes. There are 12 replicated tanks. In each of the first 6 tanks there is a even mix of male and female fish (100 of each sex in each tank); 3 of these ...
- 51
3
votes
1
answer
891
views
model specification: crossed random effect for item and subject with fixed effect nested (??) within items
In a previous thread I got the advice to run a crossed random effects linear mixed model with my data. Whilst working on the model specification, I came across a new question.
In short, all ...
- 683
3
votes
2
answers
455
views
How to deal with nestedness of fixed factors in a linear mixed effects model (lmer in lme4)?
I am new to analyzing complex datasets using mixed models in R, so please forgive me if I am asking something very basic.
I'm currently trying to write a linear mixed model using the ...
- 41
3
votes
1
answer
81
views
specifying random effects in an intensive longitudinal design
I conducted a study where participants made 15 decisions (which could be correct or incorrect) per trial (or block). There were 10 identical trials (so the same 15 decisions were made 10 times). All ...
- 65
3
votes
1
answer
319
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Nesting random effect within fixed effect, with additional nested random effect. Nominal logistic
Very new to R so please pardon my naivety.
I am trying to run a sort of mixed effects nominal logistic regression model with my insect response data.
I have 2 rearing treatments (hot and cold) and 3 ...
3
votes
0
answers
46
views
nested mixed effect ANOVA (lme4): can a factor be a fixed effect AND a nesting term for a random effect? [duplicate]
I study fish in a single large river and want to know if fish length differs between 3 large sampling 'sections' of the river. To answer this question, I measured hundreds of fish lengths within five ...
3
votes
0
answers
743
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 ...
- 126
3
votes
0
answers
534
views
Mixed Effects Model with Nesting - RNAseq differential expression
I'm new in the RNAseq differential expression analysis and I'd like to know which is the best way to treat my data.
I have RNAseq data collected from iPSCs organized as follows:
I have 2 groups of ...
- 31
3
votes
0
answers
2k
views
LMER: specify interaction between main fixed effect and nested random effect
I have an experiment where I tested the influence of mycorrhizal fungi on plant growth, in six populations of a plant species. Each population had 10 maternal lines (families, Fam) in it. I'm ...
- 313
3
votes
0
answers
1k
views
Can including an observation level random effect (OLRE) create nested random factors in a GLMM?
I have data from an observational study on insect parasitism rates from 42 sites. Some sites were sampled only once and others were sampled multiple times across different years. For each sampling ...
- 31
3
votes
1
answer
4k
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Specifying Cross-Level Interactions in LMER [closed]
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 ...
- 31
2
votes
2
answers
2k
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mixed effects and lme4: Do I need nesting?
I am analyzing data from a field experiment, and I am interested in the effects of fauna and altitude (fixed). Altitude has two levels, and at each site I have 5 blocks for the three levels of fauna (...
2
votes
1
answer
465
views
2
votes
1
answer
354
views
mixed-models in "nlme" package using lme() - nested data structure - error in model fitting - system is computationally singular
Cross-posting from stackoverflow
I am working with a dataset having the following structure (download data here).
The variable resp is a physiological response measured once for every subject during ...
- 107
2
votes
1
answer
653
views
ANOVA represenation of mixed model with crossed random effects and uncorrelated variance structure
I was expecting this to be simple when I started, it seems to not be the case.
I am trying to model yield of bean genotypes. There were only 6 genotypes included. 3 trials were carried out in separate ...
- 155
2
votes
1
answer
2k
views
Repeatability estimation using a mixed model with repeated measures by four raters
I am a medical doctor and definitely not an expert in statistics, although I think I do okay and I am familiar with R.
I have discussed the following issue with a statistician but I am still not sure ...
- 21
2
votes
1
answer
1k
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Grouped/Nested data in logistic regression
Update:
Added more meaningful example data
Setting:
In my study, each of three randomly chosen readers (A, B,...
- 120
2
votes
1
answer
568
views
How to interprate random effects in an lme model in R [closed]
I am having trouble understanding the results of my lme model. Could someone tell me how to understand the random effects?
Here is my model:
...
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