All Questions
Tagged with lme4-nlme nested-data
123 questions
3
votes
0
answers
743
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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
4
votes
1
answer
60
views
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
0
votes
0
answers
204
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How to write model with fixed factors nested in random one?
I'm at the beginning of models understanding so this question is maybe childish, excuse me, please. It is close to this but there are some differences and I'm not sure how to implement that solution ...
- 1
1
vote
1
answer
130
views
Mixed Effect Models - choice of the random intercept
I'm using the glmer function from lme4 package to model a binomial phenomena in a human DNA dataset. An allele can be missing (1) or not (0).
The dataset is created with 10 different samples. Each ...
- 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
1
vote
0
answers
2k
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How to build a LME with nested random effects? A study with a very comlicated experimental design
I am trying to analyse the data on the climbing behaviour of flies. The design of the experiment was rather complicated, so I am currently struggling to build a propper LME model.
The flies have ...
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
1
vote
0
answers
48
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Mathematical description of covariance matrix
Using the nlme R package, I specified a model of the form
...
- 45
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
2
votes
1
answer
873
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Mixed effects model failing to converge - better to remove the random intercept? slope?
I have data for classes that are nested within schools
There are two classes for most schools (n = 240), but
I also have some schools with which I have more than two classes.
i.e., 20 schools with ...
- 381
2
votes
1
answer
465
views
2
votes
1
answer
850
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Mathematical notation / formula of a mixed effect model
I am unsure how to define the mathematical notation of a mixed model of R.
I built the model in this way:
...
- 23
1
vote
1
answer
636
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Specifying random slope in a nested random effects
I collected crop yield and rainfall data from multiple counties and year ( > 30 years).
Each county can only belong to one province and each province can only belong to one region. I am interested in ...
- 991
0
votes
1
answer
246
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Linear Mixed Model in R: Rep. Measures, Nested, Random Effects
I ran a study with the following design: Subjects were presented 100 different stimuli and asked to indicate their liking (scaled from 0-10) for each stimulus. Each stimulus was part of only one of 4 ...
- 129
1
vote
1
answer
1k
views
Multilevel nested glmer model (logistic regression) with 4 groups
I have 3 level nested data that is causing convergence problems (glmer function in lme4, R for multilevel logistic regression).
The Data
Country(4 groups) -> School(100 groups) -> respondent
A ...
1
vote
0
answers
61
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Multi-level modeling using lmer in R
I have nested data as followed: 'Learning group sessions' in 'students' in 'learning groups' (each learning group consisted of different students and the learning groups chose to have between 3 and 10 ...
- 21
0
votes
0
answers
763
views
Error when using lmer but not lme (specifying nested data in random-effects structure)
I have a dataset with participants' scores on three exams. Each participant completed each of the three exams. So the dataset looks something like (for a total of 945 rows):
...
- 491
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
1
vote
1
answer
1k
views
Modeling repeated measures with a second layer of nesting using lmer
I am doing a longitudinal repeated measures study looking at the effect of age (maturation) on my test result (Y - a type of hearing test). My outcome Y, is numeric, and the main effect is age (age....
- 155
3
votes
0
answers
534
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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
4
votes
0
answers
593
views
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
2
votes
1
answer
151
views
Specification of linear mixed-effects model
my apologies if this is a very basic question or if similar questions have been asked before. I am relatively new to this kind of modelling and did not find anything yet that resolves my question.
...
- 21
3
votes
0
answers
2k
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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
2
votes
0
answers
183
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GLMM Seedling Survivorship (binary outcome) - glmer & nested effects in R
I am attempting to fit a generalized linear mixed effects model in R using lme4, but am new to mixed models. I'd like to model Survivorship as the outcome of Treatment + Environmental Factors (...
- 21
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
1
vote
1
answer
104
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Logistic GLMM coefficients blow up when adding nested random effects?
I have some data (here) that I was hoping to analyse using lme4. It consists of a binary outcome variable that has been calculated at a number of locations in each of a number of images, which ...
- 805
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
2
votes
0
answers
1k
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Clarification on nesting fixed effects within random effects in an mixed effect model
Before I go into my question I'd like some clarification on fixed and random effects. From what I understand "Effects are fixed if they are interesting in themselves or random if there is interest in ...
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
1
vote
0
answers
51
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Specifying mixed model for temperature measurements of termite mounds during the day in different soils
I've got a problem while trying to specify the 'right' nesting of the random effects of my dataset. The dataset registers hourly variations in temperature inside termite mounds:
Sampling was ...
4
votes
1
answer
75
views
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
0
votes
1
answer
3k
views
Mixed effects model with random and nested effects in lmer
I want to run a linear mixed effects model with nested and random effects using lmer in R, but continue getting errors. Two questions: what is causing the errors and how can I fix my model to run the ...
11
votes
1
answer
2k
views
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
6
votes
1
answer
1k
views
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
2
votes
1
answer
1k
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Correlation structure of nested nonlinear mixed model
I would appreciate any help. I am trying to fit a nonlinear mixed model to some experiments. I have adopted a Gompertz function (y=Asym*exp(-b2*b3^x)), and the data used is 3 years of experiments (the ...
- 123
1
vote
0
answers
277
views
Fitting distribution in R with bimodally distributed data from bimodal dataset (with repeated measures)
I am having problems analysing a data set from a study with unbalanced design and that contains repeated measures...I inherited the data and I'm a bit lost.
The response variable is core body ...
- 11
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 ...
1
vote
0
answers
474
views
Nesting fixed effects within random effect in lmer in R
I am a masters student in phonetics currently looking at voice onset time values (VOT) for voiced consonants in French.
I am intending to use a linear mixed effects regression to evaluate the effect ...
1
vote
0
answers
239
views
Fitting a nested experimental design in R
I am analyzing experimental growth data where I have fixed effects A and B (two levels each), an interaction between them (AxB) and 5 culture replicates for each combination of A and B. Numerical ...
- 11
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
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
1
vote
0
answers
561
views
Degrees of freedom for post-hoc comparisons in lmerTest
I have some experimental data in which treatments are nested within sessions which are nested within groups. It's tricky, because it seems like a simple between subjects comparison (TX1 vs TX2 vs TX3),...
- 11
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
0
votes
1
answer
5k
views
glmer.nb with weights and nested random effects - Convergence Error [closed]
I have a dataset of behavioural observations in an experiment on free ranging breeding birds. I'd like to calculate GLMMs.
The dataset has the following parameters:
Behaviour (count data)
Behaviour ...
- 11
7
votes
1
answer
3k
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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
1
vote
1
answer
659
views
How to specify factors nested within treatments using a glmm
I have behavioral response data (counts of acts within an hour trial) that I would like to analyze using a GLMM. I'm new to GLMM's but after months of digging through papers and forums, I've concluded ...
- 11
0
votes
1
answer
3k
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Using lme to perform a nested ANCOVA in r
I want to perform a nested ANCOVA using the function lme in r. My data concerns the growth rate (sgr) of fish at different temperatures (temp). In the trial there were 3 replicate tanks each housing 8 ...
- 3
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
0
votes
1
answer
316
views
Fitting a model on continuous response variable using lme4 package in R? Factorial or Nested design?
I am trying to find the effect of plant traits on water infiltration and did some analysis using lme4 with the help of 2 statisticians, both of them suggest different models to check it. I can't ...
- 131
4
votes
1
answer
2k
views
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 ...
