All Questions
Tagged with lme4-nlme nested-data
42 questions with no upvoted or accepted answers
4
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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, <...
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4
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0
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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
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0
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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
3
votes
0
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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
3
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1k
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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
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0
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139
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Equivalence test with random effects
I am designing an experiment where I will test different subjects’ multiple times under two different conditions (lab and real life)
My hypothesis Is that that the subject will perform equivalent in ...
2
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0
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68
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How to deal with the rank deficiency in lmer for nested variable
Data and background of the study:
The data is a repeat measurement of metabolite levels in responses to 2 types of stimuli.
The data measured in 4 sessions— ...
- 21
2
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0
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26
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Using multilevel modeling to test differences in the ability of trait and state measures to predict outcomes
I'm currently trying to test whether trait is better at predicting overall/mean job performance than state anxiety and whether state anxiety is better at predicting daily job performance than trait ...
- 71
2
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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
2
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0
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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 ...
2
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98
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Syntax for unbalanced block design with nesting?
I am trying to run a model in which I have site as a blocking factor, and two layers of nested random effects due to sub-sampling.
The nesting layers are -> plant[flower[robbing status]].
My response ...
- 805
2
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1k
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Fixed, random effect and nested factor in lme
I have a dataset with the following variables:
Treatment : (fixed,3 levels)
Location : (fixed, 4 levels)
Sample (random, 5 levels): 5 samples are taken in each location (randomly)
Subsample (...
- 21
1
vote
1
answer
30
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How to specify a model with multiple treatment groups, measured twice, repeatedly across a time period (lme4)?
I have 30 animals (factor: animal_id, 30 levels) which have been treated with a drug or a vehicle (factor: treatment, 2 levels). ...
1
vote
1
answer
127
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LMER random effects
I have a question regarding a linear mixed-effects model, specifically the random effects. I have taken one core in each zone (three Zones (U,L,P)) across five transects (T1-T5) and three ...
- 11
1
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0
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28
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Hierarchical linear model in the context of an experiment
In an experimental study, I randomly assign participants to one of two conditions: Condition A (which they read Text A), and Condition B (in which they read Text B). After reading their assigned text, ...
- 33
1
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0
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148
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Two factorial time series mixed effect model using lmer
I'm facing a problem regarding the the selection of an appropriate model and right synthax using lmer()-command (lme4-package). But first let me explain the design of the study:
Study design: I ran an ...
- 21
1
vote
1
answer
99
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Does linear mixed effect models fit to analyse nested data?
I am searching for correlations between symptoms severity and the parameters of neural activity in a disease model. As predictors, I have two (slightly collinear) measures of disease severity on each ...
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1
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0
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728
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Need help: nested fixed effects in nlme()
I have two fixed effects in a nonlinear mixed effect model. One is nested in the other, as the case here: "Specie" is nested in 'category'.
...
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1
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0
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225
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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 ...
- 65
1
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0
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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 ...
1
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0
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48
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Mathematical description of covariance matrix
Using the nlme R package, I specified a model of the form
...
- 45
1
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0
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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 ...
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1
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0
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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 ...
1
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0
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277
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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 ...
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1
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0
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474
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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
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0
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239
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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
1
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0
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561
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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
1
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0
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221
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Using lme4 correctly for a nested mixed model
I'm trying to create a nested model in lme4 and would like feedback on whether I've understood its use correctly.
Every individual (n = 144) had two proteins measured after 0, 12 and 72 hours. At ...
- 146
1
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0
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103
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How to specify a simple model in lmer/lme4: do I need explicit nesting?
I am measuring response time RT_log for 3 experimental manipulations (Conditions), and there are 4 ...
- 1,280
1
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0
answers
85
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Correct specification of a nested mixed effect model in lmer
I have experiments where we tested 4 substances at different days. We have substance 1 tested 10 times at day 1, substance 1 tested 10 times at day 2, substance 2 tested 10 times at day 3, etc.
We see ...
- 11
1
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0
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110
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Linear mixed model construction validation
I have 6 groups of fish made up of 8 individuals. Each group is tested three times under different treatments. These group level treatments are hungry , ...
- 11
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0
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1k
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including interactions in a mixed linear model in R (lme)
I'm trying to test for the effect of soil moisture on transpiration rates. I have plot-level data for 18 plots in 6 different stands of trees (3 plots x 6 stands). I want to treat "stand" as a random ...
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0
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0
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41
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How do I correctly formulate the random effects with repeated measures in a paired design
Sorry if this is a cross-posting, but I haven't found the exact solution for my problem yet.
Let us assume I have an experiment with 20 households, with 2 people each (1 female + 1 male).
Over the ...
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0
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0
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31
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Mixed effect model for two levels of repeated measures
I have a repeated measures dataset that I am attempting to analyze using linear mixed effects regression. I would like to compare the effects of different products (A and B) on a dependent variable (y)...
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0
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0
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59
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lmer (lme4) nested random structure gives singular fit
I'm running the following model on some reaction time data:
...
0
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0
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57
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Mixed effects model specification lmer
I am quite new to mixed effects modelling but am starting to explore more complex designs for hypothesis testing using lmer in R. The model specification is ...
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0
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44
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lmer applicable for nested unbalanced experimentel design?
My experimental design causes me some headache. It consists of three sites (A, B, C). Each site contains two treatments (Treat1 and Treat2). Obtained data (resp1 and resp2) were recorded at eight ...
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0
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101
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Choosing between nested and crossed design
I'm looking to use a linear mixed effects model. Each participant will rate a given item using 9 scales, 1 of which is the outcome variable. There are 6 items in total. The aim is to determine which ...
- 93
0
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1
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217
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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 ...
0
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0
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545
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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 ...
- 115
0
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0
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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
0
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0
answers
763
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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):
...
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