All Questions
3,532 questions
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9
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Statistical Inquiry. Overdispersion issue or abundance of 0s
Trying to go over some data and its half presence absence while the other half is count data. The model I've been working on lately is a mix of lmer and glmer.nb as that seems to be the approach for ...
- 1
0
votes
1
answer
32
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Fitting a Nonlinear Mixed Model
I’m trying to fit a nonLinear Mixed Model (nLMM) to test whether the abundance of certain organisms was affected by the sampling period after an event that caused a significant increase.
The data show ...
- 33
1
vote
0
answers
38
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How to estimate population variance from a mixed model with a categorical variable?
I supposed it is a basic question, but I'm stuckle on it and I can't find the solution.
I have a date base with the slurry dry matter content from different pig production stages (CATEGORY), also, ...
- 41
3
votes
2
answers
108
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R: How to fit a linear mixed model with a custom covariance structure for two random intercepts
Suppose I have a dataset with repeated measurements on q clusters. I want to fit an LMM with two random intercepts, on the same cluster, with a non-diagonal covariance structure on the random effects (...
- 172
1
vote
1
answer
48
views
Estimating mixed model with identical response value but different covariate values within a pair
Say we have a dataset with individuals. Each individual performed a task, either in solo or with another individual (variable condition), and we measured the ...
- 65
0
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0
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11
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DHARMa bootstrap testOutliers unexpected p-values
I am checking the assumptions of multiple univariate logistic mixed models each with a predictor and covariates.
Due to the following error:
...
- 1
1
vote
0
answers
29
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Nested design with fixed and random effects: Is my R model correct?
I am trying to analyze a nested experimental design in R, but I am unsure whether I am approaching it correctly. I have a following data:
Set
Sample
Repet.
Response
1
1
1
y1
1
1
2
y2
1
2
1
y3
1
2
...
- 11
1
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50
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Opposite results using Bayesian (STAN) vs Multilevel model (nlme). How is this possible?
My datasets contains the median wages and the cumulative installed wind-capacity for 4000 counties over a period of 20 years. The wages tend to rise over the period and the capacity tends to highly ...
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1
vote
0
answers
69
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simr Failing to Run, "observed power calculation"
I am analyzing simulated delay-discounting data. The response variable is reaction time in milliseconds. K is the scaling factor describing how much value is affected by delay. College Year is from 1-...
- 11
2
votes
1
answer
24
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LMEM - When is it okay to not treat repeated measures as a random effect? And other related questions
Design: I have 3 groups, each subject was tested 3 times (3 trials) per time point, on three different time points.
The Independent variables are: Group (A,B, or C), Trial (1, 2, or 3), and Time (0, 2,...
- 55
4
votes
0
answers
73
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Major discordance between uncertainties estimated by `predictInterval()` and `bootMer()` for binomial GLMM with cloglog link
We have been using predictInterval() from the merTools package to bootstrap uncertainty for binomial GLMM models (complementary ...
0
votes
1
answer
49
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lmerMod vs lmerModLmerTest - what are the differences and which is correct?
I have three trials, want to know if the order of trial affected the outcome. I was checking my work with ChatGPT and noticed a discrepancy between their results and mine. This is the dummy code from ...
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1
vote
1
answer
42
views
R how best to model continuous bimodal survival data using lmer and glmmTMB that includes values of 0 and 1
I am attempting to model bimodal continuous coral survival data that includes values of 0 and 1 (0-100% survival).
I have attempted to use linear mixed effects models (lmer and glmmTMB) with a few ...
- 221
2
votes
1
answer
158
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predict() function fails for lmer in R when NAs present in dataset
The issue is not how to format/obtain data but how to run predictions for linear mixed effect model for given set os estimated fixed effects in case of NAs present in the data.
The predict() function ...
- 316
1
vote
0
answers
32
views
Would it be okay to have a predictor that overlaps with the variable used as a random effect?
I will work with a predictor based on a Countries' Tightness index (numerical), so there’s one value for each country. I'll be collecting data in 50 countries, but I expect the number of participants ...
- 375
0
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0
answers
51
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P_values of 1 in LMM
Our team had words learning experiment and we decided to process the data with LMM
That the data structure, it's event-related potential(ERP) on different time intervals and
and then different ...
4
votes
1
answer
133
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Linear Mixed-effects Modelling for Mouse Tumor Growth Data
I tried going through the available materials online for this issue, but I did not manage to find many great resources. I would greatly appreciate any guidance or advice you could provide.
I have mice ...
- 41
2
votes
1
answer
35
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How can I compare one group to the mean of all other groups in a longitudinal mixed-effects regression?
I have a longitudinal mixed-effects regression comparing change in depression between two timepoints across 12 groups. I'd like to know if the control group is significantly less effective in reducing ...
- 413
3
votes
1
answer
88
views
Interpretation lmer output with z-score standardized coefficients
I've been running lmer() (in the lme4 package) on my data using this formula:
...
- 31
0
votes
0
answers
41
views
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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7
votes
1
answer
135
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Using proportions as a measure of nest success in a glmm
I want to run a GLMM to see if a conservation intervention had an effect on the nesting success of a shore-breeding bird. I'm comparing this against a control where no intervention was used. I used ...
- 71
7
votes
3
answers
481
views
If the categorical variable is retained in my final model in R, then why does the post hoc analysis say the levels do not differ?
I am performing model selection in R with the anova() function, and my categorical variable was maintained in my final model, but when I did a post hoc analysis with the emmeans() function, it told me ...
- 71
1
vote
0
answers
26
views
How to model an alternating relationship (low, high, low, high, low, high) for mixed effects model
I'm trying to get my head around running more complex mixed models in R (only previously run time-series repeated measures). I have some data from a study where participants completed a series of ...
- 121
0
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0
answers
44
views
glmer estimate is negative, but should be positive
I'm looking at a glmer for my masters thesis research (I cannot share the data until after thesis is completed so I will try to be very explicit in the descriptions).
But to summarize, my dependent ...
0
votes
0
answers
18
views
Doubts in interpreting 2 way interaction lme [duplicate]
I have some doubts in interpreting my data. So, if I have this model ...
- 33
3
votes
1
answer
48
views
Data format for mixed effects model lme4
I have a dataset from participants that were assigned to a random condition (full factorial 3x3x3 design) that varies on Feedback (three levels), Content (three levels), and Design (three levels). ...
- 51
3
votes
1
answer
101
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Interaction as main effect in lme4 vs. nlme
Let's say I am trying to see if there are speed differences among different types of cars (e.g., jeep, SUV, truck, sports car). I also want to see whether the car store (A, B, C, D, E) has an effect ...
- 33
0
votes
0
answers
24
views
Using differential scores instead of the interaction term as the "IV" for mediation (lmer)
I’m planning to do a mediation analysis using the mediation package in R.
There are two groups of participants in my experiment (categorical IV group, between subject, two levels) completing a task ...
- 1
3
votes
2
answers
181
views
Do estimated conditional modes of random effects follow a MVN in a linear mixed-effects model?
In an example provided in the tutorial GLMM worked examples, a linear mixed-effects model is fitted to the data on tundra ecosystems (from Belshe et al., 2013) with the following specification:
...
1
vote
1
answer
61
views
How to manipulate crossed and nested random effects in nlme model
I've seen some older posts on this but I am really struggling. I am fitting nutrient data and my data is I think to large to dput for posting, I tried to sub sample the data for the purpose of posting ...
- 11
3
votes
2
answers
88
views
Using Zero inflated GlMM when you have too many zeros
I am trying to understand the influence of several predictors (n=8) on the presence or absence of a species using generalized linear mixed models. Unfortunately, I do not have great data. I have 13000 ...
- 41
4
votes
1
answer
75
views
Non normal data in a LMM; beginners question
I am new to statistics and am seeking guidance on analyzing the effects of earthworms on litter-derived carbon using R.
I conducted an experiment to assess the impact of earthworm presence (with three ...
3
votes
1
answer
252
views
Should i exclude random effects from a model if the random effect itself has missing data?
I have found a number of questions relating to missing data in fixed effects and how packages like lme4 handle this in mixed models. For example, here. However, I ...
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2
votes
2
answers
89
views
Comparing Linear Mixed Models with and without interaction terms
I would like to compare different models with and without interaction terms to see which one is the best fit for my data. I just wanted to check that my approach is correct.
I construct my models like ...
- 133
3
votes
3
answers
128
views
Contrasts for type III ANOVA on mixed effects model (lme) in R
I'm running a series of mixed effects models using nlme in R. Here is an example of my final model:
...
- 97
2
votes
1
answer
68
views
Mathematical reproduction and understanding of lme4 results for linear mixed model with one random intercept in R
The objective of this post is to MATHEMATICALLY recreate the results given by lmer for the following linear mixed model.
Suppose that we have $n$ test subjects. For ...
- 639
1
vote
1
answer
49
views
How do I compute the intra-rater intraclass correlation for a study design with some repeated measures?
How do I compute the intra-rater intraclass correlation for a study design with some repeated measures?
The study had approximately 1000 subjects rated (continuously 0-100%) by 500 raters. Each rater ...
- 131
3
votes
1
answer
75
views
Is random slope meaningful when the relevant fixed effect is not significant?
I am building a liner mixed model with the following syntax:
$$
y \sim \text{run} + (1 + \text{run} \mid \text{subjects})
$$
The summary is as follows:
The fixed effect of $\text{run}$ is not ...
- 113
1
vote
0
answers
25
views
anova.mitml.results giving high df2 when comparing nested models
I'm comparing nested models using anova.mitml.results to test my fixed effects.
I have 25 imputed datasets, 231 participants per time measure x 3 time measures. I'm ...
2
votes
1
answer
52
views
Inflated fixed effects in mixed-effects logistic regression model
I have a dataset with multiple observations per ID and a binary outcome. I am trying to fit a mixed-effects logistic regression, however, the fixed effect estimate of the intercept is extremely large ...
- 123
4
votes
1
answer
65
views
How do I best fit my linear mixed effect model with lmer() from the "lme4" R-package?
So, I'm pretty new to R and modeling with lmer from the "lme4" package. I would love some help on how to fit my model to answer my research question; if different grab types are comparable, ...
- 43
1
vote
0
answers
56
views
Error in lmerTest: The random-effects parameters and the residual variance (or scale parameter) are probably unidentifiable
I know that there have been similar questions before, but I dont still get it.
I would like to estimate a multilevel model with repeated measures in R using the package “lmerTest”. The model ...
- 11
1
vote
2
answers
46
views
Appropriate Linear Mixed Model for nested data
I'm asking for help with the structure of a linear mixed model I'm trying to run. Here is the description of my study:
I am studying the effect of different stand types (Oak pure, Pine pure and Mixed) ...
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0
votes
0
answers
19
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Linear mixed model with dependent variable range constrained by predictor
I conducted an experiment where participants rated stimuli on a visual analog scale with a range between 0 (lowest possible rating) and 100 (highest) under two viewing conditions (restricted exposure ...
- 41
1
vote
1
answer
35
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Should I Include Visit as Both a Fixed Effect and Random Effect in a Longitudinal Mixed-Effects Model with Interactions?
I'm working on a longitudinal analysis using the nlme package in R, where I'm modeling the effect of treatment (tx) and menopausal status (menscat) on a biomarker level that tested at two visits: V00 ...
- 135
0
votes
0
answers
21
views
How to interpret the output for nested random factors in glmer and how to put it in a table
I am looking at an alternation of a character in a word using a congressional Hansard. I have a binary outcome dependent variable (kuni), the date of the meeting expressed as the standardized number ...
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2
votes
1
answer
92
views
R lmer help understanding my mixed model output
Question: How does urbanization impact the body size of bee species that differ in their functional traits?
Something we may expect is that social bees are often larger and would be distributed ...
- 209
2
votes
1
answer
85
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Understanding when to use a negative binomial GLMM
I have 16 birds (191978,191984, 191977, 191980, 191986, 201446, 191983, 201447, 211598, 211590, 211595, 191981, 211591, 201441, 201445, 211592). There are 6 males and 10 females. The dataset is called ...
- 21
0
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0
answers
12
views
Meaning of lognormal in performance::check_distribution() in R [duplicate]
I modeled my data using lme4:lmer() function. Since the model's performance was not satisfactory, I used function performance::check_distribution() which suggested that both predicted distribution of ...
- 1
1
vote
1
answer
58
views
nlme crossed random effects and autoregressive covariance structure
I would like to ask you two specific questions regarding a model in which crossed random effects and autoregressive covariance structure (AR1 -->
therefore use the package ...
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