All Questions
Tagged with lme4-nlme confidence-interval
56 questions
2
votes
1
answer
99
views
Why is it recommended to keep use.u=T (in bootMer) when doing parametric bootstrap for lmer models?
I am performing a parametric bootstrap with the intention of using the simulated values to create confidence intervals for my coefficients in a mixed model. I saw that it was generally recommended to ...
- 21
2
votes
1
answer
298
views
Confidence interval for GLMM
I am conducting a GLMM for my bachelors thesis and I am wondering, how I can calculate and whether it is common to report confidence intervals for the models' estimates.
This is the model I fitted on ...
- 31
0
votes
0
answers
103
views
Plotting confidence and means from logistic regression in ggplot2
My data are for an experiment asking participants to detect a tone (Response= 1 or 0) in different (within-participant) conditions. I am interested in how participants' scores on separate ...
- 542
0
votes
1
answer
451
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Using 95% confidence intervals for pairwise comparisons in mixed effects model
I'm running mixed effects models in R using Treatment and Species as crossed predictors and Group as a random effect using the nlme package, like so:
...
- 97
3
votes
1
answer
102
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Summary output of binomial GLMM shows significant effects, but graph shows overlapping CI error bars?
I have run this binomial GLMM:
...
0
votes
0
answers
45
views
Reconciling: A mixed model with random effect shows significant differences in fixed effects but has overlapping CI?
I'm trying to reconcile with a mixed model with random effect shows significant differences in fixed effects but has overlapping confidence intervals.
Here is data computing temperature of litterfall ...
- 21
1
vote
0
answers
117
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bootstrapped confidence interval for glmer model with identity link
In an experiment Subjects decide as fast as possible whether letter strings presented on screen are real Words or non-words and reaction time (RT) in milliseconds is recorded. We want to know for ...
- 21
1
vote
1
answer
192
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Non significant difference between condition from LME model, when Confidence intervals clearly non overlapping
Edit with graph:
I am struggling a bit conceptually to make sense of a result I get when applying a linear mixed model to my reaction time data.
I have a 2x2 within subjects design. When I plot the ...
- 21
1
vote
0
answers
38
views
Limitations with effect sizes and confidence intervals (fixed effects) with lmer and effectsize in R
Background
I've been running a couple of lmer() models with different data and noticed something I cannot really grasp.
The models range from simple to more complicated
(e.g. DV ~ ...
- 11
3
votes
1
answer
662
views
p-values and confidence intervals are not matching
My model is here. I'm running a bootstrapping mixed-effects model with "case" type with lmersmapler. The thing is, now I'm using bootstrap_pvals()to ...
- 843
5
votes
2
answers
195
views
No variance in binomial glmer yields problematic CI
I have a glmer with a binomial response variable and two binary predictor variables, where there are no observations for one of the four groups. I used ...
- 329
2
votes
2
answers
900
views
What can explain large Odds Ratios 95% confidence intervals in multilevel binomial logistic regression (glmer)?
I conducted a multilevel binomial regression (glmer) and I obtain quite wide confidence intervals for my odds ratio. What could be causing such large 95% CI and what can be done to provide more ...
- 23
0
votes
0
answers
20
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What can explain large Odds Ratios 95% confidence intervals in multilevel binomial logistic regression (glmer)? [duplicate]
I conducted a multilevel binomial regression (glmer) and I obtain quite wide confidence intervals for my odds ratio. What could be causing such large 95% CI and what can be done to provide more ...
- 23
3
votes
1
answer
949
views
Interpretation glmer output and CI with interaction for non-reference level
I could use some help interpreting a glmer output? I am unsure how to get the odds of a non-reference level since there is an interaction. I have observations of ...
- 329
1
vote
0
answers
236
views
Confidence Intervals for ICC
I was wondering if anyone might know of a way to calculate confidence intervals around an ICC(1) value? I'm running a multilevel model using the lmer() function in lme4 where I'm interested in seeing ...
- 71
2
votes
1
answer
685
views
lmer fixed effects t-statistic interpretation
I'm struggling to explain some output from a linear mixed effects model. I've done a lot of reading and searching of previous questions but haven't been able to find what I'm looking for.
I have 3 ...
- 41
1
vote
1
answer
3k
views
R: Plotting lmer confidence intervals per faceted group
I am using lme4 package to run a Mixed-Effects Model followed by the predict function ot obtain fitting lines per invidual level and group level. Yet, I am ...
- 13
1
vote
0
answers
725
views
The ggpredict function returns incomplete confidence intervals for a linear mixed midel with an interaction
I am trying to create a plot showing the LMM prediction with confidence intervals using the ggpredict function from the ggeffect ...
3
votes
1
answer
2k
views
Confidence intervals in probabilities for mixed effects logistic regression
A while back I was helped to get correct confidence intervals for predicted probabilities in a logistic regression model: Correct interpretation of confidence interval for logistic regression?
Now, I ...
- 105
0
votes
0
answers
112
views
glmer r significant slope but bootstrap confidence interval includes zero
I am running a generalized linear mixed model in r using glmer. The slope (year) from the model is significant (<0.05), however, when I bootstrap the slope to get the confidence interval it ...
- 11
5
votes
1
answer
144
views
Why is the coverage of this lme4 confidence interval less than 95%?
I have data that can be described using the model $y_{i j} = \alpha_i + \epsilon_{i j}$, where $\alpha_i \sim \text{N}(\mu_{\alpha}, \sigma_{\alpha}^2)$ and $\epsilon_{i j} \sim \text{N}(0, \sigma_{\...
- 83
1
vote
0
answers
133
views
Bootstrap confidence intervals for betas in a linear mixed model
I am trying to calculate bootstrap intervals for my beta coefficients in linear mixed effect models.
I used the lme()function from the ...
- 433
0
votes
0
answers
168
views
lmer with random effects shows insignificant interaction term despite confidence intervals not overlapping
I am trying to interpret an analysis on urchin biomass and how the means differ between 2 sites (Waikiki and Hanauma Bay) and 2 experimental treatments (low and high shelter). Because of the nature ...
- 221
1
vote
1
answer
232
views
Why the variation between CIs computed with emmeans and confint are so high?
I have some strangeness going on when calculating CIs for my model.
I've found 2 ways to do this, and I decided to try them both (emmeans and confint).
I have 6 timepoint and 2 groups.
My model looks ...
- 107
0
votes
0
answers
1k
views
GLMM. Why are my confidence intervals so wide when my p-values are so small?
I am trying to find out whether there is a significant effect of Treatment (factor with 3 levels: GR, BC and WF) on the number of moths captured per night in a field experiment. I have 15 Blocks that ...
- 41
1
vote
1
answer
344
views
Why are my confidence intervals much larger in glmmADMB than glmer.nb?
I'm plotting 3-way interaction terms from a negative binomial models, and tested the models in two packages to check my work and as a sensitivity analysis. I used the effect function to extract the ...
- 658
0
votes
0
answers
95
views
R - zero biased data, glmer.nb, properly counting confidence intervals
any suggestions how to count confidence intervals from zero biased data? I've counted generalized linear model using glmer.nb function. I have to make graph but I was told that confidence intervals ...
1
vote
1
answer
2k
views
Odds ratio confidence intervals and p-values suggest different conclusions in a binary logistic mixed-effects model (glmer)
I am running a generalized linear mixed-effects model in R using the glmer function of lme4. The outcome variable is trial-level accuracy in a task (incorrect trials are 0, correct trials are 1), and ...
- 315
2
votes
1
answer
550
views
My confidence intervals for a negative binomial mixed-effect model are not right?
I'm using glmms with a negative binomial distribution from the lme4 package. I've run my model (Checked for singularity) and have plotted the fitted values along with the 95% confidence intervals for ...
- 354
1
vote
0
answers
29
views
Simulated estimate from a linear mixed model with random intercepts
I wanted to see if there was a quick way to get a bootstrapped parameter estimate and CI using confint() from merTools?
...
- 11
6
votes
1
answer
2k
views
Build confidence intervals for random effects in intercept only models
I'm building a Poisson model for a rate between an outcome and an offset (to be precise between the observed and predicted values of a phenomenon). I want to get this rate + confidence intervals (CI) ...
- 2,949
3
votes
1
answer
244
views
1
vote
0
answers
385
views
confidence intervals for GLMER model
I'm trying to calculate confidence intervals for GLMER model. I heard that there are two ways I could do it:
Number 1:
exp(Estimate Std + 1.96 * Std Error)
exp(ES - 1.96* Std Error)
Number 2:
m&...
- 47
4
votes
1
answer
848
views
R - lme4 nlmer confidence interval
I have a question regarding confidence intervals from a non-linear mixed effects model. I ran the following model on my data:
...
- 165
2
votes
0
answers
84
views
Interpreting interactions of mixed model estimates correctly?
I have data of the following form:
...
- 2,345
3
votes
1
answer
14k
views
Confidence intervals from bootMer in R, and pros/cons of different interval types [duplicate]
I've created a mixed effects model using lme4 in R:
...
- 2,345
5
votes
0
answers
2k
views
Prediction intervals for generalized least squares model with heteroscedastic errors
I wanted to model some data with heteroscedastic errors using a gls model of the form
...
- 3,417
0
votes
1
answer
580
views
GLMERTREE: confidence intervals for regression coefficients at terminal nodes and implications of fixed effects in lmer/random component
I've built a lmertree model using the GLMERTREE package with random slope and intercept, a treatment variable, and a "partitioning" variable. I've attached a toy dataset and the associated model:
...
- 35
2
votes
1
answer
3k
views
R lme4 interpret MLM confidence intervals
I'm using the lme4 package in R to run a multilevel model and to calculate confidence intervals:
...
- 2,361
1
vote
0
answers
181
views
Calculate confidence intervals for population estimates when spatially applying GLMM across a large region
What I'd like to calculate: I'm using glmer (lme4) with a poisson distribution to estimate a bird's total population across a large region (i.e. sum predictions). I'd like to obtain confidence ...
- 193
2
votes
0
answers
72
views
The slope of a mixed model
I want to know whether x2 is better than x1 in explaining y. My data frame looks like:
<...
- 51
1
vote
0
answers
563
views
How to calculate confidence intervals of lmer estimates using Parametric Bootstrap when variable has been transformed?
Parametric bootstraps are considered the gold standard to compute confidence intervals for linear mixed effects models. I think they also allow for easy re-transformation of model predictions to the ...
- 1,029
17
votes
1
answer
10k
views
Confidence intervals on predictions for a non-linear mixed model (nlme)
I would like to obtain 95% confidence intervals on the predictions of a non-linear mixed nlme model. As nothing standard is provided to do this within ...
3
votes
0
answers
337
views
How to calculate prediction confidence intervals for estimated mixed model change scores varying per a continuous predictor, using "lme4" in R
The Setup
I am employing a linear mixed model in R using the packages "lme4" and "lmerTest." In modeling my predicted variable, I have two time indicators set as fixed and random effects: one time ...
- 31
1
vote
1
answer
2k
views
R, glmer(), plot bootstrapped CI in graph
Using the glmer() function in the LME4-library in R I computed logistic models, of the form: $Y ~ cat1 * cont1 + (1|Subject)$ where, obviously, Y is the binomial ...
- 15
1
vote
0
answers
645
views
Bootstrapped confidence intervals for predicted probabilities seem too small (using glmer in lme4)
I am using logistic regression to examine factors affecting female reproductive status (0=inactive, 1=active) in a rodent species.
My top model includes the fixed effect of "year" and a random ...
- 41
2
votes
0
answers
309
views
Generating predicted mean values and CIs across different groups in lme4
I’ve run a mixed-effects model with crossed random effects in glmer and ultimately want to show a bar graph depicting mean predicted values (and associated confidence intervals) across years within ...
- 21
3
votes
1
answer
3k
views
R lmer confint: theta values not the same as summary values
I've been using lmer's confint procedure to compute bootstrapped confidence intervals for random effects. I noticed that extracting the theta values using "getME" produces estimates that are slightly ...
- 121
1
vote
0
answers
512
views
95% CI in nonlinear mixed-effect model {lme4} with two or more crossed random effects
I have fisheries-independent data and am interesting in estimating maturity patterns across 50 lakes that are sampled (with bias) by 4 types of gear-collections. The sampling pattern is very ...
- 11
4
votes
0
answers
2k
views
Profile likelihood confidence intervals = (-Inf Inf) in a glmer {lme4_1.1-7}
I fitted a mixed logit model with crossed random effects in lme4_1.1-7::glmer (R version 3.1.1 / OS X 10.9.4 Mavericks).
Had to simplify the maximal random-effect ...
- 133