All Questions
33 questions
18
votes
4
answers
28k
views
Interpreting random effect variance in glmer
I'm revising a paper on pollination, where the data are binomially distributed (fruit matures or does not). So I used glmer with one random effect (individual plant)...
- 313
16
votes
1
answer
21k
views
How to estimate variance components with lmer for models with random effects and compare them with lme results
I performed an experiment where I raised different families coming from two different source populations. Each family was assigned one of two treatments. After the experiment I measured several traits ...
- 381
13
votes
2
answers
5k
views
Are $R^2$ for GLMM useful for modelers but not necessarily for readers?
The short version:
1)Are there any published critiques of the use of $R^2$ for GLMMs, in particular the popular approach of Nakagawa & Schielzeth (2013) A general and simple method for obtaining $...
- 2,173
10
votes
2
answers
7k
views
How can I test for differences in variation between groups in a mixed model (lme4)?
I would like to test for differences in variation, not in means, between two sites. By looking at a boxplot of my data I see that bird song in one site look much more variable in length than in ...
- 101
9
votes
1
answer
999
views
What to do with heterogeneity of variance when spread decreases with larger fitted values
I am trying to produce a linear mixed model the R code is as follows.
lme(Average.payoff~Game+Type+Others.Type+Game:Type+Game:Others.Type+Type:Others.Type,random=~1|Subjects,method="REML", data=...
- 1,193
7
votes
2
answers
395
views
Don't understand why glmm random effect variance is zero. Have reviewed similar questions still dont get it
I study a colonially-nesting bird species. I am trying to perform an AICc evaluation of GLMMs for a nest site selection study. I collected data at nest sites and paired random sites. I want to ...
- 83
7
votes
1
answer
8k
views
Residual variance for glmer
I am running a glmer model and I want to determine the total variance. My data is for survival and it is coded as 0 and 1, where 1 represents that the individual survived and 0 represents that the ...
- 71
4
votes
1
answer
64
views
Calculating variance of a dependent variable with multiple fixed effects
I am kind of a stats noob but I figure someone here may have some insight. I am running a linear mixed effects model in R, reminiscent of what's below:
...
- 121
3
votes
1
answer
189
views
How to compute correlation of random slopes for X between two Conditions with (X*Condition|subject) model in lme4?
We have the following model:
Y ~ X*Condition + (X*Condition|subject)
Y = dichotomous variable; values 0,1
X = continous variable; values ca. 0-3000
Condition ...
- 1,782
3
votes
1
answer
1k
views
Understanding variance components with an interaction structure
Suppose that I have the following dataset in R:
library(lme4)
data(Machines,package='nlme')
mydata <- Machines[Machines$Machine!='C',]
There are 3 levels with ...
- 2,769
3
votes
1
answer
7k
views
Proper use of weights argument in linear mixed model [lme()]?
After attempting to produce a linear mixed model I was left with a great deal of heterogeneity.
...
- 1,193
2
votes
2
answers
248
views
How to estimate proportions of variance in outcome variable attributable to each individual fixed effect variable in lmer?
I am using multivariate models in lme4 to try to work out, quantify and compare the effects on a single outcome variable of a large group of fixed effects variables. Because the data are at week and ...
- 213
2
votes
1
answer
2k
views
Error with RLRsim package while testing for variance components
I am trying to fit the mixed effects model and test for a variance component using RLRsim package.
$$
Y_{ik} = \alpha + \mu_{k} + \beta G_{i} + Z_{k}G_{i} + b_{i} + \epsilon_{ik}
$$
Random ...
- 43
2
votes
1
answer
3k
views
How to get the proportion variance explained by each predictor in an lmer() model?
Is there a way to get the proportion of variance explained by individual fixed effects in a mixed effects model?
I thought that the partR2 package could do this, ...
- 2,701
2
votes
1
answer
2k
views
Partitioning variance within a level in a 3-level mixed effects model
I have a 3-level repeated measures model setup observations (level-1) nested within patients (level-2) nested within providers (level-3). One of my questions is the percentage of variance explained at ...
- 163
2
votes
0
answers
24
views
How to construct GLMM with differing random effect variance structure by group?
I have a longitudinal dataset with a normally distributed outcome variable, a normally distributed predictor variable, and a binary grouping variable. I am trying to construct a GLMM with differing ...
- 63
2
votes
0
answers
162
views
How to estimate variance for identical & fraternal twins with a mixed model
I am using the twins data from OpenMx and am curious to estimate the empirical covariance structure for BMI differences in monozygous and dizygous twins:
...
- 64.8k
2
votes
0
answers
295
views
Using lme4 and glmer (logit) to estimate variances of random intercepts
Our data set consists of a matrix with a few thousand respondents (rows), many items of ten surveys (columns), and all 0’s and 1’s for a certain survey answering behaviour (either responding ‘I don’t ...
- 21
2
votes
0
answers
452
views
Multiple comparisons for variance structure in R lme fit
How can I compare variances for different levels of a factor in a mixed effect model?
I'm fitting a mixed effects model (in R using the ...
- 121
1
vote
1
answer
85
views
Do I need a nested random effect if I do not care about decomposing variance within clusters?
Consider I have a linear mixed effect model fitted via the R package lme4 with a nested random effect structure as:
model<-lmer(y~x+(1|A/B/C))
If I look at the ...
- 89
1
vote
1
answer
3k
views
How to find variance (in %) explained within the output coefficients?
I'm not very good with technical details or equations in stats as I'm quite new to running these in R. So I hope that you won't mind me asking these perhaps simple questions and also I would ...
- 105
1
vote
1
answer
178
views
Estimation of random intercept and random slope for singleton cluster in multilevel modeling
I am performing some multilevel analyses with the R package lme4.
The study design is longitudinal with the hierachical structure of observations (L1) nested into study participants (L2). I have 215 ...
1
vote
0
answers
26
views
Can slope variance be greater than ICC in lmer results
My question is can variance of the random slope be larger than random intercept variance? And if so, what would it mean in terms of group level variation?
- 11
1
vote
0
answers
85
views
Is regression towards the mean happening when we use a control group?
I have a subset of 40000 participants in my study. From those I would like to study those with higher weight longitudinally, and compare them with those with healthy weight.
I observe, that those with ...
- 270
1
vote
1
answer
112
views
Run mixed effect model where one fixed effects shows no variation within the random factor levels
I want to run a mixed effect model to test the effect of temperature and SLA on Herbivory. In my case, the random factor is plot since my samples are nested within ...
- 11
1
vote
0
answers
288
views
Specify variance structure TOEP(1) in lmer for mixed model
How can I do the following job in R? More specific: how can I define type=toep(1) in R?
...
- 11
0
votes
1
answer
19
views
How can I get the population variance from a mixed model?
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, ...
- 33
0
votes
2
answers
310
views
Anova and mixed effect models (lm4 / nlme) return complete different effects
As a continuation of a previous topic, I would like to address a similar experience.
Subjects completed an experiment in which their electrodermal activity was recorded. For each subject there are 72 ...
AlexKas
0
votes
1
answer
225
views
Calculating a mixed model using pdIdent var-cov matrix
I have a question in mixed models. I'm quite new at this field and I'm trying to calculate a model in which "y" is predicted according to multiple covariates (Age,gender,BMI) and the random variable "...
- 1
0
votes
0
answers
29
views
Why does the ICC differ when comparing multilevel models with using log transformations of the outcome variable in R using lme4?
I'm currently working on a multilevel modeling project in R utilizing the lme4 package. The primary aim of the research is to assess the relative importance of between-family and within-family ...
- 41
0
votes
0
answers
26
views
Linear mixed models unequeal group variances and model fit
I have data from two groups (divisions) of participants that consider attention lapses. The question is, first, do the number of attention lapses change over the two testings, and second, do the ...
- 77
0
votes
0
answers
252
views
How does lme4 calculate residual variance for an LMM?
How does the lmer() function calculate residual variance for an LMM? If I code a model and then try to manually calculate residuals, the variance of the manually ...
- 63
0
votes
0
answers
53
views
difference between estmated and empirica variance matrix of lmer random effects
Does anyone know why when I perform a lmer analysis (here using the builtin sleepstudy dataset) the estimated variance matrix of the random effects from VarCorr are so different from the variance of ...
- 360