1
vote
0answers
5 views

lme / lmer - split-plot with Non orthogonal subdesign

I have an agricultural field experiment (testing a plant protection agent): Split plot design with: ...
0
votes
0answers
23 views

Cannot do Tukey test in multcomp

After performing series of linear mixed models in lme4 to justify which model with which level of interaction to be used, now I would like to do the Tukey's test for multiple comparison. So first, I ...
0
votes
0answers
14 views

Two-way interaction: interpret output from LMM in lmer

I have asked a question in this topic relating interpreting two- and three-way interactions in this link: How to interpret 2-way and 3-way interaction in lmer? ...
0
votes
0answers
14 views

Interpretation of three-way interaction in an output of lmer

I am using lme4 to run a three-way interaction model. I have three independent variables: animal (rat, lion, dog), color (red, green, blue) and sex (male, female). The baselines are as follows: ...
2
votes
2answers
66 views

A good source to understand interaction in LMM?

I would like to know more about interaction in LMM using lmer. Can you recommend me any books, articles, websites?
0
votes
0answers
14 views

Do I need a planned contrast or post-hoc analysis when doing LMM in R?

I am doing a LMM in R and would like to know if I need to do a planned contrast or a post-hoc analysis. From my understanding, the LMM in R already provideds me a planned contrasts and if I have ...
2
votes
0answers
29 views

predict() in lmer regression, but I need it only 2 categories [migrated]

I am attempting to estimate a multilevel model. My code is: ...
2
votes
0answers
40 views

Multilevel model specification for count data (with overdispersion) in R

I would like to specify a multilevel model including the following variables: DV: count data, i.e. a score value between 0 and 13 (resulting from an additive index) for each individual Individual ...
2
votes
0answers
41 views

lmer giving worse performance than lm

I am having trouble training a model for nested data about house prices. Lets say my data looks like following: ...
0
votes
0answers
42 views

LMM models with two difference reference categories yield two different results

I have run LMM models with different reference categories and this yield different results: ...
4
votes
1answer
61 views

Notation for multilevel modeling

The formula one needs to specify for training a multilevel model (using lmer from lme4 R ...
4
votes
0answers
73 views

Meaning of a convergence warning in glmer

I am using the glmer function from the lme4 package in R, and I'm using the bobyqa optimizer ...
0
votes
0answers
19 views

Subjects:condition interaction random effect in a growth model

I'm investigating the effect of 'Condition' (3 levels: Quiet, Intelligible, Unintelligible) on pupil response over time (intercept, linear, cubic, quadratic, quartic and quintic terms). When I use ...
0
votes
0answers
28 views

Growth curve analysis on orthogonal polynomial terms

I am conducting a study which is looking at the effect of 'Condition' (Quiet, Intelligible, Unintelligible) on the pupil(eye) response over time. Upon visual inspection of my data plots, pupil ...
0
votes
0answers
28 views

ANOVA in lmerTest for in-between study with repeated measurements

I have a bit of trouble understanding how to formulate a correct formula in R using the lmerTest-library. Let’s assume there is an 2x2 in-between design with repeated measurements. Those repeated ...
0
votes
0answers
52 views

Afex does not give me all p-values of all parameters. What should I do?

I have installed the package afex with this formula: ...
1
vote
0answers
40 views

How to get p-value for fixed-effects by model comparsion?

I am doing linear mixed model using lme4. According to Winter (2013, http://www.bodowinter.com/tutorial/bw_LME_tutorial2.pdf), as the new version of R does not give p-values due to inconclusion of ...
0
votes
0answers
25 views

How do we know the LMM model has to add random slope with random intercept?

When I read the literature about random intercept, random slope, and random intercept and slope model, I usually see the graph that they have lines for each participant. I do not know how to plot such ...
2
votes
0answers
47 views

What should the appropriate model for my data look like?

My research objective is that I would like to test if some sounds in languages are similar to each other in terms of duration. In my situation, I have 4 languages with 5 sounds. The first three ...
0
votes
1answer
48 views

Why does the log-likelihood change when a variable is linearly transformed in a hierarchical model?

I ran into (what I think is) an inconsistency when running a random-intercept model (using the lmer function in the lme4 package in R). Here is what I do: I first run a model with a set of ...
1
vote
1answer
129 views

How to interpret 2-way and 3-way interaction in lmer?

I have a problem with interpreting 2-way and 3-way interactions in lmer. My DV is height which is a continuous variable. All IVs are categorical variables. The first factor is animal, either rat or ...
0
votes
0answers
36 views

“non-monotonic profile”: what should I do when getting this when running confint(lmer)?

I am new to R and I have run the lmer in lme4. In the model summary, there is no any warning message, but when I ask for ...
0
votes
0answers
30 views

Do you know any paper reporting only CI instead of p value when the analysis is from LMM in lmer4?

I'm finding articles that report only CI, instead of p value. All articles I found will report p value despite its issue is inconclusive. I would like to look at how they put the important information ...
0
votes
0answers
23 views

Can I select IV from their t value and confidence intervals in LMM in lmer?

As the issue of p value is still inconclusive and many papers point out that the confidence intervals are more informative in selecting factors in fixed effects, I would like to ask about ...
0
votes
0answers
21 views

within subjects design with condition rotated across presentation lists (staggered cross-over design?)

In my field, it is common to rotate levels of an experimental condition across different presentation lists in a within-subjects design. This is done to prevent a particular participant from seeing ...
2
votes
1answer
90 views

Dropping term for correlation between random effects in lme and interpretting summary output

I want to fit a model without a correlation term between the random effects with lme. In lmer this is fairly straighforward.... ...
1
vote
1answer
63 views

lsmeans vs. differences between lsmeans

I calculated the least-squares means and standard errors for a linear mixed model. I am attempting to plot the lsmeans and standard errors for the combinations of the two factors, but I notice a ...
2
votes
1answer
72 views

Interpreting random slopes equal to 0 using lmer in R

I have just started working with mixed models and the lme4 package and was after some advice interpreting some results. I have a data set looking at the change in nest height of birds (NAP) over time ...
0
votes
0answers
51 views

Interpreting coefficients for random effects models with extremely unbalanced data

I'm currently working with a data set that has numerous samples collected over time at different sites in a study area, and I'm interested in detecting a trend over time for that area. I know that in ...
1
vote
0answers
36 views

Translating from aov to lmer or lme with three levels of nesting

I have data from a split-plot (or repeated measure) experiment with three factors: A is random, B is fixed and nested within A, and C is fixed and nested within B. I can test for the effect of B, C ...
11
votes
1answer
222 views

Likelihood ratio test - lmer R - Non-nested models

I am currently reviewing some work and have come across the following, which seems wrong to me. Two mixed models are fitted (in R) using lmer. The models are non-nested and are compared by ...
2
votes
1answer
255 views

How to fix an overdispersion in a Poisson GLMM with lmer function in R?

I want to model counts as being dependent on two nominal variables, one continuous variable (all as fixed effects) with 3rd-order interactions and one grouping variable (as random effect). However, I ...
6
votes
1answer
81 views

Dealing with correlating fixed effects in a linear mixed-effects analysis

My question is about the best way to estimate the effect of a predictor on a dependent variable, while accounting for several other predictors that may correlate with the predictor of interest. I'm ...
0
votes
0answers
64 views

Effect size in plotLMER.fnc

I'm working with linear mixed models. I used plotlmer.func, in the package lmerConvenienceFunctions to build a graphical ...
0
votes
1answer
47 views

Null GLMM Poisson underestimate the mean of the response variable. Is it indicative of poor fitting?

I want to test the fixed and random effects of some covariates on a discrete variable with non negative values. In exploratory analysis I fitted a null Poisson GLM and an null Poisson GLMM. However, ...
1
vote
1answer
245 views

Changing reference level for contrasts changes results in R 3.0.2/lme4 1.1-2 vs. R 2.15.0/lme4 .999999-0

I hope this is an appropriate forum to post this question. I recently upgraded my R software from 2.15.0 to 3.0.2. I also upgraded the lme4 package from .999999-0 to 1.1-2. After doing so, the results ...
2
votes
0answers
85 views

Why is there a dramatic difference between aov and lmer?

I have a mixed model and the data looks like this: ...
4
votes
1answer
206 views

Unable to fit repeated measures in R

I've been trying to fit a repeated measures model in R using lmer but I get an error message. I've used SAS in the past and I was able to fit a somewhat similar ...
1
vote
0answers
72 views

Multivariate Mixed model in nlme

I have two correlated response variables ($y_1,y_2$) explained by the same covariate set ($x_1,x_2$), each with mean = 0. I have a random grouping factor ('group') which is heteroskedastic ($group ...
2
votes
1answer
77 views

How do you specify a binary time-series-cross-section model in lme4?

I have a standard binary time-series–cross-section (BTSCS) model that I would like to specify as a mixed effects model using the lme4 package. I've read elsewhere that time-series–cross-section (TSCS) ...
2
votes
3answers
850 views

Checking assumptions lmer/lme mixed models in R

I ran a repeated design whereby I tested 30 males and 30 females across three different tasks. I want to understand how the behaviour of males and females is different and how that depends on the ...
0
votes
1answer
92 views

Mixed model fitted on time course data

I have some time course data which plotted looks like this: I have fitted a mixed model to my raw datapoints with R's lme4::lmer, as seen in this code. In ...
6
votes
1answer
353 views

Why can't I match lmer for family = binomial?

I'd like to match the outputs of lmer (really glmer) with a toy binomial example. I've read the vignettes and believe I understand what's going on. But apparently I do not. After getting stuck, I ...
0
votes
1answer
63 views

R linear models - category IDs as strings or ints

I am trying to fit a linear model (lme4::lmer()) to my data in R. I would like to look at a number of things, including "scrambling" of visual stimuli and ...
0
votes
0answers
31 views

Group effects where there is a single group

Suppose I have a table of subjects and measurements as follows subject measurement s1 1 s1 2 s1 3 s1 4 s1 5 s1 6 s1 7 s1 8 s1 9 s1 ...
3
votes
1answer
116 views

How to deal with collinearity in lme with categorical IV with > 2 levels

I'm analysing data from our experiment. We had participants in 4 groups, each participant was measured 4 times. We measured cortisol in saliva, so it leads us to the linear mixed models, because the ...
4
votes
0answers
300 views

What does it mean that random effects are highly correlated?

What does it mean when two random effects are highly or perfectly correlated? That is, in R when you call summary on a mixed model object, under "Random effects" "corr" is 1 or -1. ...
6
votes
0answers
560 views

What does the anova() command do with a lmer model object?

Hopefully this is a question that someone here can answer for me on the nature of decomposing sums of squares from a mixed-effects model fit with lmer (from the ...
5
votes
2answers
328 views

Have I correctly specified my model in lmer?

I have scoured lots of help sites and am still confused about how to specify more complicated nested terms in a mixed model as well. I am also confused as the use of ...