All Questions
61 questions
2
votes
1
answer
35
views
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
0
votes
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
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
79
views
How to set contrasts for contrast in post-hoc comparison of linear mixed effect model in R?
i am new in R and studying statistical analysis for experiments, please help me~
I have 3 age groups (Y/HO/LO) and 2 conditions (Related/Unrelated). I am running a linear regression model on RT (...
- 13
0
votes
0
answers
34
views
Apply custom (ANOVA-like) contrasts to all interactions in a mixed model (with a stacked dataset)
I am conducting a multilevel mediation analysis with a multicategorical X (4 levels from a 2-by-2 design) for which I want to apply custom contrasts that code two ...
- 1
1
vote
1
answer
30
views
Interpretation of Intercept in mixed model with repeated contrasts
I am running the following logistic mixed model in lme4:
...
- 542
1
vote
0
answers
46
views
Custom contrasts in piecewise mixed effects models
I have longitudinal data from a two-group RCT in which the primary outcome was assessed at baseline, each week during the intervention, post-test and 5-month follow-up (6 times total). I am modeling ...
- 11
0
votes
0
answers
299
views
R: emtrends pairwise contrast results change when testing slopes against 0 or 1
When performing post-hoc simple slope analysis on my linear mixed effect model in R using emtrends(), I noticed that pairwise slope comparisons showed differences in the significance when I tested all ...
- 1
0
votes
1
answer
36
views
Access to the interaction of two three level factors on a mixed model
Using a mixed model (either frequentist lmer or bayesian brms) I have an issue regarding an interaction in my model.
I have two factor variable of three level : condition (0-1-2) and Tps_real (0-300-...
2
votes
0
answers
74
views
R, lme4, glmer function: How to calculate significance values for Helmert contrasts? [closed]
I am running a GLMM using the glmer function from the lme4 package in R. I would like to use a Helmert contrast to test a specific difference for the factor condition. If I run that in the glmer ...
- 21
2
votes
1
answer
111
views
Interpretation of lme4 output with different contrasts for variables
I have data assessing reaction time (RT) with 2 variables:
Variable 1: 'HighLow', with 2 levels ('High' and 'Low')
Variable 2: 'Condition', with 3 levels ('Predicted', 'Implausible', 'Plaus/Unpred')
I ...
- 542
0
votes
1
answer
165
views
Three-level variable in LME analysis - output
I am currently unsure about a three-level variable in an linear mixed effects analysis in R (lme4) - I should add that I am new to LMEs and would very much appreciate some very basic advice!
I am ...
- 3
1
vote
1
answer
1k
views
emmeans: interaction contrast with continuous variable - same se, t- and p-values?
I am analysing my own data with a linear mixed model and estimated marginal means and have made a strange observation. I have run an experimental study with three treatment groups, measuring a ...
- 75
0
votes
1
answer
337
views
How do you conduct contrasts (pairwise comparisons) for a lmer() when your IV is continuous?
I am using lmer() to run an analysis with one categorical variable with 2 levels (task) and one continuous variable (farFC). Below is the model:
...
- 113
1
vote
1
answer
266
views
Correction for multiple comparisons using sum contrasts with linear regression
I am computing the following model using the lme4 package in R:
...
- 111
1
vote
1
answer
357
views
Problems with emmeans if RE-adjustment and backtransformation from logit
In an experiment (4 sessions, 2 groups), subjects try to remember words.
We want to test
H1: the overall (marginal) main effect of group
H2: the specific interaction contrast of group and sesson1 _ 2
...
- 21
1
vote
1
answer
313
views
Calculate contrasts from lme model across specified timepoints
I have an MMRM with the below structure:
...
- 125
1
vote
1
answer
875
views
planned contrast with **emmeans** on interaction term in mixed model
I think this is simple: I want to test if a treatment (that I know a priori does something) is stronger in one group vs. the other (in the presence of random effects). This seems like it should be ...
- 353
2
votes
1
answer
734
views
How to obtain contrasts for constrained longitudinal data analysis?
I would like to apply a constrained longitudinal data analysis (cLDA) with a linear response variable of the form, y ~ Time + Treatment:Time + (1 | ID). I am using &...
- 227
1
vote
0
answers
37
views
Experiment with two within-subjects and one between-subject with linear mixed models?
I need to analyze one dataset that contain two variables measured in the same subject and one across subjects.
The variables are:
id = subject id, factor with 83 levels
tissue = factor with 2 levels (...
- 175
0
votes
1
answer
2k
views
Contrasts in logistic regression using R
I am trying to use contrasts in a logistic regression using the lme4 package.
I have two between-subject categorical variables (both with 2 levels). The first distinguishes between groups 1 and 2; the ...
0
votes
0
answers
41
views
Contrasts in LMER, one IV
I am performing my first LME. In my data set, I have one fixed factor, “Consistency” (3 levels: con, inc, pro). Subject, Passage, and Stim_set are random effects (stim set just contains a particular ...
- 135
2
votes
1
answer
1k
views
How ti specify contrasts for lmer model
I am using lmer in R to check the effect of treatment and a group on some result (y).
In my data (dat), there are 3 categorical variables and a continuous response variable:
1 id
1 treatment variable ...
- 21
1
vote
0
answers
121
views
Predefined contrasts with lme4
in my current project I'm interested in setting certain contrasts ahead of analysis. I have five experimental groups, the control one (A), two groups with low dose (B and C) of chemical and two with ...
- 31
1
vote
0
answers
504
views
Contr.sums and contr.poly question?
I know that contr.poly creates orthogonal polynomials of degree 1, 2, etc. so that you can determine if there is a particularly mathematical pattern (e.g., linear, ...
- 113
1
vote
0
answers
23
views
LRT signficiant but not planned contrasts (mixed model)
I set up multiple models (each model adding a main effect and an interaction) with glmerfrom the R package lme4.
Conducting a ...
- 433
1
vote
1
answer
346
views
Can contrasts and interaction contrasts be identical in linear mixed model?
I have a doubt with respect to the estimated marginal means of a linear mixed model.
I performed a mixed model like the one in the example below:
...
- 13
0
votes
0
answers
536
views
Use predict function for average over all levels with contrast.sum
I have a model with Machine as factorial variable. The contrast is set to "contr.sum".
...
- 21
3
votes
1
answer
89
views
Is it ok to define the contrasts after building the model?
I have this mode starting model but I need to build the random structure but I am not sure if I can do that without setting the contrasts. Variable Time is a 3-...
- 526
1
vote
1
answer
373
views
Testing contrasts in multilevel models
I'm trying to think of a way to test certain hypotheses regarding an experiment I've run. It's a 2 x 3 x 4 within-subjects, repeated-measures design. I would like to fit a (cross-classified) ...
- 73
0
votes
1
answer
231
views
Mixed model contrasts for testing whether group differences increase/decrease across time points
I'm trying to fit a lmer model in order to predict whether group differences in scores on a scale increase/decrease over time.
The dataset includes the following variables:
Dependent variable: ...
1
vote
1
answer
377
views
How to report orthogonal contrast codes?
In my linear mixed effects model, I had a significant interaction, I followed up the interaction with orthogonal contrast codes to see where the difference was.
How do I report my findings, other ...
- 147
2
votes
0
answers
269
views
Planned Contrasts in Mixed models: group with 3 levels
This analysis is based on data from https://stats.idre.ucla.edu/r/seminars/repeated-measures-analysis-with-r/ with some modifications.
Pulse measurements were made at 3 time points (1,2,3) for study ...
- 31
3
votes
1
answer
2k
views
treatment and sum contrasts, inconsistent results
I am fitting a linear mixed effect models with two factors (mPair with 6 levels, and spd_des with 3 levels) and their ...
- 539
1
vote
1
answer
317
views
changing the coding system from helmert coding to difference coding changes regression results?
EDIT: I think I have mistaken the names of the coding systems, so I changed it (in bold). The content has not changed at all, though, so I would still appreciate any answer.
END EDIT
I'm running ...
- 197
2
votes
2
answers
383
views
How to model repeated measurements with mixed effect models - lme4
I have a dataset of temperature measurements within a day 6 am, 6 pm, for two groups of patients health and flue,
There are repeated measurements on the same patient and same timepoint - measurements ...
- 334
1
vote
1
answer
326
views
Combining successive and treatment contrasts in lmer
I am running a lmer mixed effects model with three fixed effects parameters, each having multiple levels:
predic1: HH LR RR LD (4 levels)
predic3: L1 L2 L3 L4 (4 levels)
predic2: A B C D E F (5 ...
- 11
2
votes
0
answers
651
views
How to perform post-hoc tests with the package emmeans [closed]
After running a generalised linear mixed effect model I have estimated the logit probability by using "emtrends" from emmeans package.
The variable Condition is a factor with 3 levels(old,lure,new), ...
- 53
2
votes
0
answers
708
views
Setting contrasts in lme4: contr.treatment vs contr.sdif [closed]
In my study, each participant completed the very same Reaction Time task 3 times in 3 Sessions. I am not entirely sure if I should code the variable "Session" using ...
- 21
2
votes
0
answers
403
views
Linear mixed model: Setting custom contrasts for interactions and main effects with glht in R
I am currently learning statistics with R, and I am a bit confused about how to set custom contrasts for interaction effects. I tried removing the intercept from my model:
...
- 21
5
votes
3
answers
5k
views
Specify contrasts for lme with interactions
I have used lme to generate a mixed effect model of the response of cells to a certain stimulus. The stimulus is applied 3 times in a row (coded by the Exposure ...
- 4,591
3
votes
1
answer
4k
views
Results of Type-3 Wald Chi-Square Different for GLMM with Different Contrast Coding
I have just completed a multilevel, longitudinal logistic regression testing, at four different time points, whether participants in an experimental group are more likely to have committed any drug-...
- 2,187
1
vote
1
answer
1k
views
LMER Factor vs numeric Interaction
I am attempting to use lmer to model my data.
My data has 2 independent variables and a dependent variable.
The first is "Morph" and has values "Identical", "Near", "Far".
The second is "Response" ...
- 133
4
votes
1
answer
7k
views
How to interpret sum contrast in regression (LMM)?
I am having difficulty understanding how the results from Linear Mixed Effects model. I am examining the three different types of learning condition, condition A, B, and C. My formula using Lme4 ...
- 616
2
votes
1
answer
734
views
Calculating ratios for contrasts after lmer model
I have performed lmer on my data and, to be generic, my model has 3 fixed effects (A,B,C) and 3 nested random effects (d,e,f) following the response variable y: <...
- 21
1
vote
1
answer
470
views
ANOVA contrast estimates in R
I'm doing a contrast anova on a dataset, and I'm just not sure what to do to get the lsmeans estimates relating to one particular contrast (c1).
Here is my code:
...
0
votes
0
answers
201
views
Interpretation of a three-level contrast in a linear mixed-effect model in R
I have a linear mixed effect model in R where my fixed effect consists of three levels: Yes, No and ...
- 211
1
vote
1
answer
2k
views
Within-subjects contrasts in repeated measures anova with unbalanced design [closed]
I would like to reproduce the standard output of a repeated measures anova in SPSS with R. For a balanced design (i.e. equal group sizes) I can exactly reproduce the SPSS output of the within-subjects ...
- 33
2
votes
0
answers
332
views
Contrasts are giving wrong estimates using glht in R
The problem: glht is giving the direct differences between the estimates of the summary table (i.e., not summing each estimate with the intercept to obtain the estimated value).
...
- 78
1
vote
0
answers
272
views
How to design a contrast matrix with a continuous variable
I was wondering if someone could help me designing a contrast matrix when you have a continuous variable.
My model looks like this:
...
- 11