Repeated Measures ANOVA in R || lme4
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- Опубликовано: 11 сен 2024
- How to do a repeated measures ANOVA n R using lme4 and lmerTest.
Also the difference between repeated measures ANOVA and ANOVA.
Reddit: / thesassystatistician
Twitter: / chelseaparlett
This is the best way to do a repeated measures analysis. However, it's not an ANOVA. ANOVA use the generalized least squares method. This is an Multi-level linear model (MLM) utilizing the maximum likelihood method. They're roughly the same until you get incomplete or unbalanced data and that's when the methods differ with the MLM method being much better.
Finally an easy explanation for R, thanks alot! I searched for it like forever. I don't know if you're aware but base R returns type I SS, which doesn't matter if you have a balanced design like you showed here, but if it's unbalanced you'd need to use a different function to compare the results of lme4::lmer with the conventional anova. So in addition to the difference between these two functions you've already stated, there'd be another one caused by the different SS (again, only if the design is unbalanced). One example to get type III SS out of a conventional ANOVA model would be like this:
library(car)
options(contrasts = c("contr.sum", "contr.poly"))
Anova(nonRMModel, type = 3)
Hey there, thanks a lot for pointing this out! Could you please also write where can I read more about assigning the SS type in case of balanced and unbalanced designs? I checked my design by means of VCA:::isBalanced(RT ~ F1 + F2 + F3 + F4, mydata) and it is balanced. However, assigning the Anova(model, type =2) vs. Anova(model, type = 3) produces different results (p and F values). Do you know why this IS and in case if the data IS balanced, what type should I assign in this case (i.e., balanced data) if any? Thank you!
Great tutorial, thanks a bunch!
Hey Chelsea, thanks a lot for the video, this was really helpful! Could you please also comment if one should additionally indicate the type of SS (I, II or III) in the last anova(nonRMModel)? And if yes, would you always use Type II or Type III and why?
Thank you for this well made video.
Can I ask why you use anova(model) instead of summary (model)?
Also, a follow up video on model diagnostics would be great.
Thanks!
There wasn't a specific reason, I believe in a simple model either will give you what you need. That's a good point though, I should show what both include.
And, you got it! That's a great idea for a follow up video. I'll put it on my list.
Awesome! I´ll subscribe and wait for the video.
I didn´t now lmerTest package - its realy good :-)
Maybe you will give your opinion on this - My mixed models are quite simple models with only 1 independent variable, and patient ID as random effect. I test my models in the following way: Assumption of linear dependency. Normal distribution of residuals and normal distribution of random effects. Do you think there is something I should add to that?
Thanks in advance
Thank You
This is great! Thank you so much!
How can I find the previous video that you showed the data?
ruclips.net/video/zaba5xtaHlE/видео.html
Do you know a way to calculate eta squared for lme4 S4 objects? heplots::etasq seems to work only with the Anova() function from the car package, which is way more difficult to set up.
RiseAgainst24 I just figured this out. Package is MuMIN
And the run r.squaredGLMM(entermodelhere)
Hi, there are some data, but I can not apply the anova with measures repeated in time, could you help me?
Thank you!!!! :)
This is a great video, thank you so much! My only issue is that I found that I receive "Error in library(lmerTest) : there is no package called ‘lmerTest’" after running install.packages(lmerTest) and library(lmerTest). Any idea what's going on here? Thanks.
Hi Zoie,
The install.packages() function needs the name of the package in " ", so in your case like install.packages("lmerTest"). Did you give it a try this way?
Regards,
Antonis
Thanks for the video upload. How do you get lme4 and lmerTest packages?
Hey Rydaholic, you can download them using install.packages() and use them by calling library(). If you're using RStudio, it's even easier to use the drop down menu to install them.
I like your voice. =)
How to do Post Hoc test in R for repeated measures ANOVA. TukeyHSD(anova_name) didn't work in this case..
I believe TukeyHSD is for between-group ANOVAs.
@@oddmentings Is there a post hoc test on the repeated measures ANOVA considering a TukeyHSD does not work?
@@checkscher3047 try .....emmeans(model1, list(pairwise ~ group), adjust = "tukey"). where group is your treatments.
Emmeans package as already mentioned. There is also multicomp. Another way, which I have done as well, is to interpret the betas usining summary(lmemodel)
Then you report like a regression.