# Questions tagged [anova]

ANOVA stands for ANalysis Of VAriance, a statistical model and set of procedures for comparing multiple group means. The independent variables in an ANOVA model are categorical, but an ANOVA table can be used to test continuous variables as well.

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### Does Greenhouse-Geisser correction influence the effect size estimation, the statistical significance treshold, or both of them?

I discussed recently with one of my colleagues about the Greenhouse-Geisser correction for non-sphericity. I told him first that this correction is very conservative and that it would be more ...
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### Comparing two F-test statistics

I have two groups A and B, each of which consists of 5 samples. Each sample is described in a vector of length (>1000) of continuous numeric values (characteristics). I want to test if the sample in ...
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### How the Error() term in aov() decides what goes in which stratum?

I am trying to understand how the principles of nested anova in R, but I am having extreme difficulty with the error term. Imagining the simplest case. I measured plant growth in two places, A and B. ...
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### Will Tukey multiple comparison be the same for different types of Sum Of Squares of ANOVA for an unbalanced design

I am working on Two-Way ANOVA for an unbalanced design. Will Tukey multiple comparison be the same for different types (I, II & III) of Sum Of Squares of ANOVA for an unbalanced design. I am ...
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### Missing cells with Type III SS

I have a linear model of the form y ~ x + z + x:z. I have unbalanced data and further have a few missing cells (data would be unbalanced even without those missing cells). My understanding of the ...
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### How does R's aov function 'work better' with orthogonal contrasts?

The help page for R's aov function states: The default ‘contrasts’ in R are not orthogonal contrasts, and aov and its helper functions will work better with such ...
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### Orthogonality in ANOVA and Regression Analysis

I read the following (Wikipedia) regarding contrast coding of categorical variables: Unlike when used in ANOVA, where it is at the researcher’s discretion whether they choose coefficient values ...
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### Why do we need to model lower-order effects in models with interactions?

I recently saw a paper with a four-way interaction. That already is difficult to interpret (maybe if you have 1 or more categorical variables but definitely near impossible to interpret if all ...
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### Seeking authoritative references on weighted ANOVA

I would be grateful for any reference, such as a textbook or peer-reviewed journal article (of any vintage), that contains explicit formulas for conducting a weighted ANOVA with arbitrary weights. ...
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### What is the logic behind ANOVA on ranks?

I've read a few sources that describe ANOVA on ranks, and I am still confused on how the calculation is done, and why. Specifically: Is ANOVA on ranks just applying a rank transformation to the data ...
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### No value or "."returned for Mauchly's Test of Sphericity in SPSS

I am learning how to do a Two-Way Repeated Measures ANOVA in SPSS but when I try to check the Mauchly's Test of Sphericity Significance value it only displays a single decimal point. It is also ...
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### AIC or ANOVA to compare models?

What are the relative merits of each approach, and which circumstances call for one rather than the other? To some extent I have a specific example in mind, which I've discussed here. In that example ...
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### How is the confidence interval for variance component in "lmer" function computed by the command "confint"?

Here is the R code : ...
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### creating contrast matrix (limma) for two factorial in R

I am attempting to construct a contrast matrix that I can run in R, using the limma bioconductor package, but I am not sure that I have coded the contrast matrix correctly. A previous post and the ...
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### When to use a chi-squared test?

This is a very basic question however I do not have a statistical background and I am currently analysing some data for my dissertation. I have constructed a survey about healthy lifestyles & ...
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### When using repeated-measures ANOVA in R, what does it mean to specify Error(subject) instead of Error(subject/(A*B))?

For a two-way repeated measures design, we can specify the model using aov in the following fashion: ...
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### Formulating a mixed model with nested fixed and random effects

I'm analysing the results of an experiment using a mixed (fixed and random-effects) ANOVA with nested effects and I just need someone to confirm that I have the right model. The effects in the design ...
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### ANOVA - probability of negative variance estimate

There is a certain probability that ANOVA provides negative variance estimates. According to [Searle et al. : Variance components] (https://onlinelibrary.wiley.com/doi/book/10.1002/9780470316856) p67 ...
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### Three versions of the independent two sample t-test (and R)

This post concerns three versions of the independent two sample t-test: Student's t-test uses a pooled standard deviation in the denominator (all equations are shamelessly copied from Wikipedia - ...
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### Geometric interpretation of the difference between the means (ANOVA)

First of all, a disclosure: I'm a medical doctor trying to understand statistics for research. Coming from a non-mathematical background I can do many mistakes. I've read some traditional books of ...
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### Randomized Block Design Models

I have been asked to fit the following models in R: The models are based on this data: I know the mediums are the blocks and the units of the active ingredient are the treatments. I understand how ...
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### Syntax differences between aov and lmer for two-way repeated measures design

I'm working with the following data frame using R. It consists of measurements obtained from 7 subjects with two independent variables (IV1 and ...
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### Why there is no agrement on power / sample size for factorial repeated measures design?

I'm not really sure to what degree this is a statistical question but thought this might be the best place to start. If my questions prove only my ignorance please vote it down and I'll delete the ...
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### How to handle crossed and nested terms in a crossover design

Here comes my case: I conducted an experiment with the following design: 30 participants, each with a unique id, were screened and classified according to a trait. Then, all participants were tested ...
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### The anova() function in R to compare a glm() and a glmer() models

I recently tested something regarding the stats::anova function in R. Assuming modglm is a model fitted with the ...
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### Computing effect size (partial eta squared) from a RM-ANOVA's F value

I want to calculate the number of participants I need in order to get a power of 0.95, when replicating an effect. The effect size of this effect is not reported in the previous study, which is why I ...
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### Is there a principled ANOVA-like approach when a "subject" factor forms a symmetric 2D matrix?

I have a dataset where the dependent variable is a similarity measure between any 2 data channels, lets call it S(i,j), with a few dozen simultaneously recorded channels (so there are quite a few ...
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### Dropping columns from an orthogonal design matrix?

Hello: I’m working with a three factor (ANOVA) design that I wish to use in an MCMC chain to estimate the parameters for the main effects and treatment interactions. I wish to run MCMC analyses ...
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### Mixed Anova in R

I am trying to do an anova anaysis in R. The experiment done had each subject tested in Method 1 and Method 2 as well a being in one of 4 different Levels (each subject in one group). The goal is to ...
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### multiple Kruskal-Wallis instead of ANOVA for non-normally distributed data

Apologies in advanced if I supply too little or vague information, since I am a complete newbie in stats and using this forum. So I did a study which evaluated psychopathic personality traits, ...
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### Testing for differences between time series with many timepoints

I think the easiest way to describe my question is with plots. I've run an experiment where I recorded data from animals' brains (EEG) at 6 depths. The animals are recorded at baseline for 25 minutes,...
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