# Tagged Questions

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### Is my random variable affecting my response?

I performed an experiment on coral colonies (10 colonies, randomly chosen in repeated measurements); manipulating aragonite/carbon chemistry and temperature (fixed effect) to analyse effects on the ...
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### Repeated measures ANOVA in R for non-orthogonal design

I have data from a two-factor within-subjects experiment design where the conditions are not orthogonal. Factor one (Location) has three levels; factor two (Stimulus) has three levels, one of which is ...
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### Simple Mixed Model with 1 Fixed and 1 Random Effect

I have various datasets I need to analyse regarding soil properties, all in the same fashion, with one fixed effect (which is a position along a transect, indicating different land uses). Now my main ...
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### Using lmer for repeated-measures linear mixed-effect model

EDIT 2: I originally thought I needed to run a two-factor ANOVA with repeated measures on one factor, but I now think a linear mixed-effect model will work better for my data. I think I nearly know ...
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### GLM with unequal sample size

I am trying to figure out how to run a GLM with a poisson distribution in R. The data has 4 treatments: A(n=16), B(n=17), C(n=16), D(n=20), and 2 time periods. This data is count/area so there are ...
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### Repeated-measures error in R ezANOVA using more levels than subjects (balanced design)

I'm having a problem running a repeated-measures ANOVA in R using the ezANOVA function. I have data from 18 subjects - each subject participated in 3 conditions, ...
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### Advice on the statistical analysis of clinical data using summary statistics, t-tests, ANOVA, and linear regression

I need some help with the statistical analysis of a study of a particular surgery to remove a particular cancer. I am using the statistical program R to conduct my analysis. My data are saved in the ...
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### What factor (trials or blocks) to use in a repeated measures ANOVA

I am conducting a psycholinguistic experiment. Each trial consists of the subject responding to a word by pressing a button.The design of my experiment is as follows: 5 blocks of a 100 trials each ...
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### What does R mean by “unbalanced design”?

I think this means an unequal sample in different conditions. But it seems to mean something else. . . I have a data set like below ...
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### Efficient way to run multiple ANOVAs on subsets of data

I have a data set that is repeated-measures ratings of four devices (two two-level variables) for 6 dimensions (ease, confidence, comfort, control, size and fit), with a two-level between-subjects ...
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### R p-value half to SPSS rANOVA

I have done rANOVA in SPSS and then in R and got two different p-values from the same model. While SPSS gives 0.032, R gives 0.0162, which when rounded is a half. Other data are exactly the same. 1. ...
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### Pretest-posttest plus control design

I am evaluating the effect of an intervention (treatment: a lecture) on the ability to spot behavioral clues of emotions using visual stimuli using pretest-posttest plus control group experimental ...
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### Question about reading an output for using ANOVA to compare two linear models

I tried to compare the following two models using "anova.lm()" in R: ...
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### Difference between a 2 factor ANOVA and mixed effects model

The lme4 package in R includes the cake dataset. ...
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### Variance associated with factors in GLS (nlme)

First time posting here, so thank you ahead of time for your help. I'd like to estimate the variances associated with two factors in a relatively simple, but unbalanced GLS model, and I am unsure how ...
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### Analysis to use with categorical response and categorical predictor variables

I have data from a randomized survey experiment in which each respondent was assigned to one of 4 groups, one of which can be considered a "control" or "no treatment" group. The key question asked in ...
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### How to interpret a non significant independent variable?

I conducted a regression analysis using R's lm() function. One of the independent variables shows no significance (p = 0.89), which contradicts the hypothesis that is should have a significantly ...
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### How can I perform an ANOVA from multiple CSV files with R?

I (or rather, my girlfriend whom I'm trying to convert to free software) am just getting started with R. She wants to do a two-way ANOVA on her data on mussels and the threads they release in ...
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### R, Differences between lm and aov

What does explain the differences in p.values in the following aov and lm ? Is the difference only due to different types of Sum of square calculations ? ...
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### Anova Repeated Measures Looking at Interactions for a BACI design in R

Here are my data: ...
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### Sphericity in GNU R for within subject design

I'm now trying to caliculate Mauchly's test, sphericity test for within subject design, using GNU R. My data, Df4 is fellow, ...
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### Tukey HSD on Two way ANOVA with Interaction

I saw an example online of a two way ANOVA followed by Tukey HSD using the ToothGrowth dataset in R (factorial, betwen subjects design), but don't know how to ...
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### Should a mixed effects model be used?

This post provides an excellent example of the inner workings of a mixed effects model: http://emhart.github.com/blog/2012/11/16/making-sense-of-random-effects/ In a hypothetical study, I have ...
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### Checking confidence intervals on user defined contrast (one-way ANOVA)

Hi is anyone able to help - I am doing this all in R Code: I have run one way analysis on some data and set up 2 contrasts (Liberarts-Finearts and also Engineering-science). I now need to calculate ...
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### One-way repeated measures anova

I tried finding an answer to this question on this and other sites but to no avail - if I am missing something please excuse my inability to locate the answer! Basically I have several dependent ...
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### two way repeated measures anova random factors missing data

I have a pretty simple time series experiment that I'd like to analyze in R. I have an experimental and control group and for each individual in each group I collected samples from them over a course ...
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### How do I cross error terms in Stata's xtmixed (examples inside) like lmer's +(a*b*c|s)?

Let's say I have an experiment with three within-subject factors, A, B, & C. Data looks like this. ...
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### Specification of error terms in aov() in R

For a two-way repeated measures design, we can specify the model using aov in the following fashion: ...
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I have two questions about Bonferroni adjustments: 1). Can one use the Bonferroni method to compare independent groups? The reason why I ask this is it seems that many examples I've encountered ...
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### Calculate F-statistic / p-value for subset of co-efficients in R

I'm wondering if there's an easy way of calculating an F-statistic / p-value for a subset of model coefficients. Particularly in R? I'm not sure what test would be needed to calculate this. For ...
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### How to interpret R output for two-way repeated measures ANOVA

How do I interpret the following output from R for a two-way repeated measures ANOVA ...
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### Between subjects repeated measures ANOVA in R - 5 brands, 11 measurements

In my research I have performed a series of measurements on 5 different brands of blocks. Each block has been inspected for deformation under incremental forces (20, 30, 40, 50, 60, 70, 80, 90, 100, ...
177 views

### How does anova.lm in R calculates “Sum Sq”?

I'm learning R and trying to understand how lm() handles factor variables & how to make sense of the ANOVA table. I'm fairly new to statistics, so please be ...
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### Between group comparison for every level of within factor

If I use lme for mixed ANOVA as follow ...
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### Test for significance in a time series using R

I've got a time series data set that looks at population numbers on a yearly basis, and I would like to know if there is a significant difference between certain years, and if so- which years are ...
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### ANOVA post hoc with concerned about the sphericity

According to this post the best way to do post hoc analysis in ANOVA in R is t-test + ptukey. Because lme + glht "essentially assumes the sphericity assumption holds". How are t-test + ptukey ...
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### Post-hoc test after 2-factor repeated measures ANOVA in R?

I have problems finding a solution regarding how to run a post-hoc test (Tukey HSD) after a 2-factor (both within-subjects) repeated-measures ANOVA in R. For the ANOVA, I've used the aov -function: ...
572 views

### ANOVA or Regression? 1 Continuous factor & 1 Categorical factor with continuous response variables

I have 1 categorical factor (3 treatments) and 1 continuous factor (weight) and then I have 5 continuous response variables. From what I have read, I should not use a two way ANOVA as one of the ...
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### R loop for anova on multiple files [closed]

I would like to execute anova on multiple datasets stored in my working directory. I have come up so far with: ...
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### Analyse unbalanced repeated measures 2x2x2x2 type II anova interactions

I have a run an unbalanced 2x2x2x2 Type II ANOVA in R and am having trouble following up on the results. Here is the output: ...
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I have the dataset that contains one continuous measure of plant leafs (PC1 scores of individual leafs), that is dependent variable and three others that I need to use as independant, explanatory. One ...
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### How would you do Bayesian ANOVA and regression in R?

I have a fairly simple dataset consisting of one independent variable, one dependent variable, and a categorical variable. I have plenty of experience running frequentist tests like ...
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### anova(model1, model2) vs. anova(model2, model1) in R

I'm trying to figure out why there is a difference when I run anova(model1, model2) versus anova(model2, model1) in R. I know ...
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### Partial, adjusted or Type-III SS of factorial experiment in R

The partial SS for two factor (N and P factors) factorial experiment with interaction can be calculated as: \begin{eqnarray*} \textrm{SS}\left(N_{i}|\mu,P_{j},\left(NP\right)_{ij}\right) & = ...
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### Nested/SplitModel - RepeatedMeasures/MixedModel ANOVA: levels of nesting & scripting in R

My data set has the following variables: Treatment (4 types- fixed) Location (8 locations- fixed) Position in Location (3 positions per location- fixed) Samples are taken in each position (3 ...
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### R model.tables() incorrect means – possible bug?

I was doing ANOVA in SPSS and then in R and to my huge surprise, the results from the latest version of R were incorrect. When I use the function ...
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### How to analyze differences of two groups with replicates?

I am trying to see if there are differences between two groups (background genetic mutants) and some values associated to them. Every group has 4 different gene types with two replicates each and its ...
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### Question with R and repeated measures

Second time I'm turning to this site, it has helped before. I am looking for some coding help to perform a repeated measures anova in R. I have a total of 4 treatments, each replicated 3 times. They ...