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Now, I am looking for an R implementation of a permutation-based equivalent of the t-test, or any other advice on what to do with the data. … I know that there are some R-packages that can do this for me (e.g., coin, perm, exactRankTest, etc.), but I don't know which one to pick. …

J., Levy, R., Scheepers, C., & Tily, H. J. (2013). Random effects structure for confirmatory hypothesis testing: Keep it maximal. … Analyzing linguistic data : a practical introduction to statistics using R. Cambridge, UK; New York: Cambridge University Press. …

I am trying to move from using the ez package to lme for repeated measures ANOVA (as I hope I will be able to use custom contrasts on with lme). Following the advice from this blog post I was able to …

I am currently writing a paper in which I have the pleasure to conduct both between and within subjects comparisons. After discussion with my supervisor we decided to run t-tests and use the pretty si …

You may also want to see this post on the R-mailing list, and this blog post for specifying a repeated measures ANOVA in R. …

A sketch of one solution (for another see below): Data needs to be in the long format (i.e., on value per row) instead of in the wide format as in SPSS (i.e., one subject per row), see the reshape p …

Great web resources are: Quick-R for Graphs: 1, 2, and 3. …

Instead of using the KS test you could simply use a permutation or resampling procedure as implemented in the oneway_test function of the coin package. Have a look at the accepted answer to this quest …

My question is based on this response which showed which lme4::lmer model corresponds to a two-way repeated measures ANOVA: require(lme4) set.seed(1234) d <- data.frame( y = rnorm(96), subjec …

The full quote from our chapter also provides an answer to your second question (i.e., the why): A common contrast scheme, which is the default in R, is called treatment contrasts (i.e., contr.treatment …

I am trying to run a repeated measures Anova in R followed by some specific contrasts on that dataset. I think the correct approach would be to use Anova() from the car package. … Update: I already asked a very similar question on R-help, there was no answer. A similar questions was posed on R-help some time ago. However, the answers did also not solve the problem. …

For me, grep is more R-ish. Strongly related is the recent package by Hadley Wickhem: stringr, A package for "modern, consistent string processing" including grep like functions. … He recently published a paper on it in the R Journal. See also my answer on stackoverflow on an identical issue. …

Next to optim there is another function in base R that allows for what you want: nlminb. Check ?nlminb and ?optim for examples of the usage. There are a bunch of packages that can do optimizations. …

You should note that T is none of your model's a random effects terms, but a fixed effect. Random effects are only those effects that appear after the | in a lmer formula! A more thorough discussion …

Update: Since I now know that my problem is called quasi-complete separation I updated the question to reflect this (thanks to Aaron). I have a dataset from an experiment in which 29 human particip …