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I want to know of any repositories that contain complete experimental design in R covering basic test and analyses?

I want to take a top-buttom approach to learn step by step through a real project how that works. Do you know of any places to find that, such as an R notebook?

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I suggest you take a look at the TidyTuesday repo, where every week they post a raw dataset, a chart or article related to that dataset, and ask you to explore the data. The repo also contains other resources, like data science books.

Together with the repo, I suggest the TidyTuesday videos by David Robinson, where he creates screencasts of complete data analyses in R for the TidyTuesday datasets.

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