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I don’t have a lot of experience with this particular package, but if a package provides vignettes I like to look through those. ggtree seems to provide an entire book, which may be helpful to you. You could also look at the examples in the docs, or other scripts people have written. If you find some, read through them line by line and try to understand what they’re doing. Run each line and look at what the output is. See if you can reproduce the example analyses on your own, maybe with different data. That’ll help you learn the packages with more training wheels than just striking out on your own, and then once you get more comfortable you should be able to branch out more.
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