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Looking forward to reading this post but just wanted to say that the work Tyler has done on ray tracing in R is phenomenal. I highly recommend checking out this package website: https://www.rayshader.com
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JetBrains
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rayrender
A pathtracer for R. Build and render complex scenes and 3D data visualizations directly from R
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My personal favorite resource is "R for Data Science" by Hadley Wickham. It covers lots of nice data manipulation and visualization examples, and provides a good introduction to the tidyverse, which is a particular dialect of R that's well-suited for data analysis. It's available for free at:
https://r4ds.hadley.nz/
For more specialized analytical methods there are lots of textbooks out there that provide a deep dive into packages for a specific field (e.g. survival analysis, machine learning, time series), but for general data manipulation and visualization it's hard to beat R4DS.