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aumath-advancedr2019 / simDNA

An R package for simulating DNA sequences.
https://aumath-advancedr2019.github.io/simDNA/
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Feedback #3

Open KimHochreuter opened 4 years ago

KimHochreuter commented 4 years ago

Purpose of the package

The purpose of the package is pretty obvious for anyone that follows Asgers course. So anyone that has worked with coalescent theory, will probably see the purpose of the package aswell. I could not access anything purpose related (vignette or some sort of description) in R after installing the package. But i could find it through github. The title of the package is maybe a litle bit misleading, since i expected it would be focused on simulating DNA.

Code Quality & Documentation

The package installed without any problems and i tried all the functions in different (but fairly simple) setups without any hiccups. All of the functions are very well documented and with nice examples, that make it clear how to use them. I like that there are many functions with sparse output. The vignettes are well written and gives a nice overview of the theoretical background, without feeling overwhelming. Sadly they are not accessible directly through R.

Interface

Since there are many functions with little output, the functions themselves have very few arguments which is nice! This makes them very easy to use. The vignette also explains very clear what to use the functions for and how. The error messages are good!

Conclusion

All in all a pretty useful package for calculating standard statistics in a coalescent setup. I do not have anything in particular in mind that could improve the package, without having to add more functions with new functionalities.

maikenbak commented 4 years ago

Thank you for the feedback. We agree that the name of the package could be changed. Note that in order to obtain the vignettes directly in R, you should run devtools::install_github("aumath-advancedr2019/simDNA", build_vignettes=TRUE).