Hi everyone, My apologies if this isn�t the right place to submit this�I�m new to the R-devel community and still figuring out what is where.
If people want to skip my writeup and just look at the code, I�ve made a repository for it here: https://github.com/ahl27/new_dendrapply/tree/master. I�m not quite sure how to integrate it into a fork of R-devel; the package structure is different from what I�m used to. I had written a slightly improved version of dendrapply for one of my research projects, and my advisor encouraged me to submit it to the R project. It took me longer than I expected, but I�ve finally gotten my implementation to be a drop-in replacement for `stats::dendrapply`. The man page for `stats::dendrapply` says �The implementation is somewhat experimental and suggestions for enhancements (or nice examples of usage) are very welcome,� so I figured this had the potential to be a worthwhile contribution. I wanted to send it out to R-devel to see if this was something worth pursuing as an enhancement to R. The implementation I have is based in C, which I understand implies an increased burden of maintenance over pure R code. However, it does come with the following benefits: - Completely eliminates recursion, so no memory overhead from function calls or possibility of stack overflows (this was a major issue reported on some of the functions in one of our Bioconductor packages that previously used `dendrapply`). - Modest runtime improvement, around 2x on my computer (2021 MBP, 32GB RAM). I�m relatively confident this could be optimized more. - Seemingly significant reduction in memory reduction, still working on a robust benchmark. Suggestions for the best way to do that are welcome. - Support for applying functions with an inorder traversal (as in `stats::dendrapply`) as well as using a postorder traversal. This implementation was tested manually as well as running all the unit tests in `dendextend`, which comprises a lot of applications of `dendrapply`. The postorder traversal would be a significant new functionality to dendrapply, as it would allow for functions that use the child nodes to correctly execute. A toy example of this is something like: ``` exFunc <- function(x){ attr(x, 'newA') <- 'a' if(is.null(attr(x, 'leaf'))){ cat(attr(x[[1]], 'newA'), attr(x[[2]], 'newA')) cat('\n') } x }) dendrapply(dend, exFunc) ``` With the current version of dendrapply, this prints nothing, but the postorder traversal version will print �a� twice for each internal branch. If this would be a worthwhile addition, I can refactor the code for brevity and add a `how=c("in.order", "post.order")`, with the default value �in.order� to maintain backwards compatibility. A preorder traversal version should also be possible, I just haven�t gotten to it yet. I think the runtime could be optimized more as well. Thank you in advance for looking at my code and offering feedback; I�m excited at the possibility of helping contribute to the R project! I�m happy to discuss more either here, on GitHub, or on the R Contributors Slack. Sincerely, Aidan Lakshman ----------------------- Aidan Lakshman (he/him)<https://www.ahl27.com/> Doctoral Candidate, Wright Lab<https://www.wrightlabscience.com/> University of Pittsburgh School of Medicine Department of Biomedical Informatics ah...@pitt.edu (724) 612-9940 [[alternative HTML version deleted]]
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