[Rd] `dendrapply` Enhancements

Fri Feb 24 13:42:52 CET 2023

Hi Toby,

Thanks for your reply! I haven�t heard about the R project sprint, but I�ll definitely check it out. UK is going to be a little hard for me to get to funding-wise, but I�ll try to apply for funding.

I appreciate your other comments. As far as coding style, I did do everything I could think of to make sure it�s a drop-in replacement for the current version with the default settings, so all the user-exposed arguments/variables should be identical. I used the conventions in https://github.com/wch/r-source/wiki/Contributing for commenting and whitespace, so hopefully that all looks okay. I�m realizing there may be some differences in tab widths, but I can fix that later today.

-Aidan

-----------------------
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
ahl27 using pitt.edu
(724) 612-9940

From: Toby Hocking <tdhock5 using gmail.com>
Date: Friday, February 24, 2023 at 06:57
To: Lakshman, Aidan H <AHL27 using pitt.edu>
Cc: R-devel using r-project.org <R-devel using r-project.org>
Subject: Re: [Rd] `dendrapply` Enhancements
Hi Aidan, I think you are on the right email list.
I'm not R-core, but this looks like an interesting/meaningful/significant contribution to base R.
I'm not sure what the original dendrapply looks like in terms of code style (variable names/white space formatting/etc) but in my experience it is important that your code contribution makes minimal changes in that area.
Did you hear about the R project sprint 2023? https://contributor.r-project.org/r-project-sprint-2023/<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcontributor.r-project.org%2Fr-project-sprint-2023%2F&data=05%7C01%7CAHL27%40pitt.edu%7C41b702f139034cd7165608db165e4530%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C638128366414606277%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=oB%2BBivUsBjIgBtZNU8mh%2Fz2rujD3bv9MbWdxqNtyUFk%3D&reserved=0> Your work falls into the "new developments" category so I think you could apply for that funding to participate.
Toby

On Fri, Feb 24, 2023 at 3:47 AM Lakshman, Aidan H <AHL27 using pitt.edu<mailto:AHL27 using pitt.edu>> wrote:
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<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fahl27%2Fnew_dendrapply%2Ftree%2Fmaster&data=05%7C01%7CAHL27%40pitt.edu%7C41b702f139034cd7165608db165e4530%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C638128366414606277%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=QI%2B5t1C%2BJB15D8o8noZra4W87fgyITm12nluGN%2BFNoE%3D&reserved=0>. 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/<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ahl27.com%2F&data=05%7C01%7CAHL27%40pitt.edu%7C41b702f139034cd7165608db165e4530%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C638128366414606277%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=7KUpJpdulSIzSXbpDJlyUV8pMJm%2BSVFvDOJTlVs9lhc%3D&reserved=0>>
Doctoral Candidate, Wright Lab<https://www.wrightlabscience.com/<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wrightlabscience.com%2F&data=05%7C01%7CAHL27%40pitt.edu%7C41b702f139034cd7165608db165e4530%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C638128366414606277%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=JMgw%2BMiQ6xdp3OokToJ2nyyco%2BryiFH%2B9ap5iU3yJH8%3D&reserved=0>>
University of Pittsburgh School of Medicine
Department of Biomedical Informatics
ahl27 using pitt.edu<mailto:ahl27 using pitt.edu>
(724) 612-9940

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