adds new cpp funs

[Nowosad]

I will open a new issue soon.

[HajkD]

Hi Jakub,

Thank you so much for your fantastic work!!! I truly appreciate all your efforts and I will try to perform a thorough code review in the next days so that I can give you some more feedback and incorporate all your new features into philentropy.

You will hear from me soon :)

Many thanks,
Hajk

[HajkD]

Btw: I just added a new argument epsilon to the philentropy::distance() and philentropy::KL() functions (see #26).

Would it be possible to add these changes to your pull request?

Your help is very much appreciated!

Many thanks!

[Nowosad]

Hi @HajkD - I will wait for your code review. If you give me the green light, then I will incorporate the epsilon argument, add all of the possible distance measures to single_distance(), and write some documentation.

There is also one other important change to discuss. I have noticed that you use the src/philentropy_init.c file, which I assume you create by hand. If you look at my PR, you will see this file removed, and its content is now in src/RcppExports.cpp. The RcppExports.cpp is created automatically with devtools::document(). Let me know what you think about this approach. If you do not like it, I can go back to the way it was before.

[HajkD]

Hi Jakub,

Everything looks excellent and we can remove the src/philentropy_init.c file if it continues to pass all rhub checks.

Do you already want to add the rest and then I merge, or shall I merge first and then you add the rest?

Would it also be possible to add the fantastic benchmark and motivation in #28 to the vignettes so that users can swiftly see the advantages of using the new functions?

Many thanks!!!
Hajk

[HajkD]

Also feel free to add your changes to NEWS.md for the next release.

[Nowosad]

Hi Hajk,
I plan to find some time tomorrow to work on this (adding the rest of the metrics, vignette, and update the news file). I will let you know when it is ready to be merged.
Best,
Jakub

[Nowosad]

Hi Hajk,
I think this PR is ready for your final review (and merge). To sum up:

1. It adds three new functions - dist_one_one(), dist_one_many(), dist_many_many()
2. These functions are exported and documented
3. NEWS are updated
4. There is also a vignette explaining all of them - Many_Distances.Rmd
5. It also fixes some existing issues with documentations
6. Finally, I hide the last part of the existing Distances.Rmd vignette, as it seems unfinished

Best, J

[HajkD]

Hi Jakub,

Absolutely brilliant! I already reviewed your changes after you committed and everything looks fantastic. I will now merge everything and we shall run a quick integration test. Do you think it would make sense to add some unit tests with testthat so that we can always run automated checks as we continue to grow the package?

I was also wondering whether you would be interested (and/or have time) to look into the parallel support feature #24? This would also speed up big computations.

In either case, I am more than happy to add you as official contributor to the package and let me know if you have other ideas that we could integrate before submitting the new package version to CRAN.

You wonderful help is greatly appreciated!

Many thanks,
Hajk

[Nowosad]

Hi Hajk,

1. new tests are now added - 228e67f
2. I will try to look at the parallel support some time in the future, but I cannot promise anything (as my C++ skills are just good enough to barely survive;))