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rrrlw / TDAstats

R pipeline for computing persistent homology in topological data analysis. See https://doi.org/10.21105/joss.00860 for more details.
https://rrrlw.github.io/TDAstats
GNU General Public License v3.0
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Permutation Test Code for TDAstats #17

Closed shaelebrown closed 3 years ago

codecov-io commented 4 years ago

Codecov Report

Merging #17 into master will not change coverage. The diff coverage is n/a.

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  Coverage   93.15%   93.15%           
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  Files           6        6           
  Lines         570      570           
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  Hits          531      531           
  Misses         39       39

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rrrlw commented 4 years ago

Hey @shaelebrown, thank you for your patience. I have reviewed & edited the pull request (see above commits). Overall, this looks phenomenal! Thank you for contributing to TDAstats. I am not done reviewing the code yet, but have a couple of questions that I'd like to run by you before reviewing the rest: (1) I don't quite understand the d() (renamed to wass()) function and would love to chat more about how it works (likely Skype); in particular, it doesn't match up with the output produced by TDA::wasserstein in the code below:

a <- TDA::circleUnif(n = 20)
b <- TDA::circleUnif(n = 20)
phom1 <- calculate_homology(a)
phom2 <- calculate_homology(b)
wass(B1 = phom1, B2 = phom2, dim = 1, p = 1)
TDA::wasserstein(phom1, phom2, dimension = 1, p = 1)

(2) I don't understand how loss() works either and would love to chat more about it (likely Skype)

Note: the above questions are primarily a result of my limited knowledge, I would appreciate any explanations you can provide. Thanks!

rrrlw commented 3 years ago

Merging into permtest branch of rrrlw/TDAstats and will put code into R package format in that branch; thanks for the contribution, @shaelebrown! Will tag or email you when permtest is ready for merging into master