ripser options (format, dim, threshold, modulus, …)

[mattearnshaw]

do you have any plan to support these options via your interface?

[rrrlw]

Absolutely; unfortunately, due to other commitments, this will likely not happen until June/July 2018. :(

[paigero]

Thanks so much for creating ripserr. I need to compute persistent homologies of dimension 2 and higher. How can I get ripserr to do this?

[rrrlw]

Hello, thank you for the interest in ripserr! Assuming your data is at least 3-dimensional, ripserr should (with default options) calculate persistent homologies of dimension 2 and higher. Do you have a minimal dataset that should definitely have features of dim 2 or higher that are not showing up?

[paigero]

Dear Raoul,

Thank you for the quick reply.

When I run ripserr on the attached data set I get 0-cycles and 1-cycles but no 2-cycles.

On the other had when I run a standard R TDA command;

Diag = ripsDiag(X = data, maxdimension, maxscale,library = "GUDHI", printProgress = TRUE)

Then I get 0-cycles, 1-cycles and 2-cycles.

Thanks much in advance,

Rob Paige

From: Raoul W. [mailto:notifications@github.com] Sent: Saturday, June 9, 2018 7:25 PM To: rrrlw/ripserr ripserr@noreply.github.com Cc: Paige, Robert paigero@mst.edu; Comment comment@noreply.github.com Subject: Re: [rrrlw/ripserr] ripser options (format, dim, threshold, modulus, …) (#1)

Hello, thank you for the interest in ripserr! Assuming your data is at least 3-dimensional, ripserr should (with default options) calculate persistent homologies of dimension 2 and higher. Do you have a minimal dataset that should definitely have features of dim 2 or higher that are not showing up?

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/rrrlw/ripserr/issues/1#issuecomment-396008827, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AIaE_mxpYNPJoZfKmuvtU0IZqWy8FYqoks5t7GdcgaJpZM4T06xT.

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[rrrlw]

Yes, you are correct, this is definitely a bug in ripserr. Thank you for pointing it out! I will try to get it fixed as soon as possible.

[paigero]

Dear Raoul,

Thank you so much in advance,

Rob Paige

From: Raoul W. [mailto:notifications@github.com] Sent: Sunday, June 17, 2018 12:34 AM To: rrrlw/ripserr ripserr@noreply.github.com Cc: Paige, Robert paigero@mst.edu; Comment comment@noreply.github.com Subject: Re: [rrrlw/ripserr] ripser options (format, dim, threshold, modulus, …) (#1)

Yes, you are correct, this is definitely a bug in ripserr. Thank you for pointing it out! I will try to get it fixed as soon as possible.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/rrrlw/ripserr/issues/1#issuecomment-397855960, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AIaE_sRkJK_MYwI7yMzt6YBOR2BDkTJgks5t9epFgaJpZM4T06xT.

[rrrlw]

@mattearnshaw The dim and threshold options have been implemented in the TDAstats R package (https://github.com/rrrlw/TDAstats) that is intended to replace the ripserr package. The modulus option should be added soon as well. I am unsure how many formats I will support apart from point cloud; is there a particular format that would be useful in your work?

[rrrlw]

@paigero The TDAstats R package (https://github.com/rrrlw/TDAstats) is intended to replace the ripserr R package, as it has more functionality (visualization and inference, in addition to calculation of persistent homology). The TDAstats::calculate_homology function is used to calculate persistent homology (with the C++ Ripser library doing the work behind the R code); it has a parameter named dim, which represents the maximum dimension for which to calculate persistent homology. Thus, the function call calculate_homology(point.cloud, dim = 2) should do the trick. Please let me know if this works for you.

[mattearnshaw]

@rrrlw thanks for the heads up! point cloud alone works for me.

[paigero]

Raoul,

The point cloud format is most useful in my work.

Thanks much in advance for your hard work,

Rob

From: Raoul W. [mailto:notifications@github.com] Sent: Monday, July 16, 2018 1:24 PM To: rrrlw/ripserr ripserr@noreply.github.com Cc: Paige, Robert paigero@mst.edu; Mention mention@noreply.github.com Subject: Re: [rrrlw/ripserr] ripser options (format, dim, threshold, modulus, …) (#1)

@mattearnshawhttps://github.com/mattearnshaw The dim and threshold options have been implemented in the TDAstats R package (https://github.com/rrrlw/TDAstats) that is intended to replace the ripserr package. The modulus option should be added soon as well. I am unsure how many formats I will support apart from point cloud; is there a particular format that would be useful in your work?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/rrrlw/ripserr/issues/1#issuecomment-405330037, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AIaE_nT77eGQyY91XLEU7OPdxJDBQW_Zks5uHNpDgaJpZM4T06xT.

[paigero]

Raoul,

Great!! Thank you so much.

Rob

From: Raoul W. [mailto:notifications@github.com] Sent: Monday, July 16, 2018 1:25 PM To: rrrlw/ripserr ripserr@noreply.github.com Cc: Paige, Robert paigero@mst.edu; Mention mention@noreply.github.com Subject: Re: [rrrlw/ripserr] ripser options (format, dim, threshold, modulus, …) (#1)

@paigerohttps://github.com/paigero The TDAstats R package (https://github.com/rrrlw/TDAstats) is intended to replace the ripserr R package, as it has more functionality (visualization and inference, in addition to calculation of persistent homology). The TDAstats::calculate_homology function is used to calculate persistent homology (with the C++ Ripser library doing the work behind the R code); it has a parameter named dim, which represents the maximum dimension for which to calculate persistent homology. Thus, the function call calculate_homology(point.cloud, dim = 2) should do the trick. Please let me know if this works for you.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/rrrlw/ripserr/issues/1#issuecomment-405330693, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AIaE_vA9qW_D5pl5Np1Hum4-hwl8vgd_ks5uHNqEgaJpZM4T06xT.

[rrrlw]

Thank you, @paigero, appreciate the kind words. Please let me know if there are any issues with TDA stats at https://github.com/rrrlw/TDAstats/issues.

[rrrlw]

@mattearnshaw apologies, but upon a closer look, it appears that the modulus option will not be supported as it required the USE_COEFFICIENTS flag during C++ compilation of Ripser (which is not used in TDAstats). See https://github.com/Ripser/ripser for details. Thank you for using TDAstats, let me know if there are any issues at https://github.com/rrrlw/TDAstats/issues!