Package: ripserr 0.2.0

Raoul Wadhwa

ripserr: Calculate Persistent Homology with Ripser-Based Engines

Ports the Ripser <arxiv:1908.02518> and Cubical Ripser <arxiv:2005.12692> persistent homology calculation engines from C++. Can be used as a rapid calculation tool in topological data analysis pipelines.

Authors:Raoul Wadhwa [aut, cre], Matt Piekenbrock [aut], Jacob Scott [aut], Jason Cory Brunson [aut], Emily Noble [ctb], Takeki Sudo [cph, ctb], Kazushi Ahara [cph, ctb], Ulrich Bauer [cph, ctb], Xinyi Zhang [aut]

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ripserr.pdf |ripserr.html✨
ripserr/json (API)

# Install 'ripserr' in R:

install.packages('ripserr', repos = c('https://tdaverse.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rrrlw/ripserr/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

aegypti - _Aedes aegypti_ occurrences in Brazil in 2013
case_predictors - State-level predictors of mosquito-borne illness in Brazil

On CRAN:

algebraic-topology cohomology cpp cubical-complex persistent-homology pixel point-cloud r-language r-programming rcpp rips-complex ripser simplicial-complex simplicial-homology topological-data-analysis topology vietoris-complex voxel

5.50 score 7 stars 5 scripts 160 downloads 13 exports 2 dependencies

Last updated 1 months agofrom:d08c080dfe. Checks:OK: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 09 2024
R-4.5-win-x86_64	WARNING	Nov 09 2024
R-4.5-linux-x86_64	WARNING	Nov 09 2024
R-4.4-win-x86_64	WARNING	Nov 09 2024
R-4.4-mac-x86_64	WARNING	Nov 09 2024
R-4.4-mac-aarch64	WARNING	Nov 09 2024
R-4.3-win-x86_64	WARNING	Nov 09 2024
R-4.3-mac-x86_64	WARNING	Nov 09 2024
R-4.3-mac-aarch64	WARNING	Nov 09 2024

Exports:as.PHom cubical cubical.array cubical.matrix is.PHom PHom vietoris_rips vietoris_rips.data.frame vietoris_rips.default vietoris_rips.dist vietoris_rips.matrix vietoris_rips.numeric vietoris_rips.ts

Dependencies:magrittr Rcpp

Calculating Persistent Homology with a Cubical Complex

Raoul R. Wadhwa, Jacob G. Scott

Rendered fromcubical.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2020-11-16
Started: 2020-08-31

Calculating Persistent Homology with a Vietoris-Rips Complex

Raoul R. Wadhwa, Matthew Piekenbrock, Jacob G. Scott

Rendered fromvietoris-rips.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2020-11-03
Started: 2020-08-31

Modeling Cases of Mosquito-Borne Disease Using Persistent Homology

Xinyi Zhang, Jason Cory Brunson

Rendered frommodeling-disease-using-PH.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2021-11-29
Started: 2021-11-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
_Aedes aegypti_ occurrences in Brazil in 2013	aegypti
Convert to PHom Object	as.PHom
State-level predictors of mosquito-borne illness in Brazil	case_predictors
Calculating Persistent Homology via a Cubical Complex	cubical cubical.array cubical.matrix
First Part of PHom Object	head.PHom
Check PHom Object	is.PHom
Persistence Data Container	PHom
Printing Persistence Data	print.PHom
Calculate Persistent Homology with Ripser-Based Engines	ripserr-package ripserr
Last Part of PHom Object	tail.PHom
Calculate Persistent Homology via a Vietoris-Rips Complex	vietoris_rips vietoris_rips.data.frame vietoris_rips.default vietoris_rips.dist vietoris_rips.matrix vietoris_rips.numeric vietoris_rips.ts