ripserr: Calculate Persistent Homology of Vietoris-Rips and Cubical Complexes using Ripser in R

Overview

ripserr ports the Ripser and Cubical Ripser persistent homology calculation engines from C++ via Rcpp. It can be used as a convenient and rapid calculation tool in topological data analysis pipelines.

Installation

# install development version
devtools::install_github("tdaverse/ripserr")

# install from CRAN
install.packages("ripserr")

Sample code

Ripser (Vietoris-Rips filtration) can be used as follows for data with dimension greater than or equal to 2.

# load ripserr
library("ripserr")

set.seed(42)
SIZE <- 100

# 2-dimensional example
dataset2 <- rnorm(SIZE * 2)
dim(dataset2) <- c(SIZE, 2)
vr_phom2 <- vietoris_rips(dataset2)
head(vr_phom2)
#>   dimension birth      death
#> 1         0     0 0.01004861
#> 2         0     0 0.02923702
#> 3         0     0 0.04550504
#> 4         0     0 0.06829826
#> 5         0     0 0.06853393
#> 6         0     0 0.07187663
tail(vr_phom2)
#>     dimension     birth     death
#> 113         1 0.3916344 0.4239412
#> 114         1 0.3906769 0.5577989
#> 115         1 0.3880186 0.4029842
#> 116         1 0.3703398 0.5007011
#> 117         1 0.3330234 0.3416054
#> 118         1 0.2418318 0.2504820

# 3-dimensional example
dataset3 <- rnorm(SIZE * 3)
dim(dataset3) <- c(SIZE, 3)
vr_phom3 <- vietoris_rips(dataset3, max_dim = 2) # default: max_dim = 1
head(vr_phom3)
#>   dimension birth     death
#> 1         0     0 0.1282935
#> 2         0     0 0.1421812
#> 3         0     0 0.1516424
#> 4         0     0 0.1819928
#> 5         0     0 0.1858051
#> 6         0     0 0.2114116
tail(vr_phom3)
#>     dimension     birth     death
#> 133         1 0.5212961 0.5233529
#> 134         2 1.1829207 1.1999911
#> 135         2 1.1194324 1.3245908
#> 136         2 1.0707409 1.0914850
#> 137         2 0.9433034 0.9867254
#> 138         2 0.6882204 0.6913078

Cubical Ripser (cubical filtration) can be used as follows for data with dimension equal to 2, 3, or 4.

# load ripserr
library("ripserr")

set.seed(42)
SIZE <- 10

# 2-dimensional example
dataset2 <- rnorm(SIZE ^ 2)
dim(dataset2) <- rep(SIZE, 2)
cub_phom2 <- cubical(dataset2)
head(cub_phom2)
#>   dimension      birth      death
#> 1         0 -1.1943289 -0.8607926
#> 2         0 -2.4142076 -0.8509076
#> 3         0 -0.8113932 -0.7844590
#> 4         0 -1.7170087 -0.7844590
#> 5         0 -0.7272921 -0.5428288
#> 6         0 -0.9535234 -0.5428288
tail(cub_phom2)
#>    dimension     birth     death
#> 22         1 0.8217731 0.9333463
#> 23         1 0.7681787 1.0385061
#> 24         1 0.7581632 1.5757275
#> 25         1 0.7208782 1.3025426
#> 26         1 0.6792888 1.4441013
#> 27         1 0.6359504 1.8951935

# 3-dimensional example
dataset3 <- rnorm(SIZE ^ 3)
dim(dataset3) <- rep(SIZE, 3)
cub_phom3 <- cubical(dataset3)
head(cub_phom3)
#>   dimension     birth     death
#> 1         0 -1.926167 -1.737728
#> 2         0 -1.737297 -1.439229
#> 3         0 -1.924950 -1.439229
#> 4         0 -1.500221 -1.354600
#> 5         0 -2.277778 -1.354600
#> 6         0 -1.682481 -1.306676
tail(cub_phom3)
#>     dimension     birth    death
#> 324         2 1.2488637 1.258482
#> 325         2 1.2009654 2.036972
#> 326         2 1.0452759 1.199978
#> 327         2 0.9885968 1.809382
#> 328         2 0.9310749 1.179696
#> 329         2 0.8447922 1.709689

# 4-dimensional example
dataset4 <- rnorm(SIZE ^ 4)
dim(dataset4) <- rep(SIZE, 4)
cub_phom4 <- cubical(dataset4)
head(cub_phom4)
#>   dimension     birth     death
#> 1         0 -1.986299 -1.923519
#> 2         0 -1.822606 -1.816506
#> 3         0 -1.776392 -1.710786
#> 4         0 -1.833663 -1.710387
#> 5         0 -1.947054 -1.704791
#> 6         0 -1.701462 -1.639160
tail(cub_phom4)
#>      dimension    birth    death
#> 4329         3 1.676609 2.019277
#> 4330         3 1.675766 1.932152
#> 4331         3 1.669449 2.149646
#> 4332         3 1.662486 1.863734
#> 4333         3 1.535361 1.963609
#> 4334         3 1.349235 2.263581

Functionality

1. Calculation of persistent homology of Vietoris-Rips filtrations using Ripser (function named vietoris_rips).
2. Calculation of persistent homology of cubical filtrations using Cubical Ripser (function named cubical).

Citation

If you use the ripserr package in your work, please consider citing the following (based on use):

• General use of ripserr: Wadhwa RR, Piekenbrock M, Brunson JC, Zhang X, Zhang A, Phipps K, Hershkowitz S (2025). ripserr: Calculate Persistent Homology with Ripser-Based Engines. R package version 1.0.0, https://github.com/tdaverse/ripserr/.
• Calculation using Vietoris-Rips filtrations: Bauer U (2021). Ripser: Efficient computation of Vietoris-Rips persistence barcodes. arXiv: 1908.02518.
• Calculation using cubical filtrations: Kaji S, Sudo T, Ahara K (2020). Cubical Ripser: Software for computing persistent homology of image and volume data. arXiv: 2005.12692.

Contribute

To contribute to ripserr, you can create issues for any bugs/suggestions on the issues page. You can also fork the ripserr repository and create pull requests to add useful features.

Acknowledgments

The upgrade to Ripser version 1.2.1 (ripserr version 1.0.0) was funded by an ISC grant from the R Consortium. It was done based on preliminary work by and in collaboration with Sean Hershkowitz, Alice Zhang, and Kent Phipps, in coordination with Aymeric Stamm and with guidance from Bertrand Michel and Paul Rosen.