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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# ripserr: Calculate Persistent Homology of Vietoris-Rips and Cubical Complexes using Ripser in R
[](https://travis-ci.org/rrrlw/ripserr)
[](https://ci.appveyor.com/project/rrrlw/ripserr)
[](https://codecov.io/gh/rrrlw/ripserr?branch=master)
[](https://www.gnu.org/licenses/gpl-3.0)
[](https://CRAN.R-project.org/package=ripserr)
[](https://CRAN.R-project.org/package=ripserr)
## Overview
ripserr ports the [Ripser](https://arxiv.org/abs/1908.02518) and [Cubical Ripser](https://arxiv.org/abs/2005.12692) persistent homology calculation engines from C++ via [Rcpp](https://CRAN.R-project.org/package=Rcpp).
It can be used as a convenient and rapid calculation tool in topological data analysis pipelines.
## Installation
```{r install, eval=FALSE}
# install development version
devtools::install_github("rrrlw/ripserr")
# install from CRAN (not available yet)
# install.packages("ripserr")
```
## Sample code
Ripser (Vietoris-Rips complex) can be used as follows for data with dimension greater than or equal to 2.
```{r sample-vr}
# 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)
tail(vr_phom2)
# 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)
tail(vr_phom3)
```
Cubical Ripser (cubical complex) can be used as follows for data with dimension equal to 2, 3, or 4.
```{r sample-cub}
# 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)
tail(cub_phom2)
# 3-dimensional example
dataset3 <- rnorm(SIZE ^ 3)
dim(dataset3) <- rep(SIZE, 3)
cub_phom3 <- cubical(dataset3)
head(cub_phom3)
tail(cub_phom3)
# 4-dimensional example
dataset4 <- rnorm(SIZE ^ 4)
dim(dataset4) <- rep(SIZE, 4)
cub_phom4 <- cubical(dataset4)
head(cub_phom4)
tail(cub_phom4)
```
## Functionality
1. Calculation of persistent homology of Vietoris-Rips complexes using Ripser (function named `vietoris_rips`).
1. Calculation of persistent homology of cubical complexes 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, Scott JG. ripserr: Calculate Persistent Homology with Ripser-based Engines; version 0.1.0. URL https://github.com/rrrlw/ripserr.
* **Calculation using Vietoris-Rips complex:** Bauer U. Ripser: Efficient computation of Vietoris-Rips persistence barcodes. 2019; arXiv: 1908.02518.
* **Calculation using cubical complex:** Kaji S, Sudo T, Ahara K. Cubical Ripser: Software for computing persistent homology of image and volume data. 2020; arXiv: 2005.12692.
## Contribute
To contribute to ripserr, you can create issues for any bugs/suggestions on the [issues page](https://github.com/rrrlw/ripserr/issues).
You can also fork the ripserr repository and create pull requests to add useful features.