rgudhi

The goal of rgudhi is to provide an R interface to the Python package gudhi. The GUDHI library is a generic open source C++ library, with a Python interface, for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding. The library offers state-of-the-art data structures and algorithms to construct simplicial complexes and compute persistent homology.

Installation

You can install the development version of rgudhi from GitHub with:

# install.packages("devtools")
devtools::install_github("LMJL-Alea/rgudhi")

Example: Persistence diagram using an Alpha complex

library(rgudhi)
n <- 10
X <- seq_circle(n)
ac <- AlphaComplex$new(points = X)
st <- ac$create_simplex_tree()
st$persistence()
#> # A tibble: 13 × 3
#>    dimension  birth    death
#>        <int>  <dbl>    <dbl>
#>  1         1 0.0955   1.00  
#>  2         1 1        1     
#>  3         1 1        1     
#>  4         0 0      Inf     
#>  5         0 0        0.0955
#>  6         0 0        0.0955
#>  7         0 0        0.0955
#>  8         0 0        0.0955
#>  9         0 0        0.0955
#> 10         0 0        0.0955
#> 11         0 0        0.0955
#> 12         0 0        0.0955
#> 13         0 0        0.0955