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