get_persistence_diagrams {LOMAR}

get_persistence_diagrams

Description

Compute persistence diagrams for a list of point sets. By default, compute persistent homology from the Vietoris-Rips filtration. If use.dtm is TRUE, compute instead the persistent homology of the sublevel set of the distance to measure evaluated over a grid.

Usage

get_persistence_diagrams(
  point.sets = NULL,
  maxdimension = NULL,
  maxscale = NULL,
  use.dtm = FALSE,
  m0 = NULL,
  grid.by = NULL,
  ncpu = 1,
  cluster.type = "PSOCK"
)

Arguments

point.sets

list of point sets, each as a data frame with columns x,y,z

maxdimension

maximum dimension of the homological features to be computed

maxscale

limit of the Vietoris-Rips filtration

use.dtm

logical (default: FALSE), whether to use the distance to measure function

m0

parameter for the dtm function

grid.by

vector of space between points of the grid for the dtm function along each dimension

ncpu

number of parallel threads to use for computation

cluster.type

type of multicore cluster to use, either PSOCK (default) or FORK

Value

a list of persistence diagrams as n x 3 matrices. Each row is a topological feature and the columns are dimension, birth and death of the feature.

Examples

PS <- list(data.frame(x = c(2.4,-6.9,4.6,-0.7,-3.3,-4.9,-3.5,-3.5,4.2,-7),
                      y = c(5.7,1.9,4.8,3.4,-3,-2.1,7.2,1.8,6.1,-1.6),
                      z = c(2.7,-0.1,-0.7,-0.6,0.4,-1.5,-0.6,-0.9,2.2,0.7)),
           data.frame(x = c(0,0,3.1,-5.6,-5,-7.4,-0.7,-7.7,-6.7,4,4.2,0.2,5.8,3.9,3.9),
                      y = c(6.3,-6.1,-3.5,4.6,-4.1,0.3,8.8,-2.3,2.9,3.7,-1.4,-3.9,5.5,-1.2,-6.7),
                      z = c(-1.5,1.7,-0.4,-1.4,1.8,1.7,-0.9,-1.8,-0.5,1.7,1.3,0.5,-1.4,1.6,-0.1)))
Diags <- get_persistence_diagrams(point.sets = PS, maxdimension = 1, maxscale = 5, ncpu = 1)