simplex-tree.md
In rgudhi: An Interface to the GUDHI Library for Topological Data Analysis

Class `SimplexTree` works

Code
  st$filtration(1:2)
Output
  [1] 0.618034

Code
  st$extended_persistence()
Output
  $Ordinary
  list()

  $Relative
  list()

  $`Extended+`
  $`Extended+`[[1]]
  $`Extended+`[[1]][[1]]
  [1] 0

  $`Extended+`[[1]][[2]]
  $`Extended+`[[1]][[2]][[1]]
  [1] 0

  $`Extended+`[[1]][[2]][[2]]
  [1] 0.618034




  $`Extended-`
  $`Extended-`[[1]]
  $`Extended-`[[1]][[1]]
  [1] 1

  $`Extended-`[[1]][[2]]
  $`Extended-`[[1]][[2]][[1]]
  [1] 0.618034

  $`Extended-`[[1]][[2]][[2]]
  [1] 0

Code
  st$flag_persistence_generators()
Output
  [[1]]
        [,1] [,2] [,3]
   [1,]    3    3    2
   [2,]    4    4    3
   [3,]    5    5    4
   [4,]    6    6    5
   [5,]    7    7    6
   [6,]    8    8    7
   [7,]    9    9    0
   [8,]    0    9    8
   [9,]    1    1    0
  [10,]    2   10    1

  [[2]]
  [[2]][[1]]
        [,1] [,2] [,3] [,4]
   [1,]   10    0   10    0
   [2,]   10    2   10    2
   [3,]   10    3   10    3
   [4,]   10    4   10    4
   [5,]   10    5   10    5
   [6,]   10    6   10    6
   [7,]   10    7   10    7
   [8,]   10    8   10    8
   [9,]   10    9   10    9
  [10,]    2    1   10    9


  [[3]]
  [1] 10

  [[4]]
  list()

Code
  st$get_boundaries(1:2)
Output
  # A tibble: 2 x 2
    simplex   filtration
    <list>         <dbl>
  1 <int [1]>         -1
  2 <int [1]>         -2

Code
  st$get_filtration()
Output
  # A tibble: 41 x 2
     simplex   filtration
     <list>         <dbl>
   1 <int [1]>         -3
   2 <int [1]>         -2
   3 <int [1]>         -2
   4 <int [1]>         -2
   5 <int [2]>         -2
   6 <int [1]>         -2
   7 <int [2]>         -2
   8 <int [1]>         -2
   9 <int [2]>         -2
  10 <int [1]>         -2
  # i 31 more rows

Code
  st$get_simplices()
Output
  # A tibble: 41 x 2
     simplex   filtration
     <list>         <dbl>
   1 <int [3]>          2
   2 <int [2]>         -1
   3 <int [3]>          2
   4 <int [2]>         -2
   5 <int [2]>          2
   6 <int [1]>         -2
   7 <int [3]>          2
   8 <int [2]>         -1
   9 <int [2]>          1
  10 <int [1]>         -1
  # i 31 more rows

Code
  st$get_skeleton(0)
Output
  # A tibble: 11 x 2
     simplex   filtration
     <list>         <dbl>
   1 <int [1]>         -2
   2 <int [1]>         -1
   3 <int [1]>         -2
   4 <int [1]>         -2
   5 <int [1]>         -2
   6 <int [1]>         -2
   7 <int [1]>         -2
   8 <int [1]>         -2
   9 <int [1]>         -2
  10 <int [1]>         -2
  11 <int [1]>         -3

Code
  st$lower_star_persistence_generators()
Output
  [[1]]
  [[1]][[1]]
       [,1] [,2]
  [1,]    2   -1

  [[1]][[2]]
       [,1] [,2]
  [1,]    1   -1


  [[2]]
  [[2]][[1]]
  [1] 10

Code
  st$persistence()
Output
  # A tibble: 3 x 3
    dimension birth death
        <int> <dbl> <dbl>
  1         1    -1     2
  2         0    -3   Inf
  3         0    -2     1

Code
  st$persistence_intervals_in_dimension(0)
Output
  # A tibble: 2 x 2
    birth death
    <dbl> <dbl>
  1    -2     1
  2    -3   Inf

Code
  st$persistence_pairs()
Output
  [[1]]
  [[1]][[1]]
  [1] 2

  [[1]][[2]]
  [1] 10  1


  [[2]]
  [[2]][[1]]
  [1] 2 1

  [[2]][[2]]
  [1] 10  9  8


  [[3]]
  [[3]][[1]]
  [1] 10

  [[3]][[2]]
  list()