Efficient Format for Persistence Data (Diagrams)

Transform persistence data to the format used by plt.

as_persistence(x, ...)

# S3 method for default
as_persistence(x, modulus = NULL, max_dim = NULL, threshold = NULL, ...)

# S3 method for persistence
as_persistence(x, ...)

# S3 method for list
as_persistence(x, ...)

# S3 method for diagram
as_persistence(x, ...)

# S3 method for PHom
as_persistence(x, ...)

# S3 method for persistence
print(x, ...)

# S3 method for persistence
format(x, ...)

get_pairs(x, degree, ...)

# S3 method for persistence
as.data.frame(x, row.names = NULL, optional = TRUE, ...)

Arguments

x: Persistence data to be transformed; either a \(\geq 3\)-column matrix (or object coercible to one) with dimension/degree, start/birth, and end/death columns, a list whose first element is such an object, an object of class 'PHom' as returned by [ripserr::vietoris_rips()], or (a list as returned by a *Diag() function in TDA (e.g. [TDA::ripsDiag()]) whose first element is) an object of class 'diagram'.
...: Parameters passed to methods.
modulus, max_dim, threshold: Possibly missing parameters of the calculation of the persistence data x to be included in the 'persistence' object.
degree: Non-negative integer; the homology degree for which to recover a matrix of persistence pairs.
row.names: NULL or a character vector giving the row names for the data frame. Missing values are not allowed.
optional: logical. If TRUE, setting row names and converting column names (to syntactic names: see make.names) is optional. Note that all of R's base package as.data.frame() methods use optional only for column names treatment, basically with the meaning of data.frame(*, check.names = !optional). See also the make.names argument of the matrix method.

Value

Persistence data in the form of a list with named entries:

pairs: A list of 2-column matrices containing birth-death pairs in each dimension/degree, starting with zero.
modulus: The (integer) modulus of the prime field in which homology coefficientts were calculated.
max_dim: The (integer) maximum dimension of calculated features.
threshold: The (real) maximum length of an edge in the simplicial filtration.

Details

This class and function will soon be spun off to a lower-level package that can be imported by others as needed. Refer to http://adv-r.had.co.nz/S3.html for guidance on methods to make available.

Examples


# sample from a cylinder
x <- tdaunif::sample_cylinder_elliptical(n = 60)
# calculate PH using {ripserr}
ph <- ripserr::vietoris_rips(x, dim = 1)
#> Warning: `dim` parameter has been deprecated; use `max_dim` instead.
as_persistence(ph)
#> 'persistence' data computed up to degree 1:
#> 
#> * 0-degree features: 59
#> * 1-degree features:  8 
# calculate PH using {TDA}
ph <- TDA::alphaComplexDiag(x, maxdimension = 1)
as_persistence(ph)
#> 'persistence' data computed up to degree 1:
#> 
#> * 0-degree features: 60
#> * 1-degree features: 36
#> 
#> threshold = 1.004018 
# create a 'persistence' object directly from a matrix
as_persistence(unclass(ph$diagram))
#> 'persistence' data computed up to degree 2:
#> 
#> * 0-degree features: 60
#> * 1-degree features: 36
#> * 2-degree features: 20