perhomology: Topological Analysis using Persistent Homology

In BenjaminDelory/topotree: Topological Analysis of Tree Architectures using Persistent Homology

Description

Computing the birth and death of homology group components (path-connected components) using tree architecture data found in QSM files.

Usage

perhomology(x)

Arguments

x	A qsmToTable object. Mandatory.

Details

In mathematics, homology refers to homology groups. Because tree branches are path-connected components, only zero order homology (H0) branches are considered here.

The persistence of each H0 branch is computed using a geodesic distance function. More information can be found in Li et al (2017).

Value

Returns a matrix. The matrix is a barcode object and has the following columns:

dimension: the homology group (0 for path-connected components).

birth: the birth of an H0 branch along the distance function.

death: the death of an H0 branch along the distance function.

Author(s)

Benjamin M. Delory

References

Li M., Duncan K., Topp C.N., Chitwood D.H. (2017) Persistent homology and the branching topologies of plants, American Journal of Botany, DOI: 10.3732/ajb.1700046.

See Also

qsmToTable, plot.barcode.

BenjaminDelory/topotree documentation built on Sept. 28, 2019, 7:15 a.m.