bottleneckdist {archiDART}

Computing a Pairwise Bottleneck Distance Matrix

Description

Computing a pairwise distance matrix using a bottleneck distance method for the comparison of persistence barcodes. More information can be found in Li et al (2017) and Delory et al (2018).

Usage

bottleneckdist(x, show.progress=FALSE)

Arguments

x

A perhomology object created with the perhomology function of this package. Mandatory.

show.progress

A logical value. Should a progress bar be shown in the R console? Yes is TRUE, No is FALSE.

Details

The bottleneck distance between two persistence barcodes is calculated with the bottleneck function of the TDA package (Fasy et al (2017)). This package is now listed in the “Suggests” field of the description file and must be available in your R session (see https://archidart.github.io/drat/). An error message will be returned if TDA is not available.

show.progress=TRUE can only be used if x contains more than one element.

Value

Returns a pairwise distance matrix.

Author(s)

Benjamin M. Delory, Guillaume Lobet

References

Delory B.M., Li M., Topp C.N., Lobet G. (2018). archiDART v3.0: a new data analysis pipeline allowing the topological analysis of plant root systems, F1000Research, 7:22, DOI: doi: 10.12688/f1000research.13541.1

Fasy B.T., Kim J., Lecci F., Maria C., Rouvreau V. (2017). TDA: Statistical Tools for Topological Data Analysis. https://CRAN.R-project.org/package=TDA.

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

perhomology.

Examples

## Locate folder with RSML file
path <- system.file("extdata", package="archiDART")

table<-rsmlToTable(inputrsml=path, unitlength="cm", rsml.date="age")

#Persistent homology
ph<-perhomology(table)

#Compute pairwise distance matrix
if (requireNamespace("TDA", quietly=TRUE)) {distance<-bottleneckdist(ph)}