Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/bottleneckdist.R
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).
1 | bottleneckdist(x, show.progress=FALSE)
|
x |
A perhomology object created with the |
show.progress |
A logical value. Should a progress bar be shown in the R console? Yes is TRUE, No is FALSE. |
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.
Returns a pairwise distance matrix.
Benjamin M. Delory, Guillaume Lobet
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: http://dx.doi.org/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.
1 2 3 4 5 6 7 8 9 10 | ## 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)}
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