perhomology: Topological Analysis using Persistent Homology
In archidart/archidart: Plant Root System Architecture Analysis Using DART and RSML Files

Description Usage Arguments Details Value Author(s) References See Also Examples

Computing the birth and death of homology group components (path-connected components) using root system architecture data encoded with the Root System Markup Language (RSML) or exported by Data Analysis of Root Tracings (DART). More information can be found in Le Bot et al (2010), Lobet et al (2015), Li et al (2017), and Delory et al (2018).

1	perhomology(x, show.progress=FALSE)

`x`	A rsmlToTable or dartToTable object. Mandatory.
`show.progress`	A logical value. Should a progress bar be shown in the R console? Yes is TRUE, No is FALSE.

In mathematics, homology refers to homology groups. Because roots 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).

show.progress=TRUE can only be used if more than one root system is stored in x.

Returns a list of matrices. The list is a perhomology object. Each matrix of the list is a barcode object. Each element of the list is named as its corresponding RSML/DART file. Each matrix is associated with one root system only and possesses 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.

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

Le Bot J., Serra V., Fabre J., Draye X., Adamowicz S., Pages L. (2010) DART: a software to analyse root system architecture and development from captured images, Plant and Soil, DOI: 10.1007/s11104-009-0005-2.

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.

Lobet G., Pound M.P., Diener J., Pradal C., Draye X., Godin C., Javaux M., Leitner D., Meunier F., Nacry P., Pridmore T.P., Schnepf A. (2015) Root System Markup Language: Toward a Unified Root Architecture Description Language, Plant Physiology, DOI: 10.1104/pp.114.253625.

dartToTable, rsmlToTable, plot.barcode.

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

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

#Persistent homology
ph1<-perhomology(table)
plot(ph1$'monocot-archisimple_1', las=1, xlab="Geodesic distance (cm)")