aRchi: Make_Path – R documentation

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Make_Path

Make the path of a QSM in an aRchi object

Description

Identify and record the paths of a QSM in an object of class aRchi. The path are needed for several tree metrics estimation of the aRchi package.

Usage

Make_Path(aRchi)

## S4 method for signature 'aRchi'
Make_Path(aRchi)

Arguments

aRchi

a file of class aRchi

Details

A path is a continuous succession of cylinders from a terminal segment (i.e a branch tip) to the trunk base. Thus, there is as many path as terminal segments in a QSM.

This function fill the slot Paths of an object of class aRchi with a data.table of the paths. This data.table contains the same variables as a classic QSM plus an ID_path column. This table is thus larger than the QSM table as each cylinder is repeated as many times as it appears in a path. For example, the first cylinder of the QSM (i.e the beginning of the trunk) is repeated N path times, with N path the number of path of the QSM.

Many function of the aRchi packages request a path table (check see also).

Value

The aRchi object with the table of paths

Examples

# Read a QSM file
file=system.file("extdata","Tree_1_TreeQSM.txt",package = "aRchi")
QSM=read_QSM(file,model="treeQSM")
# Build an object of class aRchi
Tree1_aRchi<-build_aRchi(QSM=QSM)
Tree1_aRchi
# Make the path table
Tree1_aRchi<-Make_Path(Tree1_aRchi)
Tree1_aRchi
PathFraction(Tree1_aRchi)

aRchi

Quantitative Structural Model ('QSM') Treatment for Tree Architecture

v1.0.5

CeCILL

Authors

Olivier Martin

Initial release