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rsml (version 1.3)

Plant Root System Markup Language (RSML) File Processing

Description

Read and analyse Root System Markup Language (RSML) files, used to store plant root system architecture data. More information can be found at the address .

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Version

Install

install.packages('rsml')

Monthly Downloads

24

Version

1.3

License

GPL-2

Maintainer

Guillaume Lobet

Last Published

January 5th, 2016

Functions in rsml (1.3)

anagallis

Root system of a anagallis plant in 3D
addNodeToRoot

Add a node to an existing root
root

Root constructor
print.node

Print the node
lupin

Root system of a lupin plant in 2D
getInsertionPosition

Compute the insertion of the root on its parent
summary.plant

Summary of the plant
print.plant

Print the plant
primLength

Compute the length of the primary root based on the coordinates of its nodes
totalLength

Compute the length of the root and its children based on the coordinates of its nodes
zrangePlant

Compute the zrange of the plant
plot.plant

Plot the root system
rsmlToPlant

Import a single RSML file into a Plant object
maize

Root system of a maize plant in 3D
nRoot

Compute the total number of roots in the plant
nChild

Get the number of children in a root
nPrimRoot

Compute the number of primary roots in the plant
length.root

Compute the length of the root based on the coordinatres of its nodes
meanInterbranch

Compute the mean interbranch distance of the children (lateral) roots
meanInsertionAngle

Compute the mean insertion angle of the children (lateral) roots
node

Node constructor
yrangePlant

Compute the yrange of the plant
nLatRoot

Compute the number of lateral roots in the plant
xrangePlant

Compute the xrange of the plant
addChildToRoot

Add a child root (lateral) to an existing root
length.plant

Compute the length of the root based on the coordinates of its nodes
meanInsertionAnglePlant

Compute the mean insertion angle of all the laterals in the plant
rsmlToList

Import a single RSML file into a List. Work only if the roots in the rsml file have properties associated with them.
meanInterbranchPlant

Compute the mean interbranch distance of all the primary roots in the image
addRootToPlant

Add a root to an existing plant. Returns the plant with the added root
xrange

Compute the xrange of the root
plant

Plant object, containing a root system, composed of roots
latLength

Compute the length of the lateral root based on the coordinates of its nodes
coords

Get the coordinates of the root nodes
yrange

Compute the xrange of the root
zrange

Compute the xrange of the root
nNode

Get the number of nodes in a root
getInsertionAngle

Compute the insertion angle of the root on its parent