dartToTable: Import DART Files Into a Single Data Frame

Description Usage Arguments Details Value Author(s) References Examples

View source: R/dartToTable.R

Description

Import DART files located in a folder into a single data frame. More information about DART files can be found in Le Bot et al (2010) and Delory et al (2018).

Usage

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dartToTable(inputrac, inputlie, inputtps, res=NULL, unitlength="px",
            unitangle="d", fitter=FALSE)

Arguments

inputrac

A character string specifying the path to the folder containing the rac files created by DART. This argument could be the same as inputlie/inputtps.

inputlie

A character string specifying the path to the folder containing the lie files created by DART. This argument could be the same as inputrac/inputtps.

inputtps

A character string specifying the path to the folder containing the tps files created by DART. This argument could be the same as inputrac/inputlie.

res

If images were acquired with a flatbed scanner: a numeric value specifying the resolution of the images used to vectorize the root systems with DART (resolution is expressed in dots/inch). If images were acquired with a digital camera: the ratio between the length of a reference object located on the image expressed in pixels and the actual length of the same object expressed in inches. This argument must be specified if unitlength="mm" or unitlength="cm".

unitlength

A character string specifying the unit of length that must be used in the final data frame. The value acceptable for this argument could be either “px” for pixels, “cm” for centimetres or “mm” for millimetres. The function will use the metadata inside each RSML file (unit and resolution) to make the conversion.

unitangle

A character string specifying the unit that must be used to express the calculated angles. The value acceptable for this argument could be either “d” for degrees (default value) or “r” for radians.

fitter

A logical value. Should the Fitter topological indices be computed? Yes is TRUE, No is FALSE. See details.

Details

To run dartToTable efficiently, DART files must have been saved with their appropriate extension (.rac, .lie, and .tps).

If fitter=TRUE, topological indices described in Fitter (1986, 1987) will be calculated. Here, we define each topological index as in Fitter (1986, 1987). We recommend the reading of these papers for more information.

The magnitude of a link is equal to the number of external links that feed into that link.

The path length of a link is equal to the number of links between a given link and the root system base.

Value

Returns a dartToTable object. Each line of the data frame gives the attributes of one segment. The data frame includes the following columns:

file: the name of each DART file located in inputrac.

root: the root identification number.

order: the root branching order.

parentroot: the identification number of the parent root.

time: the date of apparition.

bran: the branching state (‘true’ denotes a branching link while ‘false’ denotes a continuing link).

apic: the apical state (‘true’ denotes a segment ending a root).

x1: the X coordinate of the node starting the segment (expressed in unitlength).

y1: the Y coordinate of the node starting the segment (expressed in unitlength).

z1: the Z coordinate of the node starting the segment (expressed in unitlength).

x2: the X coordinate of the node ending the segment (expressed in unitlength).

y2: the Y coordinate of the node ending the segment (expressed in unitlength).

z2: the Z coordinate of the node ending the segment (expressed in unitlength).

length: the length of the segment (expressed in unitlength).

blength: the cumulative length measured along each root (expressed in unitlength).

orientation: the angle between each segment and a vertical direction vector (expressed in unitangle).

growth: the growth rate value of each segment (expressed in unitlength).

geodesic: the geodesic distance measured along the roots (expressed in unitlength).

magnitude: the magnitude of the segment (see Fitter et al (1987)). Computed only if fitter=TRUE.

pathlength: the external path length of the segment (see Fitter et al (1987)). Computed only if fitter=TRUE.

Author(s)

Benjamin M. Delory, Guillaume Lobet

References

Delory B.M., Baudson C., Brostaux Y., Lobet G., du Jardin P., Pages L., Delaplace P. (2016) archiDART: an R package for the automated computation of plant root architectural traits, Plant and Soil, DOI: 10.1007/s11104-015-2673-4.

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

Fitter A.H. (1986) The topology and geometry of plant root systems: influence of watering rate on root system topology in Trifolium pratense, Annals of Botany, 58, 91-101.

Fitter A.H. (1987) An architectural approach to the comparative ecology of plant root systems, New Phytologist, 106, 61-77.

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.

Examples

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

table<-dartToTable(inputrac=path, inputlie=path, inputtps=path, res=75, unitlength="cm")

archidart/archidart documentation built on May 20, 2018, 2:29 a.m.