Row And Position Tracheid Organizer
Description:
Performs wood cell anatomical data analyses on spatially explicit xylem (tracheids) data sets derived from wood anatomical thin sections. The package includes functions for the visualization, alignment and detection of continuous tracheid radial file (defines as rows) and tracheid position within an annual ring of coniferous species. This package is designed to use elaborate cell output, like provided with ROXAS (von Arx and Carrer, 2014). The package has been validated for Picea abies, Larix Siberica, Pinus cembra and Pinus sylvestris.
Important Notes:
This repository contains the release version of RAPTOR for submission to the Comprehensive R Archive and Network (CRAN) and accompanies the manuscript Peters et al. (2018). This document outlines the package installation process and provides initial steps for using the package’s functions via examples provided in the package documentation.
Installation:
A development version of RAPTOR can be installed and used via
remotes::install_github("the-Hull/RAPTOR")
library(RAPTOR)The stable CRAN version can be installed using
install.packages("RAPTOR")
library(RAPTOR)Usage:
The package’s functions are to be executed sequentially (cf. manuscript):
- is.raptor()
- graph.cells()
- align()
- first.cell()
- pos.det()
- write.output()
- batch.mode() is a convenient ‘wrapper’ function streamlining steps 1 through 6
- anatomy.data calls complimentary example data sets
Each function is complimented by detailed documentation, which can be accessed by calling a function’s name preceded by a question mark, i.e.:
“?is.raptor()”.
Simple examples illustrating each function’s usage are provided at the bottom of each documentation file. The functions can be tested and explored using the complimentary example data sets (see manuscript or execute “?anatomy.data” in an R session.)
To begin exploring the package, navigate to Examples in the documentation of “?is.raptor()”:
#validating example data
input<-example.data(species="LOT_PICEA")
input<-is.raptor(input, str=TRUE)
inputContributors:
- Richard L. Peters richardlouispeters3@hotmail.com [aut, cre, cph]
- Daniel Balanzategui [ctr]
- Alexander G. Hurley [ctr]
- Georg von Arx [ctr]
- Angela Luisa Prendin [ctr]
- Henri E. Cuny [ctr]
- Jesper Bjoerklund [ctr]
- David C. Frank [ctr]
- Patrick Fonti [ths, ctr, fnd]
Please note that the ‘RAPTOR’ project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
