RAPTOR: Row and position tracheid organizer in R

• Published in: Dendrochronologia (Verona) Vol. 47; pp. 10 - 16
• Main Authors: Peters, Richard L., Balanzategui, Daniel, Hurley, Alexander G., von Arx, Georg, Prendin, Angela Luisa, Cuny, Henri E., Björklund, Jesper, Frank, David C., Fonti, Patrick
• Format: Journal Article
• Language: English
• Published: Elsevier GmbH 01.02.2018
• Subjects: Conifers; Local-search algorithm; Quantitative wood anatomy; Tracheidogram; Tree ring; Quantitative wood anatomy; Conifers; Tree ring; Tracheidogram; Local-search algorithm
• ISSN: 1125-7865; 1612-0051
• DOI: 10.1016/j.dendro.2017.10.003

Mechanistic understanding of tree-ring formation and its modelling requires a cellular-based and spatially organized characterization of a tree ring, moving from whole rings, to intra-annual growth zones and individual cells. A tracheidogram is a radial profile of conifer anatomical features, such as lumen area and cell wall thickness, of sequentially- and positionally-ranked tracheids. However, its construction is tedious and time-consuming since image-analysis-based measurements do not recognize the position of cells within a radial file, and present-day tracheidograms must be constructed manually. Here we present the R-package RAPTOR that complements tracheid anatomical data obtained from quantitative wood anatomy software (e.g., ROXAS, WinCELL, ImageJ), with the specific positional information necessary for the automated construction of tracheidograms. The package includes functions to read and visualize tracheid anatomical data, and uses local search algorithms to ascribe a ranked position to each tracheid in identified radial files. The package also provides functions to ensure that tracheids are adequately aligned for identifying the first tracheid in each radial file, and obtaining the correct ranking of tracheids along each radial file. Additional functions allow automating the analyses for multiple samples and rings (batch mode) and exporting data and plots for quality control. RAPTOR allows tracheidogram users to take advantage of the latest generation of cell anatomical measuring systems. With this R-package we aim to facilitate the construction of more robust and versatile tracheidograms for the benefit of the research community.