xRing—An R package to identify and measure tree-ring features using X-ray microdensity profiles |
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| Institution: | 1. CFE – Centre for Functional Ecology – Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal;2. University of Natural Resources and Life Sciences, Vienna - BOKU, UFT Tulln, Konrad Lorenz Strasse 24, 3430, Tulln, Austria;1. Tribhuvan University, Kathmandu, Nepal;2. WSL Swiss Federal Research Institute, CH-8903 Birmensdorf, Switzerland;1. Charles University, Faculty of Science, Department of Physical Geography and Geoecology, Albertov 6, 12843 Prague, Czech Republic;2. The Silva Tarouca Research Institute for Landscape & Ornamental Gardening, Department of Forest Ecology, Lidicka 25-27, 60200 Brno, Czech Republic;1. Laboratório de Botânica, Anatomia Vegetal e Dendrocronologia, Universidade Federal de Sergipe, Av. Marechal Rondon s/n, Rosa Elze, São Cristóvão, Sergipe, 49100-000, Brazil;2. CFE – Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal;3. Departamento de Ciências Florestais, Universidade de São Paulo / ESALQ – Escola Superior de Agricultura “Luiz de Queiroz”, Avenida Pádua Dias, 11, Piracicaba, São Paulo, 13418-900, Brazil;4. Departamento de Ecologia, Universidade Federal de Sergipe, Av. Marechal Rondon, s/n, Rosa Elze, São Cristovão, Sergipe, 49100-000, Brazil;1. Department of Geography, 207 Old Mill Building, 94 University Place, University of Vermont, Burlington, VT 05405 USA;2. Forest Ecosystem Monitoring Cooperative, 705 Spear Street, South Burlington, VT 05403 USA;3. Rubenstein School of the Environment and Natural Resources, University of Vermont, Burlington, VT 05405 USA;4. Forest Service, U.S. Department of Agriculture, Northern Research Station, Burlington, VT 05405 USA;1. Institute of Geography, Friedrich-Alexander University Erlangen-Nuremberg, Wetterkreuz 15, 91058, Erlangen, Germany;2. Department of Forestry and Environmental Science, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh |
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| Abstract: | Climate influences tree-ring density and ring-density variables extracted from X-ray images have been widely used for climate reconstructions. The R package xRing was developed to identify and measure tree rings on X-ray microdensity profiles automatically. This package is available for free and it offers functions to visualize and calibrate X-ray images, to detect tree-ring borders and to identify earlywood-latewood transition using wood density variations at the inter- and the intra-ring scale. The most important functions are calibrateFilm, detectRings, correctRings, detectEwLw, and getDensity. Outputs of these functions are S3 objects, for which specific methods are provided, including plot and print. The non-linear relationship between optical density of the film and wood density is defined by the function calibrateFilm. The function detectRings detects tree rings using wood density profiles as input. This function uses the difference between local maximum and minimum values to identify tree-ring borders automatically. The correctRings function is used to call a Graphical User Interface (GUI) to visualize and to correct tree-ring borders manually. After correcting tree-ring borders, the detectEwLw function is used to compute earlywood and latewood widths by dividing rings according to relative intra-ring density changes. The getDensity function computes for each tree ring the minimum (maximum) density and the mean earlywood, latewood and whole-ring density. Finally, a list with dataframes with tree-ring width and density variables can be obtained using the function getRwls. One of the major advantages of xRing package is that requires little knowledge of R language, but at the same time it can be easily changed or adapted by experienced users. |
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| Keywords: | Automatic ring detection Dendrochronology Tree-ring proxies Wood density X-ray densitometry |
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