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tracheideR—An R package to standardize tracheidograms

Campelo, Filipe, Nabais, Cristina, Carvalho, Ana, Vieira, Joana
Dendrochronologia 2016 v.37 pp. 64-68
Mediterranean climate, Pinus pinaster, conifers, growing season, growth rings, image analysis, soil temperature, soil water, soil water content, tracheids, weather
Here we present the package tracheideR to standardize profiles of tracheid features, using the R computing environment. This package contains a collection of functions to transform the raw data obtained from image analysis into a tracheidogram to better visualize the radial intra-ring variation of histometric parameters. This procedure is crucial when estimating past weather conditions with a sub-annual resolution, since tracheidograms reflect the influence of fluctuations in weather conditions throughout the growing season (such as temperature and soil water content). The main function of this package is tracheider, which takes as input raw tracheidograms and standardizes them using three different methods. The first method standardizes the number of tracheids from different radial files to the mean number of cells, allowing that different annual rings have different number of cells. The second method normalizes the number of cells of different annual rings to the same number. Finally we present a new method to standardize histometric parameters considering the relative position of the cells within the tree ring. This package was tested using two rings of Pinus pinaster to demonstrate variations between the three methods. According to our results species with high intra- and inter-annual variability, as shown by conifers species growing under Mediterranean climate, should be standardized using the “relative position” method. Finally, we suggest that this new method should be applied to other species to check its potential to detect intra-ring fluctuations in tracheid features and to improve our capacity to detect intra-annual climatic signals.