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Functions presented in this repository were developed for the assessment of growth trends, patterns of climatic limitations, and the identification of extreme growth reductions for dominant forest tree species across the Czech Republic. Their functionality was designed for processing tree-ring width series stored in the TreeDataClim database.
Acknowledgements and credits
The repository contains scripts and functions developed under the project funded by TAČR SS03010134 Tree-ring database as a tool for description and prediction of responses of the main forest tree species to climate change.
The development of the modified version of the VS-Lite process-based model of wood formation was largely inspired by the work of Dr. Suzan Tolwinski-Ward, mainly by Octave codes of the original model made available at NOAA. Similarly, individual R functions use few publicly-available packages contributing to specific data processing steps and plotting charts. We are grateful to all authors of these packages for making them freely available.
Functionality
This repository represents a compilation of stand-alone functions that were developed to process tree-ring width data following the methodology of the TreeDataClim project. The individual functions are grouped in the following folders:
Reductions: functions to identify, evaluate, and extrapolate events of extreme growth reductionsLimitations: a process-based model of intra-annual wood formation and its application to assess the type and the intensity of climatic limitation of wood formation on an intra-annual scaleTrends: functions to quantify recent growth trends and to extrapolate their patterns across spaceMisc (aka miscellaneous): pre-processing of dendrometer data required for subsequent functions, plotting of climatic diagrams
Each folder contains separate readme files explaining individual steps of the functions’ application. Most functions were developed in R language except the VS-Lite process-based model of wood formation, which is written in Octave. Both languages are open-source. We recommend using the latest versions of both programming environments with our scripts.
The functions were developed and tested reflecting the structure of the TreeDataClim dataset and methodology, i.e., a dense network of tree-ring width series across the Czech Republic. However, the procedures can be directly applied to any other region of the world with available tree-ring width datasets. The functions’ target period was 1961-2010 since we found it to be an optimal balance between the timespan of the analysis and the quality of the data (mainly the availability of reliable climatic data). Details about the required inputs and the way to apply each function are given as annotations in the specific script. Some functions require a prior installation of open-source packages and extensions both in R and Octave languages. Required packages and extensions are indicated at the beginning of each script.
Inputs
Individual functions serve to process tree-ring width data following the methodology developed as a part of the TreeDataClim project. Individual inputs differ depending on each function and are indicated at the beginning of each script. The template of each input file can be found in the Input folder. This folder contains example data from 16 sites of two species (Picea abies and Quercus robur) distributed across the northern part of the Czech Republic.
Contact and bug reporting
Jan Tumajer tumajerj@natur.cuni.cz
Charles University, Faculty of Science, Department of Physical Geography and Geoecology, Albertov 6, 12843 Prague, Czech Republic
Jakub Kašpar kaspar@vukoz.cz
Department of Forest Ecology, Silva Tarouca Research Institute, Blue Cat Team