TY - JOUR
T1 - Assimilate, process and analyse thermal dissipation sap flow data using the TREX r package
AU - Peters, Richard L.
AU - Pappas, Christoforos
AU - Hurley, Alexander G.
AU - Poyatos, Rafael
AU - Flo, Victor
AU - Zweifel, Roman
AU - Goossens, Willem
AU - Steppe, Kathy
N1 - Funding Information:
We thank Patrick Fonti for providing constructive comments on an earlier version of the manuscript and supplying the example dataset collected at the Lötschental transect. We thank Dirk J. W. De Pauw and Ana Stritih for their discussions on uncertainty analyses. We also thank all researchers and their funding agencies, whose work was essential for obtaining all the calibration experiment data. R.L.P. acknowledges the support of the Swiss National Science Foundation (SNSF), Grant P2BSP3_184475. C.P. acknowledges the support of the SNSF (Grants P2EZP2_162293 and P300P2_174477), the Canada Research Chair in Atmospheric Biogeosciences in High Latitudes and the Global Water Futures project Northern Water Futures. R.P. acknowledges the support of the Spanish grant RTI2018‐095297‐J‐I00 and of a Humboldt Research Fellowship for Experienced Researchers. Data collection was performed in the framework of the SNSF projects INTEGRAL (121859) and LOTFOR (150205). All authors declare that there is no conflict of interest.
Publisher Copyright:
© 2020 British Ecological Society
Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.
PY - 2020
Y1 - 2020
N2 - A key ecophysiological measurement is the flow of water (or sap) along the tree's water-transport system, which is an essential process for maintaining the hydraulic connection within the soil–plant–atmosphere continuum. The thermal dissipation method (TDM) is widespread in the scientific community for measuring sap flow and has provided novel insights into water use and its environmental sensitivity, from the tree- to the forest-stand level. Yet, methodological approaches to determine sap flux density (SFD) from raw TDM measurements remain case-specific, introducing uncertainties and hampering data syntheses and meta-analyses. Here, we introduce the r package TREX (TRee sap flow EXtractor), incorporating a wide range of sap flow data-processing procedures to quantify SFD from raw TDM measurements. TREX provides functions for (a) importing and assimilating raw measurements, (b) data quality control and filtering and (c) calculating standardized SFD outputs and their associated uncertainties according to different data-processing methods. A case study using a Norway spruce tree illustrates TREX's functionalities, featuring interactive data curation and generating outputs in a reproducible and transparent way. The calculations of SFD in TREX can, for instance, use the original TDM calibration coefficients, user-supplied calibration parameters or calibration data from a recently compiled database of 22 studies and 37 species. Moreover, the package includes an automatic procedure for quantifying the sensitivity and uncertainty of the obtained results to user-defined assumptions and parameter values, by means of a state-of-the-art global sensitivity analysis. Time series of plant ecophysiological measurements are becoming increasingly available and enhance our understanding of climate change impacts on tree functioning. TREX allows for establishing a baseline for data processing of TDM measurements and supports comparability between case studies, facilitating robust, transparent and reproducible large-scale syntheses of sap flow patterns. Moreover, TREX facilitates the simultaneous application of multiple common data-processing approaches to convert raw data to physiological relevant quantities. This allows for robust quantification of the impact (i.e. sensitivity and uncertainty) of user-specific choices and methodological assumptions, which is necessary for process understanding and policy making.
AB - A key ecophysiological measurement is the flow of water (or sap) along the tree's water-transport system, which is an essential process for maintaining the hydraulic connection within the soil–plant–atmosphere continuum. The thermal dissipation method (TDM) is widespread in the scientific community for measuring sap flow and has provided novel insights into water use and its environmental sensitivity, from the tree- to the forest-stand level. Yet, methodological approaches to determine sap flux density (SFD) from raw TDM measurements remain case-specific, introducing uncertainties and hampering data syntheses and meta-analyses. Here, we introduce the r package TREX (TRee sap flow EXtractor), incorporating a wide range of sap flow data-processing procedures to quantify SFD from raw TDM measurements. TREX provides functions for (a) importing and assimilating raw measurements, (b) data quality control and filtering and (c) calculating standardized SFD outputs and their associated uncertainties according to different data-processing methods. A case study using a Norway spruce tree illustrates TREX's functionalities, featuring interactive data curation and generating outputs in a reproducible and transparent way. The calculations of SFD in TREX can, for instance, use the original TDM calibration coefficients, user-supplied calibration parameters or calibration data from a recently compiled database of 22 studies and 37 species. Moreover, the package includes an automatic procedure for quantifying the sensitivity and uncertainty of the obtained results to user-defined assumptions and parameter values, by means of a state-of-the-art global sensitivity analysis. Time series of plant ecophysiological measurements are becoming increasingly available and enhance our understanding of climate change impacts on tree functioning. TREX allows for establishing a baseline for data processing of TDM measurements and supports comparability between case studies, facilitating robust, transparent and reproducible large-scale syntheses of sap flow patterns. Moreover, TREX facilitates the simultaneous application of multiple common data-processing approaches to convert raw data to physiological relevant quantities. This allows for robust quantification of the impact (i.e. sensitivity and uncertainty) of user-specific choices and methodological assumptions, which is necessary for process understanding and policy making.
KW - calibration
KW - global sensitivity analysis
KW - sap flux density
KW - thermal dissipation method
KW - transpiration
KW - uncertainty analysis
KW - whole-tree water use
UR - http://www.scopus.com/inward/record.url?scp=85096694308&partnerID=8YFLogxK
U2 - 10.1111/2041-210X.13524
DO - 10.1111/2041-210X.13524
M3 - Artículo
AN - SCOPUS:85096694308
JO - Methods in Ecology and Evolution
JF - Methods in Ecology and Evolution
SN - 2041-210X
ER -