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Assimilate, process and analyse thermal dissipation sap flow data using the TREX r package

Richard L. Peters,Christoforos Pappas,Alexander G. Hurley,Rafael Poyatos,Victor Flo,Roman Zweifel,Willem Goossens,Kathy Steppe,

Abstract

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. 

利用TREX r软件包同化、处理和分析散热sap流量数据

摘要

一个关键的生态生理参数是测量沿着树木水分输送系统的水流（或树液），这是维持土壤-植物-大气连续体中水力连接的一个基本过程。热耗散法（TDM）在科学界广泛用于测量树液流量测量，并从树木到森林水平的用水及其环境敏感性角度提供了新的见解。但从原始TDM测量确定液流通量密度（SFD）的方法是针对具体情况的，会引入不确定性并阻碍数据合成和元分析。 

本研究中介绍了r软件包TREX（TRee sap flow EXtractor），它包含了一系列sap flow数据处理程序，用于从原始TDM测量中量化SFD。TREX提供以下功能：（a）输入和同化原始测量值，（b）数据质量控制和过滤，（c）根据不同的数据处理方法计算标准SFD输出及其相关不确定性。 

本研究以挪威云杉树为例，描述了TREX的功能，其特点是交互式数据整理，并以可复制和透明的方式生成输出。例如，TREX中SFD的计算可以使用原始TDM校准系数、用户提供的校准参数或最近编纂的22项研究和37种物种数据库中的校准数据。此外，该软件包还包括一个自动程序，通过先进的全局灵敏度分析，将所得结果的灵敏度和不确定性量化为用户定义的假设和参数值。

目前研究获得了越来越多的植物生态生理测量的时间序列信息，加深了气候变化对树木功能影响的理解。TREX允许建立TDM测量数据处理的基线，并支持案例研究之间的可比性，促进稳健、透明和可复制的液流模式大规模综合。此外，TREX有助于同时应用多种常用数据处理方法，将原始数据转换为生理相关量。允许对用户特定选择和方法假设的影响（即敏感性和不确定性）进行稳健量化，这对于过程理解和政策制定是必要的。