Published August 6, 2024
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Sap Flow Analyzer: A tool to standardize sap flow estimation and scaling to whole-tree water use using the HFD method
Description
This article discusses the development of the Sap Flow Analyzer (SFA), an open-source application designed to estimate sap flow rates and tree water use from heat field deformation (HFD) measurements. The tool aims to improve the accuracy and reproducibility of sap flow estimates by offering features like regression models, data visualizations, and methods to upscale sap flow to whole-tree water use. The SFA was tested by multiple participants, demonstrating its effectiveness in processing data consistently, even for users with varying expertise.
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Methods Ecol Evol - 2024 - Wimmler - Sap Flow Analyzer A tool to standardize sap flow estimation and scaling to whole‐tree.pdf
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2024
References
- Arachchige, C. N. P. G., Prendergast, L. A., & Staudte, R. G. (2022). Robust analogs to the coefficient of variation. Journal of Applied Statistics, 49(2), 268–290. https://doi.org/10.1080/02664763.2020.1808599
- Chang, W., Cheng, J., Allaire, J. J., Sievert, C., Schloerke, B., Xie, Y., Allen, J., McPherson, J., Dipert, A., & Borges, B. (2022). shiny: Web application framework for R (R package version 1.7.4). https://CRAN.R-project.org/package=shiny
- Coopman, R. E., Nguyen, H. T., Mencuccini, M., Oliveira, R. S., Sack, L., Lovelock, C. E., & Ball, M. C. (2021). Harvesting water from unsaturated atmospheres: Deliquescence of salt secreted onto leaf surfaces drives reverse sap flow in a dominant arid climate mangrove, Avicennia marina. New Phytologist, 231(4), 1401–1414. https://doi.org/10.1111/NPH.17461
- David, T. S., David, J. S., Pinto, C. A., Cermak, J., Nadezhdin, V., & Nadezhdina, N. (2012). Hydraulic connectivity from roots to branches depicted through sap flow: Analysis on a Quercus suber tree. Functional Plant Biology, 39, 103–115.
- Foken, T., Serafimovich, A., Eder, F., Hübner, J., Gao, Z., & Liu, H. (2017). Energy and matter fluxes of a spruce Forest ecosystem. In Energy and matter fluxes of a spruce Forest ecosystem. Springer Cham. https://doi.org/10.1007/978-3-319-49389-3
- Granier, A. (1987). Evaluation of transpiration in a Douglas-fir stand by means of sap flow measurements. Tree Physiology, 3(4), 309–320. https://doi.org/10.1093/treephys/3.4.309
- Hatton, T. J., Catchpole, E. A., & Vertessy, R. A. (1990). Integration of sapflow velocity to estimate plant water use. Tree Physiology, 6(2), 201–209. https://doi.org/10.1093/treephys/6.2.201
- Link, R. M., Fuchs, S., Arias Aguilar, D., Leuschner, C., Castillo Ugalde, M., Valverde Otarola, J. C., & Schuldt, B. (2020). Tree height predicts the shape of radial sap flow profiles of Costa-Rican tropical dry forest tree species. Agricultural and Forest Meteorology, 287, 107913. https://doi.org/10.1016/j.agrformet.2020.107913
- Liu, Z., Yu, S., Xu, L., Wang, Y., Yu, P., & Chao, Y. (2023). Differentiated responses of daytime and nighttime sap flow to soil water deficit in a larch plantation in Northwest China. Agricultural Water Management, 289, 108540. https://doi.org/10.1016/j.agwat.2023.108540
- Looker, N., Martin, J., Jencso, K., & Hu, J. (2016). Contribution of sapwood traits to uncertainty in conifer sap flow as estimated with the heat-ratio method. Agricultural and Forest Meteorology, 223, 60–71. https://doi.org/10.1016/j.agrformet.2016.03.014
- Nadezhdina, N. (2012). A simplified equation for sap flow calculation based on the heat-field deformation (HFD) measurements. Acta Horticulturae, 951, 117–120.
- Nadezhdina, N. (2018). Revisiting the heat field deformation (HFD) method for measuring sap flow. iForest, 11, 118–130.
- Nadezhdina, N., Čermák, J., & Ceulemans, R. (2002). Radial patterns of sap flow in woody stems of dominant and understory species: Scaling errors associated with positioning of sensors. Tree Physiology, 22(13), 907–918. https://doi.org/10.1093/treephys/22.13.907
- Nadezhdina, N., Cermak, J., Downey, A., Nadezhdin, V., Perämäki, M., Soares David, J., Pinto, C. A., & Soares, D. T. (2015). Sap flow index as an indicator of water storage use. Journal Of Hydrology And Hydromechanics, 63, 124–133.
- Nadezhdina, N., Cermak, J., & Nadezhdin, V. (1998). The heat field deformation method for sap flow measurement. In 4th International Workshop on Measuring Sap Flow in Intact Plants (pp. 72–92). Brno, Czech Republic: Publishing House of Mendel University.
- Nadezhdina, N., Ferreira, M. I., Silva, R., & Pacheco, C. A. (2008). Seasonal variation of water uptake of a Quercus suber tree in Central Portugal. Plant and Soil, 305, 105–119.
- Oishi, A. C., Hawthorne, D. A., & Oren, R. (2016). Baseliner: An open-source, interactive tool for processing sap flux data from thermal dissipation probes. SoftwareX, 5, 139–143. https://doi.org/10.1016/j.softx.2016.07.003
- Peters, R. L., Fonti, P., Frank, D. C., Poyatos, R., Pappas, C., Kahmen, A., Carraro, V., Prendin, A. L., Schneider, L., Baltzer, J. L., Baron-Gafford, G. A., Dietrich, L., Heinrich, I., Minor, R. L., Sonnentag, O., Matheny, A. M., Wightman, M. G., & Steppe, K. (2018). Quantification of uncertainties in conifer sap flow measured with the thermal dissipation method. New Phytologist, 219(4), 1283–1299. https://doi.org/10.1111/nph.15241
- Peters, R. L., Pappas, C., Hurley, A. G., Poyatos, R., Flo, V., Zweifel, R., Goossens, W., & Steppe, K. (2021). Assimilate, process and analyse thermal dissipation sap flow data using the TREX R package. Methods in Ecology and Evolution, 12(2), 342–350. https://doi.org/10.1111/2041-210X.13524
- Poyatos, R., Granda, V., Flo, V., Adams, M. A., Adorján, B., Aguadé, D., Aidar, M. P. M., Allen, S., Alvarado-Barrientos, M. S., Anderson-Teixeira, K. J., Aparecido, L. M., Arain, M. A., Aranda, I., Asbjornsen, H., Baxter, R., Beamesderfer, E., Berry, Z. C., Berveiller, D., Blakely, B., … Martínez-Vilalta, J. (2021). Global transpiration data from sap flow measurements: The SAPFLUXNET database. Earth System Science Data, 13(6), 2607–2649. https://doi.org/10.5194/essd-13-2607-2021
- R Core Team. (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing. https://www.r-project.org/
- Süli, E., & Mayers, D. F. (2003). An introduction to numerical analysis. Cambridge University Press.
- Wimmler, M. C. (2024). Analysis of a user study with the Sap Flow Analyzer (SFA). https://doi.org/10.5281/zenodo.12771340
- Wimmler, M. C., Vovides, A. G., Bowen, H., & Nadezhdina, N. (2024). Sap Flow Analyzer (SFA): an R Shiny tool for processing heat field deformation measurements (v0.3.3). https://doi.org/10.5281/zenodo.12755464