sapfluxr: An R package for the processing and analysis of multi-method heat pulse velocity sap flow data

Grant W Joyce

Heat pulse velocity (HPV) methods are the preferred approach for long-term, ecologically interpretable measurement of tree water use, yet no open-source software has existed to process raw HPV temperature traces into whole-tree water-use estimates. Researchers have instead depended on proprietary tools whose correction algorithms and processing steps cannot be inspected or reproduced. This thesis presents sapfluxr, the first R package to integrate the complete HPV processing chain, paired with shiny-sapfluxr, a graphical interface that creates a reproducible R script to document each workflow. The package also introduces four methodological innovations in sap flow processing software: (1) a Dual-Stable Calibration that proposes candidate zero-flow periods from a co-located vapour pressure deficit record and from the stability of the velocity signal within an astronomically computed predawn window, (2) a temporal wound correction that models the widening of the wound across a deployment instead of applying a single static coefficient, (3) a cross-method correction transfer that carries the Heat Ratio Method's corrections onto a secondary method, and (4) a Selectable Dual Method Approach that pairs the Heat Ratio Method with the Maximum Heat Ratio method and switches between them using the Péclet number. Processed output from sapfluxr was validated against data processed using the proprietary Sap Flow Tool software. A worked example was then used to demonstrate the processing steps and corrections implemented in sapfluxr, using a 342-day deployment in a Banksia attenuata on the Murdoch University campus. Using the Dual Method Approach reduced errors in quantifying daily water use, particularly on high-demand summer days, when compared to using the Heat Ratio Method alone. Furthermore, the workflow was captured and documented with shiny-sapfluxr. By making each correction explicit, documented, and open to inspection, sapfluxr converts a previously hidden source of methodological uncertainty into a transparent and reproducible component of sap flow analysis.