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pyTEF: A Python package for the Total Exchange Flow (TEF) analysis framework |
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15 July 2021 |
paper.bib |
Estuarine circulation describes the water exchange between an estuary and the open ocean. The circulation is characterized by an inflow and outflow at different depths. Typically, the brackish water flows into the ocean near the surface, whereas more saline, thus denser, bottom water flows into the estuary. The TEF framework uses a continous isohaline framework rather than spatial coordinates [@Walin_1977] and combines it with the bulk concept of [@Knudsen_1900]. TEF was first introduced by @MacCready_2011 and allows a profound understanding of the exchange flow of an estuary. For example, the full salinity range during a tidal cycle is only captured in the bulk values by using the isohaline framework.
The pyTEF package provides the necessary tools to apply the TEF framework and is built on top of xarray [@hoyerxarray]. The pyTEF API allows an easy to use package that guides the user through a typical TEF analysis that can be applied to any given estuary. The implemented functions of pyTEF are based on code used for the scientific publications of @Lorenz_etal_2019; @Lorenz_etal_2020 which have been improved to be quicker by suing the numpy library [@harris2020array] . Further, the package uses a numerically converging method to compute the bulk values which also allows for proper quantifaction of exchange flow of more than two layers as presented in @Lorenz_etal_2019. In addition, the package supports the analysis of exchange flow in more than one coordinate, e.g., temperature and salinity coordinates as presented in @Lorenz_etal_2020.
pyTEF is an oceangraphic affiliated Python package for analyzing estuarine exchange flows. TEF is a well-established analysis framework in the estuarine community. It has been applied to several estuarine systems and based on it relationships between salt mixing and the exchange flow have been derived [@MacCready_etal_2018;@Burchard_etal_2019]. But a consistent application tool is still missing. Due to it's not intuitive nature TEF may be very intimidating to start with. It further takes some time to do the coding that is needed to get the desired results. pyTEF tries to solve these issues by providing all necessary functions to successfully apply the method and quantify the exchange flow. This allows a quick and easy analysis within a few lines of code based on open source code. This further leads to an easier and more transparent reproducibility of results.
The technical, mathematical documentation and their references can be found under https://florianboergel.github.io/pyTEF/ and docs/ as HTML. Furthermore, two detailed examples are included which provide a guide on how to use the functionality of the package.
The authors like to thank the communities xarray[@hoyerxarray], the fastai nbdev and numpy [@harris2020array]