In nielsjdewinter/ShellTrace: Bivalve Growth and Trace Element Accumulation Model

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shelltrace

The goal of shelltrace is to provide the user with an open-source, widely accessible version of the ShellTrace model that is described in the Geoscientific Model Development Paper "ShellTrace v1.0 - A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas)". The model reconstructs growth rates and the rates of incorporation of trace elements into the shells of bivalves. The goal of the model is to reconstruct uptake rates of various trace elements in order to shed light on the processes that influence these uptake rate and to enable the discussion of trace element concentrations in bivalve shells in relation to their environment.

Instructions

The way this package works is slightly different from a regular R package. Most of the functions contained in this package are not meant to run individually. Instead, they form a sequence of steps that need to be followed for the model to work. Examples of all functions and a detailed explanation of their mathmatics are found in the paper which explains the model. Some functions, such as "Oyster_plot_cross_section" are meant to be run by itself, but all functions are embedded in larger functions, such as "Oyster_combined_run" that run all functions of the model in the right order.

Availability

Besides being uploaded to the CRAN database, the source code of this entire package will also be made available online as a supplement to the paper in Geoscientific Model Development and as an entry in the open source research data repository Zenodo (http://doi.org/10.5281/zenodo.817258).

nielsjdewinter/ShellTrace documentation built on May 7, 2019, 2:55 a.m.