Oyster_run_sec5: Runs complete Step 5 of the trace element model

In shelltrace: Bivalve Growth and Trace Element Accumulation Model

Description

Function that combines all functions in Step 5 of the bivalve trace element model and runs them consecutively given the right input. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>

Usage

Oyster_run_sec5(phases_name, image_name, image_ext)

Arguments

phases_name	String of full name (including extension!) of the CSV file that contains information about the phases in the map
image_name	String of full name of the BMP that needs to be imported, excluding extension
image_ext	Extention of phase map file ("BMP" or "TIF")

Details

This function runs the functions Oyster_import_phases, Oyster_phase_matrix_BMP, Oyster_phase_matrix_TIF and Oyster_phase_stat consecutively

Value

List of two items:

phasemat	matrix of phases of each pixel sorted by X- and Y-coordinate of the pixel
phase_stat	matrix of statistics of trace elements and phases in the total map
phases	Matrix containing colour, density and trace element data of the phases in the XRF phase map

Note

Please cite Geoscientific Model Development paper dealing with the ShellTrace model

Author(s)

Niels J. de Winter

Source

GitHub
Manuscript
Supplementary data
Author website

References

de Winter, N. J.: 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), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.

shelltrace documentation built on May 2, 2019, 2:25 a.m.