Oyster_run_sec5 function

Runs complete Step 5 of the trace element model

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

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

Returns

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

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.

Author(s)

Niels J. de Winter

Note

Please cite Geoscientific Model Development paper dealing with the ShellTrace model

Source

GitHub

Manuscript

Supplementary data

Author website