Oyster_phase_run: Runs the entire trace element model
In shelltrace: Bivalve Growth and Trace Element Accumulation Model

Description Usage Arguments Details Value Note Author(s) Source References

Function that runs all functions contained in Step 5 and 6 of the trace element model. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>

1 2	Oyster_phase_run(LOG=T, phases_name, image_name, image_ext, IncG, pixelsize, subincr_matrix, npma=10, name_shell, name_file)

`LOG`	Boolean parameter specifying if a LOG should be printed detailing the parameters entered into this function
`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")
`IncG`	Matrix of X- and Y-coordinates of all interpolated sub-increments
`pixelsize`	Size of pixels in phase map in micrometeres
`subincr_matrix`	Revised version of the "yearly_matrix" data frame that contains characteristics calculated for every sub-increment
`npma`	Window size of the moving average used to smooth mass gain record from the bivalve growth model
`name_shell`	string indicating the name that should be added to all exported model results
`name_file`	string indicating the name of the exported results file

Runs Oyser_run_sec5, Oyser_run_sec6 and Oyster_phase_export

XLSX files of all result matrices of the trace element model as well as a list containing these matrices:

`phase_stat`	matrix of statistics of trace elements and phases in the total map
`el_time`	Matrix of trace element concentrations through time
`M_el_mat`	Matrix of mass accumulation per trace element
`M_el_mat_c`	Matrix of cumulative mass accumulation per trace element

Please cite Geoscientific Model Development paper dealing with the ShellTrace model

Niels J. de Winter

GitHub
Manuscript
Supplementary data
Author website

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.