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>
Oyster_phase_run(LOG=T, phases_name, image_name, image_ext, IncG,
pixelsize, subincr_matrix, npma=10, name_shell, name_file)Boolean parameter specifying if a LOG should be printed detailing the parameters entered into this function
String of full name (including extension!) of the CSV file that contains information about the phases in the map
String of full name of the BMP that needs to be imported, excluding extension
Extention of phase map file ("BMP" or "TIF")
Matrix of X- and Y-coordinates of all interpolated sub-increments
Size of pixels in phase map in micrometeres
Revised version of the "yearly_matrix" data frame that contains characteristics calculated for every sub-increment
Window size of the moving average used to smooth mass gain record from the bivalve growth model
string indicating the name that should be added to all exported model results
string indicating the name of the exported results file
XLSX files of all result matrices of the trace element model as well as a list containing these matrices:
matrix of statistics of trace elements and phases in the total map
Matrix of trace element concentrations through time
Matrix of mass accumulation per trace element
Matrix of cumulative mass accumulation per trace element
Runs Oyser_run_sec5, Oyser_run_sec6 and Oyster_phase_export
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.