Oyster_phase_run() R function from [shelltrace]

Runs the entire trace element model

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)

Arguments

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

Details

Runs Oyser_run_sec5, Oyser_run_sec6 and Oyster_phase_export

Returns

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

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.