Oyster_phase_run {shelltrace}

Runs the entire trace element model

Description

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>

Usage

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

Value

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

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.