Oyster_run_sec6 function

Runs complete Step 6 of the trace element model

Function that combines all functions in Step 6 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_sec6(phasemat, IncG, pixelsize, phases, subincr_matrix, npma,
  name_file)

Arguments

• phasemat: matrix of phases of each pixel sorted by X- and Y-coordinate of the pixel
• IncG: Matrix of X- and Y-coordinates of all interpolated sub-increments
• pixelsize: size of pixels in the phase map in micrometer
• phases: Matrix containing colour and trace element data of the phases in the XRF phase map
• subincr_matrix: Data frame that contains characteristics of every sub-increment
• npma: Integer n-value determining the window size of the moving average smoothing of the mass accumulation record
• name_file: string indicating the name of the exported results file

Details

This function runs the functions Oyster_subincr_phases, Oyster_Mass_gain Oyster_el_time and Oyster_accumulation consecutively

Returns

List of three items: - 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

• subincr_matrix: Data frame that contains characteristics of every sub-increment

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

Examples

## Not run:

    List6<-Oyster_run_sec6(phasemat, IncG, pixelsize, O1_phase, subincr_matrix5, npma=10,
    "test_export")
## End(Not run)