Oyster_run_sec6 {shelltrace}

Runs complete Step 6 of the trace element model

Description

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>

Usage

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

Value

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

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.

Examples

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