Oyster_run_sec6: 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>
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
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
Details
This function runs the functions Oyster_subincr_phases, Oyster_Mass_gain
Oyster_el_time and Oyster_accumulation consecutively
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.