Description Usage Arguments Details Value Note Author(s) Source References Examples
View source: R/Oyster_run_sec6.R
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>
1 2 | Oyster_run_sec6(phasemat, IncG, pixelsize, phases, subincr_matrix, npma,
name_file)
|
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 |
This function runs the functions Oyster_subincr_phases, Oyster_Mass_gain Oyster_el_time and Oyster_accumulation consecutively
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 |
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Niels J. de Winter
GitHub
Manuscript
Supplementary data
Author website
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.
1 2 3 4 5 | ## Not run:
List6<-Oyster_run_sec6(phasemat, IncG, pixelsize, O1_phase, subincr_matrix5, npma=10,
"test_export")
## End(Not run)
|
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