Oyster_combined_run() R function from [shelltrace]

Runs the growth and trace element model

Function that runs the bivalve growth and trace element model from start to finish, combining Step 2-6. de Winter, N. J. (2017) doi:10.5194/gmd-2017-137


Oyster_combined_run(raw_data, image_length, season_length=250, Xstep=0.1, Tstep=1,
Oyster_height, Oyster_length, name_file="Oyster_growth_model", phases_name,
image_name, image_ext, npma=10, name_shell)

Arguments

raw_data: Numeric data frame containing the X- and Y-coordinates digitized in Adobe Illustrator or another image processing software
image_length: Measured maximum length of the area of the cross section that is represented in "raw_data"
season_length: Length (in days) of the growth season of the studied bivalve
Xstep: The step size (dx) in X-direction used to interpolate coordinates of shell increments
Tstep: The step size (dt) in time (days) used to interpolate the existing shell increments
Oyster_height: Measured maximum height of the shell
Oyster_length: Measured maximum length of the shell in anterio-posterior direction
name_file: string indicating the name that should be added to all exported model results
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")
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

Details

Oyster_growth_run and Oyster_phase_run, bundling and exporting the model results

Returns

Exports matrices containing oyster growth parameters for each sub-increment as well as matrices containing trace element accumulation rates and concentration changes through the shells life time resulting from the trace element model. All these matrices are also exported as a list containing: - subincr_matrix: Revised version of the "incr_matrix" data frame that contains characteristics calculated for every sub-increment

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

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.