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)
Numeric data frame containing the X- and Y-coordinates digitized in Adobe Illustrator or another image processing software
Measured maximum length of the area of the cross section that is represented in "raw_data"
Length (in days) of the growth season of the studied bivalve
The step size (dx) in X-direction used to interpolate coordinates of shell increments
The step size (dt) in time (days) used to interpolate the existing shell increments
Measured maximum height of the shell
Measured maximum length of the shell in anterio-posterior direction
string indicating the name that should be added to all exported model results
String of full name (including extension!) of the CSV file that contains information about the phases in the map
String of full name of the BMP that needs to be imported, excluding extension
Extention of phase map file ("BMP" or "TIF")
Window size of the moving average used to smooth mass gain record from the bivalve growth model
string indicating the name that should be added to all exported model results
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:
Revised version of the "incr_matrix" data frame that contains characteristics calculated for every sub-increment
matrix of statistics of trace elements and phases in the total map
Matrix of trace element concentrations through time
Matrix of mass accumulation per trace element
Matrix of cumulative mass accumulation per trace element
Oyster_growth_run and Oyster_phase_run, bundling and exporting the model results
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.
"Oyster_growth_run" and "Oyster_phase_run"