Oyster_combined_run: Runs the growth and trace element model

In nielsjdewinter/ShellTrace: Bivalve Growth and Trace Element Accumulation Model

Description

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>

Usage

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

Value

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

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.

See Also

"Oyster_growth_run" and "Oyster_phase_run"

nielsjdewinter/ShellTrace documentation built on May 7, 2019, 2:55 a.m.