Oyster_combined_run {shelltrace}

Runs the growth and trace element 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"