Oyster_run_sec2 function

Runs complete Step 2 of the growth model

Function that combines all functions in Step 2 of the bivalve growth model and runs them consecutively given the right input. de Winter, N. J. (2017) doi:10.5194/gmd-2017-137

Oyster_run_sec2(raw_data, image_length, Xstep)

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
• Xstep: The step size (dx) in X-direction used to interpolate coordinates of shell increments

Details

This function runs the functions Oyster_Convert_cross_section, Oyster_plot_cross_section, Oyster_incr_area, Oyster_Shell_thickness and Oyster_Shell_height consecutively

Returns

List of three items: - cross_section: Digitized cross section of the shell with shell top, bottom and growth increments relative to a common X-axis

• incr_matrix: Matrix listing characteristics of each digitized increment

• lengthfactor: Factor of actual shell length relative to shell length in cross section, used to constrain pixelsize in phase map

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.

Author(s)

Niels J. de Winter

Note

Please cite Geoscientific Model Development paper dealing with the ShellTrace model

Source

GitHub

Manuscript

Supplementary data

Author website

Examples

List2<-Oyster_run_sec2(O1_input, image_length, Xstep=1)