Oyster_run_sec2: Runs complete Step 2 of the growth model

Description Usage Arguments Details Value Note Author(s) Source References Examples

View source: R/Oyster_run_sec2.R

Description

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>

Usage

1
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

Value

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

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.

Examples

1

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