| Oyster_run_sec2 {shelltrace} | R Documentation |
Runs complete Step 2 of the growth model
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
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
List2<-Oyster_run_sec2(O1_input, image_length, Xstep=1)