shelltrace (version 3.5.1)

Oyster_run_sec2: 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

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

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

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

# NOT RUN {
  List2<-Oyster_run_sec2(O1_input, image_length, Xstep=1)
# }