Oyster_run_sec3 function

Runs complete Step 3 of the growth model

Function that combines all functions in Step 3 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_sec3(cross_section, incr_matrix, season_length=250, Xstep=0.1,
  Tstep=1, Oyster_height, Oyster_length)

Arguments

• 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
• 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

Details

This function runs the functions Oyster_Increment_cross_section, Oyster_plot_Inc_CS, Oyster_Inc_fill, Oyster_subincr_area, Oyster_subincr_shell_height, Oyster_subincr_av_thickness and Oyster_ellipse_parameters consecutively

Returns

List of two items: - IncG: Matrix of X- and Y-coordinates of all interpolated sub-increments

• subincr_matrix: Revised version of the "yearly_matrix" data frame that contains characteristics (sub-increment number, X-value of start of increment) recalculated for every sub-increment

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

List3<-Oyster_run_sec3(cross_section, incr_matrix3, season_length=250, Xstep=1,
  Tstep=1, Oyster_height, Oyster_length)