Oyster_run_sec3: Runs complete Step 3 of the growth model
Description
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>
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
Value
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
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
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.