Oyster_growth_run {shelltrace}

Runs the entire growth model

Description

Function that runs all functions contained in Step 2-4 of the growth model. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>

Usage

Oyster_growth_run(LOG=T, raw_data, image_length, season_length=250,
  Xstep=0.1, Tstep=1, Oyster_height, Oyster_length,
  name_file="Oyster_growth_model")

Arguments

LOG

Boolean parameter specifying if a LOG should be printed detailing the parameters entered into this function

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"

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

name_file

string indicating the name that should be added to all exported model results

Details

Runs Oyser_run_sec2, Oyser_run_sec3, Oyser_run_sec4 and Oyster_Export

Value

Matrix containing all parameters of the shell calculated per sub-increment and CSV file containing this matrix

subincr_matrix

Revised version of the "incr_matrix" data frame that contains characteristics calculated for every sub-increment

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

  ## Not run: 
    GList<-Oyster_growth_run(TRUE, O1_input, image_length, season_length=250,
    Xstep=1, Tstep=1, Oyster_height, Oyster_length,name_file="test_export")
  
## End(Not run)