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dycdtools package

An R package for assisting calibration and visualising outputs of DYRESM-CAEDYM.

  • The calibration assistant function ("calib.assist") tries a large number of possible combinations of parameter values that users regard as potentially suitable for their model calibration, and calculates the values of nominated objective functions for each combination.

  • Four post-processing functions are included to visualise simulation results:

    • Scatter plot
    • Contour plot
    • Time series plot
    • Profile plot

Installation

To install the latest development version run the following code:

# install devtools
install.packages("devtools")

# install dycdTools package
devtools::install_github("SongyanYu/dycdtools")

# Remove the package zip after installation
unlink("dycdtools.zip")

Developer contact

Songyan (sunny) Yu: sunny.yu@griffith.edu.au

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Version

Install

install.packages('dycdtools')

Monthly Downloads

226

Version

0.3.1

License

MIT + file LICENSE

Maintainer

Songyan Yu

Last Published

October 18th, 2021

Functions in dycdtools (0.3.1)

objective.fun

Measure the goodness of fit for DYCD model simulations.
delete.space

Delete all whitespace until a non-whitespace character.
hgt.to.dpt

convert from height to depth
calib.assist

Assist calibration of DYRESM-CAEDYM model. Before using this function, make sure that you have set up "Bin" and "Files" sub-folders under the DYCD model folder.
plot_cont

Contour plot of simulation results of a bio-geochemical variable.
ext.output

Extract simulations from DYRESM-CAEDYM output.
output_name

Default DYCD simulation variable names with their variable name
interpol

Interpolation of simulation for a series of user-defined depths.
plot_scatter

Scatter plot of sim and obs var values
obs_temp

Example observed profiling temperature data across different depths over the period of 6-11 June 2017.
change_input_file

change parameter value of input files to DYRESM_CAEDYM model.
run.iteration

Internal function to provide parallel processing support to the calibration assistant function.
plot_cont_comp

Contour plot of a variable simulation, with observed data shown as dots in the generated contour plot.
plot_prof

Profile plot of simulated variable values vs. depth
plot_ts

Time series plot of simulated and observed values