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An R package for assisting calibration and visualising outputs of DYRESM-CAEDYM.
In the dycdtools package, there are two main function categories: calibration assistant and post-processing.
The calibration assistant function (calib_assist)
carries out simulations with 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 (i.e., statistical measures of goodness of fit) for each
combination. Based on the calculated objective function values, users
can determine the optimal set(s) of parameter values or narrow the
ranges of possible parameter values. NOTE: the
calib_assist function can only be run on Windows as it
needs to call ‘shell’ to run DYRESM-CARDYM software
executables.
Four post-processing functions provide multiple ways to visualise DYRESM-CAEDYM outputs as follows:
plot_cont displays a heat map of variable
values with depth within the water column and over time. This
visualisation is particularly suitable for displaying temporal and depth
dynamics of a variable at one lake site.plot_prof shows vertical profiles of the
simulation and corresponding observations, for all dates where
observations are available.plot_ts plots simulated values and
observations for a specified variable and depth over time. It can be
used to compare temporal changes of a variable for simulations and
observations at specific depths.plot_scatter shows observations against
simulated values for corresponding time and depth, with a colour scale
representing measured depths. It can be used to demonstrate visually the
goodness of fit for a variable across the water column.For a detailed tutorial of how to use these functions, readers are referred to a peer-reviewed paper by the developers.
IMPORTANT: It is highly recommended that first-time users of the package first run the package functions (particularly’calib_assist’) on the provided example data (see below the Application Section) to familiarise themselves.
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")Below is a minimal case study example. The example data supporting the case study can be accessed via: https://doi.org/10.5281/zenodo.7431128
Assume that you want to calibrate three model parameters: wind stirring efficiency, vertical mixing coefficient, and light extinction coefficient and each parameter have 4 possible values. The calib_assis function can be used to call DYRESM-CAEDYM to run for all possible combinations (n = 64) of the three parameters’ values. For each model run, the objective function Nash-Sutcliffe Efficiency (NSE) coefficient is calculated for temperature simulations.
library(dycdtools)
calib_assist(cal.para = "calibration_data/Calibration_parameters.csv",
combination = "all",
model.var = c("TEMP"),
obs.data = "calibration_data/Obs_data_template.csv",
objective.function = c("NSE"),
start.date = "2002-01-23",
end.date = "2016-12-31",
dycd.wd = "calibration_data/DYRESM_CAEDYM_Lake-Okareka/",
dycd.output = "calibration_data/DYRESM_CAEDYM_Lake-Okareka/DYsim.nc",
file.name = "calibration_data/Calibration_outputs.csv",
write.out = TRUE,
parallel = TRUE,
verbose = TRUE)Use a heatmap to visualise the calculated NSE values for all 64 model runs.
# Read in model calibration results
calibration <- read.csv("calibration_data/Calibration_outputs.csv")
# Heat map
library(ggplot2)
ggplot(calibration, aes(x = wse,y = vmc,fill = NSE.TEMP)) +
geom_tile() +
scale_fill_distiller(palette = "PuBu", direction = 1) +
facet_wrap(~lec, scales = "free") +
xlab("Wind stirring efficiency") +
ylab("Vertical mixing coefficient") +
labs(title = "Light extinction coefficient", fill = "NSE") +
theme_bw() +
theme(plot.title = element_text(size = 11, hjust = 0.5))Based on the 64 model runs, you can select a particular parameter value combination that generate the best performance (measured by NSE) and rerun DYRESM-CAEDYM for that particular parameter values. After that, you can use the post-processing functions in the dycdtools package to visualise the outputs of the calibrated model.
# Extract temperature simulations
var.values <- ext_output(dycd.output = "DYCD_Okareka/DYsim.nc",
var.extract = c("TEMP"))
# Interpolation of temperature across water column at an interval of 0.5 m
temp.interpolated < -interpol(layerHeights = var.values$dyresmLAYER_HTS_Var,
var = var.values$dyresmTEMPTURE_Var,
min.dept = 0, max.dept = 33, by.value = 0.5)
# Read in observed water quality data
library(lubridate)
obs.okareka <- read.csv("plotting_data/Obs_data_template.csv")
obs.okareka$Date <- as.Date(obs.okareka$Date,format="%d/%m/%Y")
# subset observed data to remain temperature observations
obs.temp <- obs.okareka[, c('Date','Depth','TEMP')]
# Contour plot
plot_cont_com(sim = temp.interpolated,
obs = obs.temp,
plot.start = "2002-01-23",
plot.end = "2006-12-31",
sim.start = "2002-01-23",
sim.end = "2016-12-31"
legend.title = "T\n(\u00B0C)",
min.depth = 0,
max.depth = 33,
by.value = 0.5,
nlevels = 20)
# Profile plot
plot_prof(sim = temp.interpolated,
obs = obs.temp,
sim.start = "2002-01-23",
sim.end = "2016-12-31",
plot.start = "2002-01-23",
plot.end = "2002-12-31",
min.depth = 0,
max.depth = 33,
by.value = 0.5,
xlabel = "Temperature \u00B0C")
# Time series plot
plot_ts(sim = temp.interpolated,
obs = obs.temp,
target.depth = c(1, 14, 30),
sim.start = "2002-01-23",
sim.end = "2016-12-31",
plot.start = "2002-01-23",
plot.end = "2012-12-31",
min.depth = 0,
max.depth = 33,
by.value = 0.5,
ylabel = "Temperature \u00B0C")
# Scatter plot
plot_scatter(sim=temp.interpolated,
obs=obs.temp,
sim.start="2002-01-23",
sim.end="2016-12-31",
plot.start = "2002-01-23",
plot.end="2012-12-31",
min.depth = 0,
max.depth = 33,
by.value = 0.5)Songyan (sunny) Yu: sunny.yu@griffith.edu.au
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.