hydromod: hydromod - Definition and execution of the model to be...

In hydroPSO: Particle Swarm Optimisation, with Focus on Environmental Models

Description

It runs a user-defined model to be calibrated/optimised and returns a goodness-of-fit value as measure of model performance, by comparing observations against simulated equivalents

Usage

hydromod(param.values, param.files = "ParamFiles.txt", model.drty = getwd(), 
         exe.fname, stdout= FALSE, stderr="", verbose = FALSE, 
         out.FUN, out.FUN.args, gof.FUN, gof.FUN.args=list(), 
         gof.Ini, gof.Fin, date.fmt = "%Y-%m-%d", obs,
         do.png=FALSE, png.fname, width = 1200, height = 600, res=90,
         main, leg.cex=1.2, tick.tstep= "auto", lab.tstep= "auto", 
         lab.fmt=NULL)

Arguments

param.values	numeric vector, a single parameter set used to run the model specified in exe.fname
param.files	character, file name (full path) storing location and names of the files that have to be modified for each parameter. By default param.files="ParamFiles.txt"
model.drty	character, path to the executable file of the model specified in exe.fname. ALL the files required to run the model have to be located within this directory (input files for the model may be located in a different directory, if properly referenced).
exe.fname	character, model command line arguments to be entered through a prompted string to execute the user-defined model
stdout, stderr	where output to ‘stdout’ or ‘stderr’ should be sent. Possible values are FALSE (discard output, the default), "", to the R console. See system2 By default stdout=FALSE and any message printed by the model code to the screen will be omitted. This setting is recommended when calibrating the model with hydroPSO. However, when trying to run the model code with hydromod by the first time, it is recommend to set stdout="", in order to detect if the model was properly executed or not. By default stderr="" and any error message of the model code will be printed to the screen
verbose	logical; if TRUE, progress messages are printed to the screen If verbose=TRUE, the following messages will appear: i) parameter values for each particle; (ii) model execution; iii) extraction of simulated values; and iv) computation of the goodness-of-fit measure
out.FUN	character, name of a valid R function to read the model outputs and transform them into a (zoo) object to be compared against obs (e.g., see read.table, read.csv
out.FUN.args	list, arguments to be passed to out.FUN
gof.FUN	character, name of a valid (goodness-of-fit) R function to obtain model performance (e.g., see NSE, rmse, etc). It MUST HAVE -at least- the following two arguments in its definition: -) sim: numeric with the value(s) simulated by the model specified in exe.fname -) obs: numeric with the observation(s) used to compute model's performance by comparison against sim
gof.FUN.args	list, arguments additional to sim and obs that need to be passed to gof.FUN (e.g., see j argument in mNSE)
gof.Ini	OPTIONAL. Character with the starting date used in the goodness-of-fit function It is used to subset obs (if necessary), AND to define the time period to compare simulated with observed values
gof.Fin	OPTIONAL. Character with the ending date used in the goodness-of-fit function It is used to subset obs (if necessary), AND to define the time period to compare simulated with observed values
date.fmt	character, format in which the dates are stored in Sim.Ini, Sim.Fin, gof.Ini, gof.Fin, e.g. %Y-%m-%d. See format in as.Date
obs	(zoo) object with the observed values
do.png	logical indicating whether a PNG image with the comparison between obs and the best simulated values has to be created If the hydroGOF package is available, the plot is produced with the ggof function. A correlation plot is produced otherwise with the plot_out function
png.fname	OPTIONAL. Used only when do.png=TRUE Name of the PNG file to be created within the model.drty directory. The default value is ‘Obs_vs_Sim.png’
width	OPTIONAL. Used only when do.png=TRUE numeric, width of the output PNG image
height	OPTIONAL. Used only when do.png=TRUE numeric, height of the output PNG image
res	OPTIONAL. Used only when do.png=TRUE numeric, resolution of the output PNG image
main	OPTIONAL. Used only when do.png=TRUE character, representing the main title of the plot comparing observed and simulated values
leg.cex	See ggof
tick.tstep	See ggof
lab.tstep	See ggof
lab.fmt	See ggof

Value

A list of two elements:

sim	numeric, with the simulated values obtained by running the model
GoF	numeric, goodness-of-fit value representing how close each one of the simulated values in sim are to their observed counterparts, by using the USER-DEFINED gof.FUN function

Author(s)

Mauricio Zambrano-Bigiarini, [e-mail]

See Also

hydroPSO

hydroPSO documentation built on April 29, 2020, 9:37 a.m.