geotopGOF: GEOtop Goodnes of fit

In ecor/geotopOptim: An R Plug-in to calibrate soil moisture output of the Distributed Hydrological Model GEOtop

Description

GEOtop Goodnes of fit

Usage

geotopGOF(x = NULL, geotop.model = NULL, approx.list = list(),
  sim = NULL, obs, layer = c("z0005", "z0020"), obs_field = "mean",
  gof.mes = NULL, gof.expected.value.for.optim = NULL, weights = NULL,
  output_simulation = FALSE, names_par = NULL,
  useSoilIntegratedValues = FALSE, temporary.runpath = FALSE,
  multiaggr = TRUE, ...)

Arguments

x	vector with parameters to calibrate. See param in geotopZProfile or geotopExec
geotop.model	a list with arguments for geotopZProfile. It is used if sim is NULL.
approx.list	list of arguments for approxfunDataFrame (optional) or integratefunDataFrame (in this case rember to specify the zrange argument).
sim	simulated data as a object returned by geotopZProfile
obs	observed data
layer	layers corresponding to soil depth at whch GOF indices are calculated
obs_field	obs field used in the observation data frame. Deafault is "mean", it is used in case varaiables are measured with different sensors at the same depth and location.
gof.mes	string(s) containing adopted numerical goodness-of-fit measure. If it is NULL (Default), all mesasures returned by gof are calculated.
gof.expected.value.for.optim	expected value for goodness-of-fit mesure, e.g. 0 or 1. It is used if this function is called by link{geotopPSO},link{hydroPSO} or link{optim}.
weights	vector of weights to assing to each layer, in case of a weigeted-averaged goodness-of-fit measure over all layers. It is NULL (Default) the gooness-of-fit measures are separately calculated for each layer. If it is "uniform", the weights are uniformly distributed in all layers.
output_simulation	logical value. If it is TRUE, function returns a list with the GOF values and the simulated time series
names_par	names of x
useSoilIntegratedValues	logical values. Default is FALSE. If it is TRUE output is integrated with a soil thckness through integratefunDataFrame.
temporary.runpath	logical value. If it TRUE GEOtop is running in a temporary sub-directory, see geotopExec. Default is FALSE.
...	further aguments for gof .

See Also

geotopZProfile,gof

Examples

data(MuntatschiniB2)
## OBSERVATION PROCESSING

obs_SWC <- MuntatschiniB2[str_detect(names(MuntatschiniB2),"SWC")]
zvalues <-  as.numeric(unlist(lapply(X=str_split(names(obs_SWC), pattern="", 
				n = Inf),FUN=function (x) {
					out <- as.numeric(x)
				    out <- out[!is.na(out)]
					out <- paste(out,collapse="")
				return(out)
})))
zformatter = "z%04d"
names(obs_SWC) <- sprintf(zformatter,zvalues)
obs_SWC <- lapply(X=obs_SWC,FUN=function(x){

				if (length(dim(x))>1) {
					max <- apply(X=x,MARGIN=1,FUN=max,na.rm=TRUE)
					min <- apply(X=x,MARGIN=1,FUN=min,na.rm=TRUE)
					mean <- apply(X=x,MARGIN=1,FUN=mean,na.rm=TRUE)
					sd <- apply(X=x,MARGIN=1,FUN=sd,na.rm=TRUE)
				} else {
				
					mean <- as.vector(x)
				 	max <-  as.vector(x)
					min <-  as.vector(x)
					sd <- NA

				}
				out <- data.frame(min=min,mean=mean,max=max,sd=sd)

				out <- as.zoo(out)
             index(out) <- as.POSIXlt(index(x))

				return(out)

})
###########
###########


simpath <- system.file("Muntatschini_pnt_1_225_B2_004",package="geotopOptim")
bin <-   '/home/ecor/local/geotop/GEOtop/bin/geotop-2.0.0' 
##### '/Ubsers/ecor/local/bin/geotop_zh'
runpath <- "/home/ecor/temp/geotopOptim_tests"

vars <- "SoilLiqContentProfileFile"

sim <- geotopZProfile(bin=bin,simpath=simpath,runpath=runpath,
clean=TRUE,variable=vars,data.frame=TRUE,level=1,zformatter=zformatter,intern=TRUE)

gof <- geotopGOF(obs=obs_SWC,sim=sim[[vars[1]]],layer=c("z0005","z0020"))

gof

### Use geotopGOF with an internal GEOtop simulation

## create a list with arguments for geotopZProfile

x <- param <- c(N=1.4,Alpha=0.0021,ThetaRes=0.05) 

geotop.model <- list(bin=bin,simpath=simpath,runpath=runpath,
clean=TRUE,variable=vars,data.frame=TRUE,level=1,zformatter=zformatter,intern=TRUE)

gof_geotop <- geotopGOF(x=x,obs=obs_SWC,geotop.model=geotop.model,layer=c("z0005","z0020"),gof.mes="KGE")

gof_geotop_ <- geotopGOF(x=x,obs=obs_SWC,geotop.model=geotop.model,layer=c("z0005","z0020"),gof.mes="KGE",useSoilIntegratedValues=TRUE,approx.list=list(zrange=c(0,500),rescaleWithDz=TRUE))

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ecor/geotopOptim documentation built on May 15, 2019, 8:54 p.m.