calibrar-package: Automated Calibration for Complex (Ecological) Models

In calibrar: Automated Parameter Estimation for Complex (Ecological) Models

Description

Automated Calibration for Complex (Ecological) Models

Author(s)

Ricardo Oliveros-Ramos Maintainer: Ricardo Oliveros-Ramos <[e-mail]>

References

calibrar: an R package for the calibration of ecological models (Oliveros-Ramos and Shin 2014)

Examples

## Not run: 
require(calibrar)
set.seed(880820)
path = NULL # NULL to use the current directory
# create the demonstration files
demo = calibrarDemo(model="PoissonMixedModel", L=5, T=100)
# get calibration information
calibrationInfo = getCalibrationInfo(path=demo$path)
# get observed data
observed = getObservedData(info=calibrationInfo, path=demo$path)
# read forcings for the model
forcing = read.csv(file.path(demo$path, "master", "environment.csv"), row.names=1)
# Defining 'runModel' function
runModel = function(par, forcing) {
output = calibrar:::.PoissonMixedModel(par=par, forcing=forcing)
# adding gamma parameters for penalties
output = c(output, list(gammas=par$gamma))
return(output)
}
# real parameters
cat("Real parameters used to simulate data\n")
print(demo$par)
# objective functions
obj  = createObjectiveFunction(runModel=runModel, info=calibrationInfo,
                               observed=observed, forcing=forcing)
cat("Starting calibration...\n")
control = list(weights=calibrationInfo$weights, maxit=3.6e5) # control parameters
cat("Running optimization algorithms\n", "\t", date(), "\n")
cat("Running optim AHR-ES\n")
ahr = calibrate(par=demo$guess, fn=obj, lower=demo$lower, upper=demo$upper, control=control)
summary(ahr)

## End(Not run)

calibrar documentation built on May 2, 2019, 10:58 a.m.