calibrarDemo: Demos for the calibrar package

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

Description

Creates demo files able to be processed for a full calibration using the calibrar package

Usage

calibrarDemo(path = NULL, model = NULL, ...)

Arguments

path	Path to create the demo files
model	Model to be used in the demo files, see details.
...	Additional parameters to be used in the construction of the demo files.

Value

A list with the following elements:

path	Path were the files were saved
par	Real value of the parameters used in the demo
constants	Constants used in the demo

Author(s)

Ricardo Oliveros–Ramos

References

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.