phenology (version 7.2)

par_init: Calculate initial set of parameters.

Description

This function is used to generate an initial set of parameters for fitting that is expected to be not to far from the final. The parameters can be:

• Min, MinE, MinB, PMin, PMinB, PMinE;

• Max;

• Begin, Peak, Flat, End;

• Length, LengthB, LengthE;

• Theta;

• Alpha, Beta, Tau, Phi, Delta;

• Alpha1, Beta1, Tau1, Phi1, Delta1;

• Alpha2, Beta2, Tau2, Phi2, Delta2;

• Alpha3, Beta3, Tau3, Phi3, Delta3;

And the name of level if a cofactor is used. The parameters Max, Min, MinE, MinB, Length, LengthB, LengthE, and Peak can be followed with _ and the name of the rookery.

Usage

par_init(data = stop("A dataset must be provided"),
  fixed.parameters = NULL, add.cofactors = NULL)

Arguments

data

Dataset generated with add_phenology()

fixed.parameters

Set of fixed parameters

add.cofactors

Names of cofactors that will be used (see fit_phenology)

Value

The initial set of parameters

Details

par_init calculates initial set of parameters.

Examples

# NOT RUN {
library(phenology)
# Read a file with data
Gratiot <- read.delim("http://max2.ese.u-psud.fr/epc/conservation/BI/Complete.txt", 
header=FALSE)
data(Gratiot)
# Generate a formatted list nammed data_Gratiot 
data_Gratiot <- add_phenology(Gratiot, name="Complete", 
		reference=as.Date("2001-01-01"), format="%d/%m/%Y")
# Generate initial points for the optimisation
parg <- par_init(data_Gratiot, fixed.parameters=NULL)
# Run the optimisation
result_Gratiot <- fit_phenology(data=data_Gratiot, 
		fitted.parameters=parg, fixed.parameters=NULL)
data(result_Gratiot)
# Plot the phenology and get some stats
output<-plot(result_Gratiot)
# }