phenology (version 3.43)

plot_phenology: Plot the phenology from a result.

Description

The function "plot_phenology" plots the phenology graph from a result.

Usage

plot_phenology(result = NULL, ..., data = NULL,
    parameters = NULL, parametersfixed = NA, pdf = FALSE,
    series = "all", moon = FALSE, replicate.CI = 1000,
    help = FALSE)

Arguments

result

A result file generated by fit_phenology

data

A dataset generated by add_format

pdf

TRUE or FALSE, indicates if a pdf file is generated.

parametersfixed

Set of fixed parameters

parameters

Set of parameters to be changed

series

Number of series to be analyzed or 'all'

...

Parameters used for graphics (xlab, ylab, ylim, cex and pch)

moon

If TRUE, the moon phase is ploted. Default is FALSE

replicate.CI

Number of replicates for estimation of confidence interval.

help

If TRUE, an help is displayed

Value

• Return a list of outputs. For each site: $site=name of the site estimate1=Estimation of counts not taking into account the observations sd1=The SD of estimation1 estimate2=Estimation of counts taking into account the observations sd2=The SD of estimation2 CI_min=The lower limit for confidence interval CI_max=The upper limit for confidence interval

Details

plot_phenology plots the phenology.

Examples

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, parametersfixed=NULL)
# Run the optimisation
result_Gratiot<-fit_phenology(data=data_Gratiot, parametersfit=parg, parametersfixed=NULL, trace=1)
data(result_Gratiot)
# Plot the phenology and get some stats
output<-plot_phenology(result=result_Gratiot, pdf=FALSE)