phenology (version 4.0.4)

plot.phenology: Plot the phenology from a result.

Description

The function plot.phenology plots the phenology graph from a result object.

Usage

## S3 method for class 'phenology':
plot(x, ..., data = NULL, parameters = NULL,
  parametersfixed = NA, series = "all", moon = FALSE,
  replicate.CI = 1000, progressbar = TRUE, help = FALSE,
  growlnotify = TRUE)

Arguments

x

A result file generated by fit_phenology

...

Parameters used by plot

data

A dataset generated by add_format

parameters

Set of parameters to be changed

parametersfixed

Set of fixed parameters

series

Number of series to be analyzed or 'all'

moon

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

replicate.CI

Number of replicates for estimation of confidence interval

progressbar

If FALSE, do not show the progress bar

help

If TRUE, an help is displayed

growlnotify

If False, does not send growl notification

Value

• Return A list of lists with formated 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

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(result_Gratiot)
# Plot only part of the nesting season
ptoutput<-plot(result_Gratiot, xlim=c(as.Date("2001-03-01"),as.Date("2001-08-31")))
# Use month names in English
Sys.setlocale(category = "LC_TIME", locale="en_GB.UTF-8")
output<-plot(result_Gratiot)
# set back the month name in local R language
Sys.setlocale(category = "LC_TIME", locale="")