Plot the phenology from a result.

Description

The function plot.phenology plots the phenology graph from a result object.
If cofactors have been added, the plot does not show their effects.

Usage

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## S3 method for class 'phenology'
plot(x, ..., data = NULL, parameters = NULL,
  parametersfixed = NULL, se = NULL, series = "all", moon = FALSE,
  replicate.CI = 1000, progressbar = TRUE, help = FALSE,
  growlnotify = TRUE, Plot = 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 replaced. Must be a named vector

parametersfixed

Set of fixed parameters to be replaced. Must be a named vector

se

Set of SE values. Must be a named vector

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

Plot

Should the plot to be shown?

Details

plot.phenology plots the phenology.

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

Author(s)

Marc Girondot

Examples

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## 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, 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="")

## End(Not run)

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