phenology (version 3.40)

plot.mcmcComposite: Plot the result of a MCMC search

Description

Plot the result of a MCMC search. The parameters to use can be called by: parameters="all" parameters=1:4 parameters=c("PAR1", "PAR2", "PAR5") parameters=c(TRUE, TRUE, FALSE, TRUE)

Usage

## S3 method for class 'mcmcComposite':
plot(x, ..., chain = 1,
    parameters = 1)

Arguments

x

A mcmcComposite object obtained after MHmcmc()

chain

The chain to use

parameters

Name of parameters or their number (see description)

...

Graphical parameters to be send to hist()

Value

• None

Details

plot.mcmcComposite plots the result of a MCMC search

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 named data_Gratiot
data_Gratiot<-add_format(origin=NULL, add=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
## not run
# result_Gratiot<-fit_phenology(data=data_Gratiot, parametersfit=parg, parametersfixed=NULL, trace=1)
## end not run
data(result_Gratiot)
# Generate set of priors for Bayesian analysis
## not run
## pmcmc <- phenology_MHmcmc_p(result_Gratiot)
## end not run
pmcmc <- structure(c("dunif", "dunif", "dunif", "dunif", "dunif", "dunif",
"dunif", "dunif", "0", "0", "0", "0", "0", "0", "0", "0", "200",
"365", "200", "50", "200", "5", "5", "10", "2", "2", "2", "2",
"2", "2", "2", "2", "0", "0", "0", "0", "0", "0", "0", "0", "200",
"365", "200", "50", "200", "5", "5", "10", "95.826796339888",
"175.36499338462", "62.4313052780003", "6.77668901451618e-05",
"33.1138407661406", "0.21779065736816", "0.424368825094697",
"3.58302217559733"), .Dim = c(8L, 7L), .Dimnames = list(c("LengthB",
"Peak", "LengthE", "Flat", "Max_Gratiot", "MinB_Gratiot", "MinE_Gratiot",
"Theta"), c("Density", "Prior1", "Prior2", "SDProp", "Min", "Max",
"Init")))
## not run
# res_mcmc <- phenology_MHmcmc(result = result_Gratiot, n.iter = 10000,
# parametersMCMC = pmcmc, n.chains = 1, n.adapt = 0, thin = 1, trace = FALSE)
# data(res_mcmc)
# plot(res_mcmc, parameters=3, xlim=c(230, 330))
## end not run