as.quantiles: Extract quantile distribution from mcmcComposite object

In HelpersMG: Tools for Environmental Analyses, Ecotoxicology and Various R Functions

Extract quantile distribution from mcmcComposite object

Description

Extract quantile distribution from mcmcComposite object

Usage

as.quantiles(
  x,
  chain = 1,
  fun = function(...) return(as.numeric(list(...))),
  probs = c(0.025, 0.975),
  xlim = NULL,
  nameparxlim = NULL,
  namepar = NULL
)

Arguments

x	A mcmcComposite obtained as a result of MHalgoGen() function
chain	The number of the chain in which to get parameters
fun	The function to apply the parameters
probs	The probability to get quantiles
xlim	The values to apply in fun
nameparxlim	The name of the parameter for xlim
namepar	The name of parameters from mcmc object to be used in fun

Value

A data.frame with quantiles

Author(s)

Marc Girondot [e-mail]

See Also

Other mcmcComposite functions: MHalgoGen(), as.mcmc.mcmcComposite(), as.parameters(), merge.mcmcComposite(), plot.PriorsmcmcComposite(), plot.mcmcComposite(), setPriors(), summary.mcmcComposite()

Examples

## Not run: 
library(HelpersMG)
require(coda)
x <- rnorm(30, 10, 2)
dnormx <- function(data, x) {
 data <- unlist(data)
 return(-sum(dnorm(data, mean=x['mean'], sd=x['sd'], log=TRUE)))
}
parameters_mcmc <- data.frame(Density=c('dnorm', 'dlnorm'), 
Prior1=c(10, 0.5), Prior2=c(2, 0.5), SDProp=c(1, 1), 
Min=c(-3, 0), Max=c(100, 10), Init=c(10, 2), stringsAsFactors = FALSE, 
row.names=c('mean', 'sd'))
mcmc_run <- MHalgoGen(n.iter=10000, parameters=parameters_mcmc, data=x, 
likelihood=dnormx, n.chains=1, n.adapt=100, thin=1, trace=1)
k <- as.quantiles(x=mcmc_run, namepar="mean")
k <- as.quantiles(x=mcmc_run, namepar="mean", 
                 xlim=c(1:5), nameparxlim="sd", 
                 fun=function(...) return(sum(as.numeric(list(...)))))

## End(Not run)

HelpersMG documentation built on Oct. 5, 2023, 5:08 p.m.