createPrior: Creates a standardized prior class

Description

Creates a standardized prior class

Usage

createPrior(
  density = NULL,
  sampler = NULL,
  lower = NULL,
  upper = NULL,
  best = NULL
)

Arguments

density: Prior density
sampler: Sampling function for density (optional)
lower: vector with lower bounds of parameters
upper: vector with upper bounds of parameter
best: vector with "best" parameter values

Author

Florian Hartig

Details

This is the general prior generator. It is highly recommended to not only implement the density, but also the sampler function. If this is not done, the user will have to provide explicit starting values for many of the MCMC samplers. Note the existing, more specialized prior function. If your prior can be created by those, they are preferred. Note also that priors can be created from an existing MCMC output from BT, or another MCMC sample, via createPriorDensity.

Examples

Run this code

# the BT package includes a number of convenience functions to specify
# prior distributions, including createUniformPrior, createTruncatedNormalPrior
# etc. If you want to specify a prior that corresponds to one of these
# distributions, you should use these functions, e.g.:

prior <- createUniformPrior(lower = c(0,0), upper = c(0.4,5))

prior$density(c(2, 3)) # outside of limits -> -Inf
prior$density(c(0.2, 2)) # within limits, -0.6931472

# All default priors include a sampling function, i.e. you can create
# samples from the prior via
prior$sampler()
# [1] 0.2291413 4.5410389

# if you want to specify a prior that does not have a default function, 
# you should use the createPrior function, which expects a density and 
# optionally a sampler function:

density = function(par){
  d1 = dunif(par[1], -2,6, log =TRUE)
  d2 = dnorm(par[2], mean= 2, sd = 3, log =TRUE)
  return(d1 + d2)
}

sampler = function(n=1){
  d1 = runif(n, -2,6)
  d2 = rnorm(n, mean= 2, sd = 3)
  return(cbind(d1,d2))
}

prior <- createPrior(density = density, sampler = sampler, 
                     lower = c(-10,-20), upper = c(10,20), best = NULL)

# note that the createPrior supports additional truncation


# To use a prior in an MCMC, include it in a BayesianSetup 

set.seed(123)
ll <- function(x) sum(dnorm(x, log = TRUE)) # multivariate normal ll
bayesianSetup <- createBayesianSetup(likelihood = ll, prior = prior)

settings = list(iterations = 100)
out <- runMCMC(bayesianSetup = bayesianSetup, settings = settings)

# use createPriorDensity to create a new (estimated) prior from MCMC output

newPrior = createPriorDensity(out, method = "multivariate",
                              eps = 1e-10, lower = c(-10,-20), 
                              upper = c(10,20), best = NULL, scaling = 0.5)