MVN_MCMC: MCMC simulation for MVN distribution

In CubicZebra/MVNBayesian: Bayesian Analysis Framework for MVN (Mixture) Distribution

Description

Function to get a MCMC simulation results based on the imported MVN distribution. It is commonly used for inquiring the specified conditional probability of MVN distribuiton calculated through Bayesian posteriori.

Usage

# Bayesian posteriori as input data
# data <- MVN_BayesianPosteriori(dataset1, pri_mean=c(80,16,3))

# run MCMC simulation using Bayesian posteriori:
MVN_MCMC(data, steps, pars, values, tol, ...)

Arguments

data	A double level list which contains the mean vector (data$mean) and the covariance matrix (data$var) of a given MVN distribution.
steps	A positive integer. The numbers of random vectors to be generated for MCMC step.
pars	A integer vector to declare fixed dimension(s). For example if the desired dimensions are 1st=7 and 3rd=10, set this argument as c(1,3).
values	A numeric vector to assign value(s) to declared dimension(s). For example if the desired dimensions are 1st=7 and 3rd=10, set this argument as c(7,10).
tol	Tolerance. A numeric value to control the generated vectors to be accepted or rejected. Criterion uses Euclidean distance in declared dimension(s). Default value is 0.3.
...	Other arguments to control the process in Gibbs sampling.

Value

return a list which contains:

AcceptRate	Acceptance of declared conditions of MCMC
MCMCdata	All generated random vectors in MCMC step based on MVN distribution
Accept	Subset of accepted sampling in MCMCdata
Reject	Subset of rejected sampling in MCMCdata

See Also

MVN_GibbsSampler, MVN_FConditional

Examples

library(mvtnorm)
library(plyr)

# dataset1 has three parameters: fac1, fac2 and fac3:
head(dataset1)

# Get posteriori parameters of dataset1 using prior of c(80,16,3):
BPos <- MVN_BayesianPosteriori(dataset1, pri_mean=c(80,16,3))

# If we want to know when fac1=78, how fac2 responses to fac3, run:
BPos_MCMC <- MVN_MCMC(BPos, steps=8000, pars=c(1), values=c(78), tol=0.3)
MCMC <- BPos_MCMC$MCMCdata
head(MCMC)

# Visualization using plot3d() if necessary:
library(rgl)
plot3d(MCMC[,1], MCMC[,2], z=MCMC[,3], col=MCMC[,5]+1, size=2)

# Visualization: 2d scatter plot
MCMC_2d <- BPos_MCMC$Accept
head(MCMC_2d)
plot(MCMC_2d[,3], MCMC_2d[,2], pch=20, col="red", xlab = "fac3", ylab = "fac2")

# Compared to the following scatter plot when fac1 is not fixed:
plot(BPos_MCMC$MCMCdata[,3], BPos_MCMC$MCMCdata[,2], pch=20, col="red", xlab = "fac3",
ylab = "fac2")

CubicZebra/MVNBayesian documentation built on May 17, 2019, 2:14 a.m.