bmrm: Bayesian Analysis of Multivariate Receptor Modeling

In bayesMRM: Bayesian Multivariate Receptor Modeling

Bayesian Analysis of Multivariate Receptor Modeling

Description

Generate posterior samples of the source composition matrix P, the source contribution matrix A, and the error variance Σ using 'JAGS', and computes estimates of A,P,Σ.

Usage

bmrm(Y, q, muP,errdist="norm", df=4,
            varP.free=100, xi=NULL, Omega=NULL,
              a0=0.01, b0=0.01,
             nAdapt=1000, nBurnIn=5000, nIter=5000, nThin=1,
             P.init=NULL, A.init=NULL, Sigma.init=NULL,...)

Arguments

Y	data matrix
q	number of sources. It must be a positive integer.
muP	(q,ncol(Y))-dimensional prior mean matrix for the source composition matrix P, where q is the number of sources. Zeros need to be assigned to prespecified elements of muP to satisfy the identifiability condition C1. For the remaining free elements, any nonnegative numbers (between 0 and 1 preferably) can be assigned. If no or an insufficient number of zeros are preassigned in muP, estimation can still be performed but the resulting estimates may be subject to rotational ambiguities. (default=0.5 for nonzero elements ).
errdist	error distribution: either "norm" for normal distribution or "t" for t distribution (default="norm")
df	degrees of freedom of a t-distribution when errdist="t" (default=4)
varP.free	scalar value of the prior variance of the free (nonzero) elements of the source composition matrix P (default=100)
xi	prior mean vector of the q-dimensional source contribution vector at time t (default=vector of 1's)
Omega	diagonal matrix of the prior variance of the q-dimensional source contribution vector at time t (default=identity matrix)
a0	shape parameter of the Inverse Gamma prior of the error variance (default=0.01)
b0	scale parameter of the Inverse Gamma prior of the error variance (default=0.01)
nAdapt	number of iterations for adaptation in 'JAGS' (default=1000)
nBurnIn	number of iterations for the burn-in period in MCMC (default=5000)
nIter	number of iterations for monitoring samples from MCMC (default=5000). nIter samples are saved in each chain of MCMC.
nThin	thinning interval for monitoring samples from MCMC (default=1)
P.init	initial value of the source composition matrix P. If omitted, zeros are assigned to the elements corresponding to zero elements in muP and the nonzero elements of P.init will be randomly generated from a uniform distrbution.
A.init	initial value of the source contribution matrix A. If omitted, it will be calculated from Y and P.init.
Sigma.init	initial value of the error variance. If omitted, it will be calculated from Y, A.init and P.init.
...	arguments to be passed to methods

Details

Model

The basic model for Bayesian multivariate receptor model is as follows:

Y_t=A_t P+E_t, t=1,\cdots,T,

where

• Y_t is a vector of observations of J variables at time t, t = 1,\cdots,T.

• P is a q \times J source composition matrix in which the k-th row represents the k-th source composition profiles, k=1,\cdots,q, q is the number of sources.

• A_t is a q dimensional source contribution vector at time t, t=1,\cdots,T.

• E_t =(E_{t1}, \cdots, E_{tJ}) is an error term for the t-th observations, following E_{t} \sim N(0, Σ) or E_{t} \sim t_{df}(0, Σ), independently for j = 1,\cdots,J, where Σ = diag(σ_{1}^2,..., σ_{J}^2).

Priors

• Prior distribution of A_t is given as a truncated multivariate normal distribution,

  • A_t \sim N(ξ,Ω) I(A_t ≥ 0), independently for t = 1,\cdots,T.

• Prior distribution of P_{kj} (the (k,j)-th element of the source composition matrix P) is given as

  • P_{kj} \sim N(\code{muP}_{kj} , \code{varP.free} )I(P_{kj} ≥ 0), for free (nonzero) P_{kj},

  • P_{kj} \sim N(0, 1e-10 )I(P_{kj} ≥ 0), for zero P_{kj},

    independently for k = 1,\cdots,q; j = 1,\cdots,J .

• Prior distribution of σ_j^2 is IG(a0, b0), i.e.,

  • 1/σ_j^2 \sim Gamma(a0, b0), having mean a0/b0, independently for j=1,...,J.

Notes

• We use the prior P_{kj} \sim N(0, 1e-10 )I(P_{kj} ≥ 0) that is practically equal to the point mass at 0 to simplify the model building in 'JAGS'.

• The MCMC samples of A and P are post-processed (rescaled) before saving so that ∑_{j=1}^J P_{kj} =1 for each k=1,...,q (the identifiablity condition C3 of Park and Oh (2015).

Value

in bmrm object

nsource

number of sources

nobs

number of observations in data Y

nvar

number of variables in data Y

Y

observed data matrix

muP

prior mean of the source composition matrix P

errdist

error distribution

df

degrees of freedom when errdist="t"

A.hat

posterior mean of the source contribution matrix A

P.hat

posterior mean of the source composition matrix P

Sigma.hat

posterior mean of the error variance Sigma

A.sd

posterior standard deviation of the source contribution matrix A

P.sd

posterior standard deviation of the source composition matrix P

Sigma.sd

posterior standard deviation of the error variance Sigma

A.quantiles

posterior quantlies of A for prob=(0.025, 0.05, 0.25, 0.5, 0.75, 0.95, 0.975)

P.quantiles

posterior quantiles of P for prob=(0.025, 0.05, 0.25, 0.5, 0.75, 0.95, 0.975)

Sigma.quantiles

posterior quantiles of Sigma for prob=(0.025, 0.05, 0.25, 0.5, 0.75, 0.95, 0.975)

Y.hat

predicted value of Y computed from A.hat*P.hat

residual

Y-Y.hat

codaSamples

MCMC posterior samples of A, P, and Σ in class "mcmc.list"

nIter

number of MCMC iterations per chain for monitoring samples from MCMC

nBurnIn

number of iterations for the burn-in period in MCMC

nThin

thinning interval for monitoring samples from MCMC

References

Park, E.S. and Oh, M-S. (2015), Robust Bayesian Multivariate Receptor Modeling, Chemometrics and intelligent laboratory systems, 149, 215-226.

Plummer, M. 2003. JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling. Proceedings of the 3rd international workshop on distributed statistical computing, pp. 125. Technische Universit at Wien, Wien, Austria.

Plummer, M. 2015. 'JAGS' Version 4.0.0 user manual.

Examples

data(Elpaso); Y=Elpaso$Y ; muP=Elpaso$muP ; q=nrow(muP)
out.Elpaso <- bmrm(Y,q,muP)
summary(out.Elpaso)
plot(out.Elpaso)

bayesMRM documentation built on Dec. 28, 2022, 1:36 a.m.