Distributions Provided by the mniw Package

Wishart Distribution

The Wishart distribution on a random positive-definite matrix \({\boldsymbol{X}}_{q\times q}\) is is denoted \({\boldsymbol{X}}\sim \textrm{Wish}({\boldsymbol{\Psi}}, \nu)\), and defined as \({\boldsymbol{X}}= ({\boldsymbol{L}}{\boldsymbol{Z}})({\boldsymbol{L}}{\boldsymbol{Z}})'\), where:

• \({\boldsymbol{\Psi}}_{q\times q} = {\boldsymbol{L}}{\boldsymbol{L}}'\) is the positive-definite matrix scale parameter,

• \(\nu > q\) is the shape parameter,

• \({\boldsymbol{Z}}_{q\times q}\) is a random lower-triangular matrix with elements

  \[ Z_{ij} \begin{cases} \overset{\;\textrm{iid}\;}{\sim}\mathcal{N}(0,1) & i < j \\ \overset{\:\textrm{ind}\:}{\sim}\chi^2_{(\nu-i+1)} & i = j \\ = 0 & i > j. \end{cases} \]

The log-density of the Wishart distribution is \[ \log p({\boldsymbol{X}}\mid {\boldsymbol{\Psi}}, \nu) = -\textstyle{\frac{1}{2}} \left[\mathrm{tr}({\boldsymbol{\Psi}}^{-1} {\boldsymbol{X}}) + (q+1-\nu)\log |{\boldsymbol{X}}| + \nu \log |{\boldsymbol{\Psi}}| + \nu q \log(2) + 2 \log \Gamma_q(\textstyle{\frac{\nu }{2}})\right], \] where \(\Gamma_n(x)\) is the multivariate Gamma function defined as \[ \Gamma_n(x) = \pi^{n(n-1)/4} \prod_{j=1}^n \Gamma\big(x + \textstyle{\frac{1}{2}} (1-j)\big). \]

Matrix-Normal Distribution

The Matrix-Normal distribution on a random matrix \({\boldsymbol{X}}_{p \times q}\) is denoted \({\boldsymbol{X}}\sim \textrm{MatNorm}({\boldsymbol{\Lambda}}, {\boldsymbol{\Sigma}}_R, {\boldsymbol{\Sigma}}_C)\), and defined as \({\boldsymbol{X}}= {\boldsymbol{L}}{\boldsymbol{Z}}{\boldsymbol{U}}+ {\boldsymbol{\Lambda}}\), where:

• \({\boldsymbol{\Lambda}}_{p \times q}\) is the mean matrix parameter,
• \({{\boldsymbol{\Sigma}}_R}_{p \times p} = {\boldsymbol{L}}{\boldsymbol{L}}'\) is the row-variance matrix parameter,
• \({{\boldsymbol{\Sigma}}_C}_{q \times q} = {\boldsymbol{U}}'{\boldsymbol{U}}\) is the column-variance matrix parameter,
• \({\boldsymbol{Z}}_{q\times q}\) is a random matrix with \(Z_{ij} \overset{\;\textrm{iid}\;}{\sim}\mathcal{N}(0,1)\).

The log-density of the Matrix-Normal distribution is \[ \log p({\boldsymbol{X}}\mid {\boldsymbol{\Lambda}}, {\boldsymbol{\Sigma}}_R, {\boldsymbol{\Sigma}}_C) = -\textstyle{\frac{1}{2}} \left[\mathrm{tr}\big({\boldsymbol{\Sigma}}_C^{-1}({\boldsymbol{X}}-{\boldsymbol{\Lambda}})'{\boldsymbol{\Sigma}}_R^{-1}({\boldsymbol{X}}-{\boldsymbol{\Lambda}})\big) + \nu q \log(2\pi) + \nu \log |{\boldsymbol{\Sigma}}_C| + q \log |{\boldsymbol{\Sigma}}_R|\right]. \]

Matrix-Normal Inverse-Wishart Distribution

The Matrix-Normal Inverse-Wishart Distribution on a random matrix \({\boldsymbol{X}}_{p \times q}\) and random positive-definite matrix \({\boldsymbol{V}}_{q\times q}\) is denoted \(({\boldsymbol{X}},{\boldsymbol{V}}) \sim \textrm{MNIW}({\boldsymbol{\Lambda}}, {\boldsymbol{\Sigma}}, {\boldsymbol{\Psi}}, \nu)\), and defined as \[ \begin{aligned} {\boldsymbol{X}}\mid {\boldsymbol{V}}& \sim \textrm{MatNorm}({\boldsymbol{\Lambda}}, {\boldsymbol{\Sigma}}, {\boldsymbol{V}}) \\ {\boldsymbol{V}}& \sim \textrm{InvWish}({\boldsymbol{\Psi}}, \nu). \end{aligned} \]

Matrix-t Distribution

The Matrix-\(t\) distribution on a random matrix \({\boldsymbol{X}}_{p \times q}\) is denoted \({\boldsymbol{X}}\sim \textrm{MatT}({\boldsymbol{\Lambda}}, {\boldsymbol{\Sigma}}_R, {\boldsymbol{\Sigma}}_C, \nu)\), and defined as the marginal distribution of \({\boldsymbol{X}}\) for \(({\boldsymbol{X}}, {\boldsymbol{V}}) \sim \textrm{MNIW}({\boldsymbol{\Lambda}}, {\boldsymbol{\Sigma}}_R, {\boldsymbol{\Sigma}}_C, \nu)\). Its log-density is given by \[ \begin{aligned} \log p({\boldsymbol{X}}\mid {\boldsymbol{\Lambda}}, {\boldsymbol{\Sigma}}_R, {\boldsymbol{\Sigma}}_C, \nu) & = -\textstyle{\frac{1}{2}} \Big[(\nu+p+q-1)\log | I + {\boldsymbol{\Sigma}}_R^{-1}({\boldsymbol{X}}-{\boldsymbol{\Lambda}}){\boldsymbol{\Sigma}}_C^{-1}({\boldsymbol{X}}-{\boldsymbol{\Lambda}})'| \\ & \phantom{= -\textstyle{\frac{1}{2}} \Big[} + q \log |{\boldsymbol{\Sigma}}_R| + p \log |{\boldsymbol{\Sigma}}_C| \\ & \phantom{= -\textstyle{\frac{1}{2}} \Big[} + pq \log(\pi) - \log \Gamma_q(\textstyle{\frac{\nu+p+q-1}{2}}) + \log \Gamma_q(\textstyle{\frac{\nu+q-1}{2}})\Big]. \end{aligned} \]

Random-Effects Normal Distribution

Consider the multivariate normal distribution on \(q\)-dimensional vectors \({\boldsymbol{x}}\) and \({\boldsymbol{\mu}}\) given by \[ \begin{aligned} {\boldsymbol{x}}\mid {\boldsymbol{\mu}}& \sim \mathcal{N}({\boldsymbol{\mu}}, {\boldsymbol{V}}) \\ {\boldsymbol{\mu}}& \sim \mathcal{N}({\boldsymbol{\lambda}}, {\boldsymbol{\Sigma}}). \end{aligned} \] The random-effects normal distribution is defined as the posterior distribution \({\boldsymbol{\mu}}\sim p({\boldsymbol{\mu}}\mid {\boldsymbol{x}})\), which is given by \[ {\boldsymbol{\mu}}\mid {\boldsymbol{x}}\sim \mathcal{N}\big({\boldsymbol{G}}({\boldsymbol{x}}-{\boldsymbol{\lambda}}) + {\boldsymbol{\lambda}}, {\boldsymbol{G}}{\boldsymbol{V}}\big), \qquad {\boldsymbol{G}}= {\boldsymbol{\Sigma}}({\boldsymbol{V}}+ {\boldsymbol{\Sigma}})^{-1}. \] The notation for this distribution is \({\boldsymbol{\mu}}\sim \textrm{RxNorm}({\boldsymbol{x}}, {\boldsymbol{V}}, {\boldsymbol{\lambda}}, {\boldsymbol{\Sigma}})\).

Hierarchical Normal-Normal Model

The hierarchical Normal-Normal model is defined as \[ \begin{aligned} {\boldsymbol{y}}_i \mid {\boldsymbol{\mu}}_i, {\boldsymbol{\beta}}, {\boldsymbol{\Sigma}}& \overset{\:\textrm{ind}\:}{\sim}\mathcal{N}({\boldsymbol{\mu}}_i, {\boldsymbol{V}}_i) \\ {\boldsymbol{\mu}}_i \mid {\boldsymbol{\beta}}, {\boldsymbol{\Sigma}}& \overset{\;\textrm{iid}\;}{\sim}\mathcal{N}({\boldsymbol{x}}_i'{\boldsymbol{\beta}}, {\boldsymbol{\Sigma}}) \\ ({\boldsymbol{\beta}}, {\boldsymbol{\Sigma}}) & \sim \textrm{MNIW}({\boldsymbol{\Lambda}}, \Omega^{-1}, {\boldsymbol{\Psi}}, \nu), \end{aligned} \] where:

• \({{\boldsymbol{y}}_i}_{q\times 1}\) is the response vector for subject \(i\),
• \({{\boldsymbol{\mu}}_i}_{q\times 1}\) is the random effect for subject \(i\),
• \({{\boldsymbol{V}}_i}_{q\times q}\) is the error variance for subject \(i\),
• \({{\boldsymbol{x}}_i}_{p\times 1}\) is the covariate vector for subject \(i\),
• \({\boldsymbol{\beta}}_{p \times q}\) is the random-effects coefficient matrix,
• \({\boldsymbol{\Sigma}}_{q \times q}\) is the random-effects error variance.

Let \({\boldsymbol{Y}}_{n\times q} = (\boldsymbol{y}_{1},\ldots,\boldsymbol{y}_{n})\), \({\boldsymbol{X}}_{n\times p} = (\boldsymbol{x}_{1},\ldots,\boldsymbol{x}_{n})\), and \({\boldsymbol{\Theta}}_{n \times q} = (\boldsymbol{\mu}_{1},\ldots,\boldsymbol{\mu}_{n})\). If interest lies in the posterior distribution \(p({\boldsymbol{\Theta}}, {\boldsymbol{\beta}}, {\boldsymbol{\Sigma}}\mid {\boldsymbol{Y}}, {\boldsymbol{X}})\), then a Gibbs sampler can be used to cycle through the following conditional distributions: \[ \begin{aligned} {\boldsymbol{\mu}}_i \mid {\boldsymbol{\beta}}, {\boldsymbol{\Sigma}}, {\boldsymbol{Y}}, {\boldsymbol{X}}& \overset{\:\textrm{ind}\:}{\sim}\textrm{RxNorm}({\boldsymbol{y}}_i, {\boldsymbol{V}}_i, {\boldsymbol{x}}_i'{\boldsymbol{\beta}}, {\boldsymbol{\Sigma}}) \\ {\boldsymbol{\beta}}, {\boldsymbol{\Sigma}}\mid {\boldsymbol{\Theta}}, {\boldsymbol{Y}}, {\boldsymbol{X}}& \sim \textrm{MNIW}(\hat {\boldsymbol{\Lambda}}, \hat {\boldsymbol{\Omega}}^{-1}, \hat {\boldsymbol{\Psi}}, \hat \nu), \end{aligned} \] where \(\hat {\boldsymbol{\Lambda}}\), \(\hat {\boldsymbol{\Omega}}\), \(\hat {\boldsymbol{\Psi}}\), and \(\hat \nu\) are obtained from the MNIW conjugate posterior formula with \({\boldsymbol{Y}}\gets {\boldsymbol{\Theta}}\).