# Distributions¶

Given in this section are distributions, as provided by the *Distributions* [2] and *Mamba* packages, supported for the specification of Stochastic nodes. Truncated versions of continuous univariate distributions are also supported.

## Univariate Distributions¶

### Distributions Package Univariate Types¶

The following univariate types from the *Distributions* package are supported.

```
Arcsine DiscreteUniform InverseGamma NoncentralChisq SymTriangularDist
Bernoulli Edgeworth InverseGaussian NoncentralF TDist
Beta Epanechnikov Kolmogorov NoncentralHypergeometric TriangularDist
BetaPrime Erlang KSDist NoncentralT Triweight
Binomial Exponential KSOneSided Normal Uniform
Biweight FDist Laplace NormalCanon VonMises
Categorical Frechet Levy Pareto Weibull
Cauchy Gamma Logistic PoissonBinomial
Chi Geometric LogNormal Poisson
Chisq Gumbel NegativeBinomial Rayleigh
Cosine Hypergeometric NoncentralBeta Skellam
```

### Flat Distribution¶

A Flat distribution is supplied with the degenerate probability density function:

```
Flat() # Flat distribution
```

### User-Defined Univariate Distributions¶

New known, unknown, or unnormalized univariate distributions can be created and added to *Mamba* as subtypes of the *Distributions* package `ContinuousUnivariateDistribution`

or `DiscreteUnivariateDistribution`

types. *Mamba* requires only a partial implementation of the method functions described in the full instructions for creating univariate distributions. The specific workflow is given below.

Create a

`quote`

block for the new distribution. Assign the block a variable name, say`extensions`

, preceded by the`@everywhere`

macro to ensure compatibility whenjuliais run in multi-processor mode.The

Distributionspackage contains types and method definitions for new distributions. Load the package and import any of its methods (indicated below) that are extended.Declare the new distribution subtype, say

`D`

, within the block. Any constructors explicitly defined for the subtype should accept un-typed or abstract-type (`Real`

,`AbstractArray`

, or`DenseArray`

) arguments. Implementing constructors in this way ensures that they will be callable with theMamba`Stochastic`

and`Logical`

types.Extend/define the following

Distributionspackage methods for the new distribution`D`

.Test the subtype.

Add the

`quote`

block (new distribution) toMambawith the following calls.using Mamba @everywhere eval(extensions)

Below is a univariate example based on the linear regression model in the Tutorial.

```
## Define a new univariate Distribution type for Mamba.
## The definition must be placed within an unevaluated quote block.
@everywhere extensions = quote
## Load needed packages and import methods to be extended
using Distributions
import Distributions: minimum, maximum, logpdf
## Type declaration
type NewUnivarDist <: ContinuousUnivariateDistribution
mu::Float64
sigma::Float64
end
## The following method functions must be implemented
## Minimum and maximum support values
minimum(d::NewUnivarDist) = -Inf
maximum(d::NewUnivarDist) = Inf
## Normalized or unnormalized log-density value
function logpdf(d::NewUnivarDist, x::Real)
-log(d.sigma) - 0.5 * ((x - d.mu) / d.sigma)^2
end
end
## Test the extensions in a temporary module (optional)
module Testing end
eval(Testing, extensions)
d = Testing.NewUnivarDist(0.0, 1.0)
Testing.minimum(d)
Testing.maximum(d)
Testing.insupport(d, 2.0)
Testing.logpdf(d, 2.0)
## Add the extensions
using Mamba
@everywhere eval(extensions)
## Implement a Mamba model using the new distribution
model = Model(
y = Stochastic(1,
(mu, s2) ->
begin
sigma = sqrt(s2)
UnivariateDistribution[
NewUnivarDist(mu[i], sigma) for i in 1:length(mu)
]
end,
false
),
mu = Logical(1,
(xmat, beta) ->
xmat * beta,
false
),
beta = Stochastic(1,
() -> MvNormal(2, sqrt(1000))
),
s2 = Stochastic(
() -> InverseGamma(0.001, 0.001)
)
)
## Sampling Scheme
scheme = [NUTS(:beta),
Slice(:s2, 3.0)]
## Sampling Scheme Assignment
setsamplers!(model, scheme)
## Data
line = Dict{Symbol, Any}(
:x => [1, 2, 3, 4, 5],
:y => [1, 3, 3, 3, 5]
)
line[:xmat] = [ones(5) line[:x]]
## Initial Values
inits = [
Dict{Symbol, Any}(
:y => line[:y],
:beta => rand(Normal(0, 1), 2),
:s2 => rand(Gamma(1, 1))
)
for i in 1:3
]
## MCMC Simulation
sim = mcmc(model, line, inits, 10000, burnin=250, thin=2, chains=3)
describe(sim)
```

## Multivariate Distributions¶

### Distributions Package Multivariate Types¶

The following multivariate types from the *Distributions* package are supported.

```
Dirichlet MvNormal MvTDist Multinomial MvNormalCanon VonMisesFisher
```

### Block-Diagonal Multivariate Normal Distribution¶

A Block-Diagonal Multivariate Normal distribution is supplied with the probability density function:

where

```
BDiagNormal(mu, C) # multivariate normal with mean vector mu and block-
# diagonal covariance matrix Sigma such that
# length(mu) = dim(Sigma), and Sigma_1 = ... = Sigma_m = C
# for a matrix C or Sigma_1 = C[1], ..., Sigma_m = C[m]
# for a vector of matrices C.
```

### User-Defined Multivariate Distributions¶

New known, unknown, or unnormalized multivariate distributions can be created and added to *Mamba* as subtypes of the *Distributions* package `ContinuousMultivariateDistribution`

or `DiscreteMultivariateDistribution`

types. *Mamba* requires only a partial implementation of the method functions described in the full instructions for creating multivariate distributions. The specific workflow is given below.

Create a

`quote`

block for the new distribution. Assign the block a variable name, say`extensions`

, preceded by the`@everywhere`

macro to ensure compatibility whenjuliais run in multi-processor mode.The

Distributionspackage contains types and method definitions for new distributions. Load the package and import any of its methods (indicated below) that are extended.Declare the new distribution subtype, say

`D`

, within the block. Any constructors explicitly defined for the subtype should accept un-typed or abstract-type (`Real`

,`AbstractArray`

, or`DenseArray`

) arguments. Implementing constructors in this way ensures that they will be callable with theMamba`Stochastic`

and`Logical`

types.Extend/define the following

Distributionspackage methods for the new distribution`D`

.Test the subtype.

Add the

`quote`

block (new distribution) toMambawith the following calls.using Mamba @everywhere eval(extensions)

Below is a multivariate example based on the linear regression model in the Tutorial.

```
## Define a new multivariate Distribution type for Mamba.
## The definition must be placed within an unevaluated quote block.
@everywhere extensions = quote
## Load needed packages and import methods to be extended
using Distributions
import Distributions: length, insupport, _logpdf
## Type declaration
type NewMultivarDist <: ContinuousMultivariateDistribution
mu::Vector{Float64}
sigma::Float64
end
## The following method functions must be implemented
## Dimension of the distribution
length(d::NewMultivarDist) = length(d.mu)
## Logical indicating whether x is in the support
function insupport{T<:Real}(d::NewMultivarDist, x::AbstractVector{T})
length(d) == length(x) && all(isfinite(x))
end
## Normalized or unnormalized log-density value
function _logpdf{T<:Real}(d::NewMultivarDist, x::AbstractVector{T})
-length(x) * log(d.sigma) - 0.5 * sumabs2(x - d.mu) / d.sigma^2
end
end
## Test the extensions in a temporary module (optional)
module Testing end
eval(Testing, extensions)
d = Testing.NewMultivarDist([0.0, 0.0], 1.0)
Testing.insupport(d, [2.0, 3.0])
Testing.logpdf(d, [2.0, 3.0])
## Add the extensions
using Mamba
@everywhere eval(extensions)
## Implement a Mamba model using the new distribution
model = Model(
y = Stochastic(1,
(mu, s2) -> NewMultivarDist(mu, sqrt(s2)),
false
),
mu = Logical(1,
(xmat, beta) -> xmat * beta,
false
),
beta = Stochastic(1,
() -> MvNormal(2, sqrt(1000))
),
s2 = Stochastic(
() -> InverseGamma(0.001, 0.001)
)
)
## Sampling Scheme
scheme = [NUTS(:beta),
Slice(:s2, 3.0)]
## Sampling Scheme Assignment
setsamplers!(model, scheme)
## Data
line = Dict{Symbol, Any}(
:x => [1, 2, 3, 4, 5],
:y => [1, 3, 3, 3, 5]
)
line[:xmat] = [ones(5) line[:x]]
## Initial Values
inits = [
Dict{Symbol, Any}(
:y => line[:y],
:beta => rand(Normal(0, 1), 2),
:s2 => rand(Gamma(1, 1))
)
for i in 1:3
]
## MCMC Simulation
sim = mcmc(model, line, inits, 10000, burnin=250, thin=2, chains=3)
describe(sim)
```

## Matrix-Variate Distributions¶

### Distributions Package Matrix-Variate Types¶

The following matrix-variate types from the *Distributions* package are supported.

```
InverseWishart Wishart
```