Package 'VecDep' reference manual

Title:	Measuring Copula-Based Dependence Between Random Vectors
Description:	Provides functions for estimation (parametric, semi-parametric and non-parametric) of copula-based dependence coefficients between a finite collection of random vectors, including phi-dependence measures and Bures-Wasserstein dependence measures. An algorithm for agglomerative hierarchical variable clustering is also implemented. Following the articles De Keyser & Gijbels (2024) <doi:10.1016/j.jmva.2024.105336>, De Keyser & Gijbels (2024) <doi:10.1016/j.ijar.2023.109090>, and De Keyser & Gijbels (2024) <doi:10.48550/arXiv.2404.07141>.
Authors:	Steven De Keyser [aut, cre] , Irène Gijbels [ctb]
Maintainer:	Steven De Keyser <[email protected]>
License:	GPL-3
Version:	0.1.3
Built:	2024-11-15 09:23:05 UTC
Source:	CRAN

betakernelestimator

Description

This function computes the non-parametric beta kernel copula density estimator.

Usage

betakernelestimator(input, h, pseudos)
betakernelestimator(input, h, pseudos)

Arguments

`input`	The copula argument at which the density estimate is to be computed.
`h`	The bandwidth to be used in the beta kernel.
`pseudos`	The (estimated) copula observations from a $q$ -dimensional random vector $\mathbf{X}$ ( $n \times q$ matrix with observations in rows, variables in columns).

Details

Given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1}, \dots, \mathbf{X}_{k})$ with $\mathbf{X}_{i} = (X_{i1}, \dots, X_{id_{i}})$ , and samples $X_{ij}^{(1)}, \dots, X_{ij}^{(n)}$ from $X_{ij}$ for $i = 1, \dots, k$ and $j = 1, \dots, d_{i}$ , the beta kernel estimator for the copula density of $\mathbf{X}$ equals, at $\mathbf{u} = (u_{11}, \dots, u_{kd_{k}}) \in \mathbb{R}^{q}$ ,

$\widehat{c}_{\text{B}}(\mathbf{u}) = \frac{1}{n} \sum_{\ell = 1}^{n} \prod_{i = 1}^{k} \prod_{j = 1}^{d_{i}} k_{\text{B}} \left (\widehat{U}_{ij}^{(\ell)},\frac{u_{ij}}{h_{n}} + 1, \frac{1-u_{ij}}{h_{n}} + 1 \right ),$

where $h_{n} > 0$ is a bandwidth parameter, $\widehat{U}_{ij}^{(\ell)} = \widehat{F}_{ij} (X_{ij}^{(\ell)})$ with

$\widehat{F}_{ij}(x_{ij}) = \frac{1}{n+1} \sum_{\ell = 1}^{n} 1 \left (X_{ij}^{(\ell)} \leq x_{ij} \right )$

the (rescaled) empirical cdf of $X_{ij}$ , and

$k_{\text{B}}(u,\alpha,\beta) = \frac{u^{\alpha - 1} (1-u)^{\beta-1}}{B(\alpha,\beta)},$

with $B$ the beta function.

Value

The beta kernel copula density estimator evaluated at the input.

References

De Keyser, S. & Gijbels, I. (2024). Hierarchical variable clustering via copula-based divergence measures between random vectors. International Journal of Approximate Reasoning 165:109090. doi: https://doi.org/10.1016/j.ijar.2023.109090.

Examples

q = 3
n = 100

# Sample from multivariate normal distribution with identity covariance matrix
sample = mvtnorm::rmvnorm(n,rep(0,q),diag(3),method = "chol")

# Copula pseudo-observations
pseudos = matrix(0,n,q)
for(j in 1:q){pseudos[,j] = (n/(n+1)) * ecdf(sample[,j])(sample[,j])}

# Argument at which to estimate the density
input = rep(0.5,q)

# Local bandwidth selection
h = hamse(input,pseudos = pseudos,n = n,estimator = "beta",bw_method = 1)

# Beta kernel estimator
est_dens = betakernelestimator(input,h,pseudos)

# True density
true = copula::dCopula(input, copula::normalCopula(0, dim = q))

q = 3
n = 100

# Sample from multivariate normal distribution with identity covariance matrix
sample = mvtnorm::rmvnorm(n,rep(0,q),diag(3),method = "chol")

# Copula pseudo-observations
pseudos = matrix(0,n,q)
for(j in 1:q){pseudos[,j] = (n/(n+1)) * ecdf(sample[,j])(sample[,j])}

# Argument at which to estimate the density
input = rep(0.5,q)

# Local bandwidth selection
h = hamse(input,pseudos = pseudos,n = n,estimator = "beta",bw_method = 1)

# Beta kernel estimator
est_dens = betakernelestimator(input,h,pseudos)

# True density
true = copula::dCopula(input, copula::normalCopula(0, dim = q))

bwd1

Description

Given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1},...,\mathbf{X}_{k})$ with $\mathbf{X}_{i}$ a $d_{i}$ -dimensional random vector, i.e., $q = d_{1} + ... + d_{k}$ , this function computes the correlation-based Bures-Wasserstein coefficient $\mathcal{D}_{1}$ between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ given the entire correlation matrix $\mathbf{R}$ .

Usage

bwd1(R, dim)
bwd1(R, dim)

Arguments

`R`	The correlation matrix of $\mathbf{X}$ .
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ .

Details

Given a correlation matrix

$\mathbf{R} = \begin{pmatrix} \mathbf{R}_{11} & \mathbf{R}_{12} & \cdots & \mathbf{R}_{1k} \\ \mathbf{R}_{12}^{\text{T}} & \mathbf{R}_{22} & \cdots & \mathbf{R}_{2k} \\ \vdots & \vdots & \ddots & \vdots \\ \mathbf{R}_{1k}^{\text{T}} & \mathbf{R}_{2k}^{\text{T}} & \cdots & \mathbf{R}_{kk} \end{pmatrix},$

the coefficient $\mathcal{D}_{1}$ equals

$\mathcal{D}_{1}(\mathbf{R}) = \frac{d_{W}^{2}(\mathbf{R},\mathbf{I}_{q}) - \sum_{i=1}^{k}d_{W}^{2}(\mathbf{R}_{ii},\mathbf{I}_{d_{i}})}{\text{sup}_{\mathbf{A} \in \Gamma(\mathbf{R}_{11}, \dots, \mathbf{R}_{kk})}d_{W}^{2}(\mathbf{A},\mathbf{I}_{q}) - \sum_{i=1}^{k}d_{W}^{2}(\mathbf{R}_{ii},\mathbf{I}_{d_{i}})},$

where $d_{W}$ stands for the Bures-Wasserstein distance, $\Gamma(\mathbf{R}_{11}, \dots, \mathbf{R}_{kk})$ denotes the set of all correlation matrices with diagonal blocks $\mathbf{R}_{ii}$ for $i = 1, \dots, k$ , and $\mathbf{I}_{q}$ is the identity matrix. The underlying assumption is that the copula of $\mathbf{X}$ is Gaussian.

Value

The first Bures-Wasserstein dependence coefficient $\mathcal{D}_{1}$ between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ .

References

De Keyser, S. & Gijbels, I. (2024). High-dimensional copula-based Wasserstein dependence. doi: https://doi.org/10.48550/arXiv.2404.07141.

Examples

q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

bwd1(R,dim)
q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

bwd1(R,dim)

bwd1asR0

Description

Given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1},...,\mathbf{X}_{k})$ with $\mathbf{X}_{i}$ a $d_{i}$ -dimensional random vector, i.e., $q = d_{1} + ... + d_{k}$ , this function simulates a sample from the asymptotic distribution of the plug-in estimator for the correlation-based Bures-Wasserstein coefficient $\mathcal{D}_{1}$ between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ given that the entire correlation matrix $\mathbf{R}$ is equal to $\mathbf{R}_{0}$ (correlation matrix under independence of $\mathbf{X}_{1},...,\mathbf{X}_{k}$ ). The argument dim should be in ascending order. This function requires importation of the python modules "numpy" and "scipy".

Usage

bwd1asR0(R, dim, M)
bwd1asR0(R, dim, M)

Arguments

`R`	The correlation matrix of $\mathbf{X}$ .
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ , in ascending order.
`M`	The sample size.

Details

A sample of size M is drawn from the asymptotic distribution of the plug-in estimator $\mathcal{D}_{1}(\widehat{\mathbf{R}}_{n})$ at $\mathbf{R}_{0} = \text{diag}(\mathbf{R}_{11}, \dots, \mathbf{R}_{kk})$ , where $\widehat{\mathbf{R}}_{n}$ is the sample matrix of normal scores rank correlations. The underlying assumption is that the copula of $\mathbf{X}$ is Gaussian.

To create a Python virtual environment with "numpy" and "scipy", run:

install_tensorflow()

reticulate::use_virtualenv("r-tensorflow", required = FALSE)

reticulate::py_install("numpy")

reticulate::py_install("scipy")

Value

A sample of size M from the asymptotic distribution of the plug-in estimator for the first Bures-Wasserstein dependence coefficient $\mathcal{D}_{1}$ under independence of $\mathbf{X}_{1},...,\mathbf{X}_{k}$ .

References

De Keyser, S. & Gijbels, I. (2024). High-dimensional copula-based Wasserstein dependence. doi: https://doi.org/10.48550/arXiv.2404.07141.

Examples


q = 5
dim = c(2,3)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

R0 = createR0(R,dim)

# Check whether scipy module is available (see details)
have_scipy = reticulate::py_module_available("scipy")

if(have_scipy){

sample = bwd1asR0(R0,dim,1000)

}

q = 5
dim = c(2,3)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

R0 = createR0(R,dim)

# Check whether scipy module is available (see details)
have_scipy = reticulate::py_module_available("scipy")

if(have_scipy){

sample = bwd1asR0(R0,dim,1000)

}

bwd1avar

Description

Usage

bwd1avar(R, dim)
bwd1avar(R, dim)

Arguments

`R`	The correlation matrix of $\mathbf{X}$ .
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ , in ascending order.

Details

The asymptotic variance of the plug-in estimator $\mathcal{D}_{1}(\widehat{\mathbf{R}}_{n})$ is computed at $\mathbf{R}$ , where $\widehat{\mathbf{R}}_{n}$ is the sample matrix of normal scores rank correlations. The underlying assumption is that the copula of $\mathbf{X}$ is Gaussian.

Value

The asymptotic variance of the plug-in estimator for the first Bures-Wasserstein dependence coefficient $\mathcal{D}_{1}$ between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ .

References

De Keyser, S. & Gijbels, I. (2024). High-dimensional copula-based Wasserstein dependence. doi: https://doi.org/10.48550/arXiv.2404.07141.

Examples

q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

bwd1avar(R,dim)
q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

bwd1avar(R,dim)

bwd2

Description

Given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1},...,\mathbf{X}_{k})$ with $\mathbf{X}_{i}$ a $d_{i}$ -dimensional random vector, i.e., $q = d_{1} + ... + d_{k}$ , this function computes the correlation-based Bures-Wasserstein coefficient $\mathcal{D}_{2}$ between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ given the entire correlation matrix $\mathbf{R}$ .

Usage

bwd2(R, dim)
bwd2(R, dim)

Arguments

`R`	The correlation matrix of $\mathbf{X}$ .
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ .

Details

Given a correlation matrix

the coefficient $\mathcal{D}_{2}$ equals

$\mathcal{D}_{2}(\mathbf{R}) = \frac{d_{W}^{2}(\mathbf{R},\mathbf{R}_{0})}{\sup_{\mathbf{A} \in \Gamma(\mathbf{R}_{11}, \dots, \mathbf{R}_{kk})} d_{W}^{2}(\mathbf{A},\mathbf{R}_{0})},$

where $d_{W}$ stands for the Bures-Wasserstein distance, $\Gamma(\mathbf{R}_{11}, \dots, \mathbf{R}_{kk})$ denotes the set of all correlation matrices with diagonal blocks $\mathbf{R}_{ii}$ for $i = 1, \dots, k$ , and the matrix $\mathbf{R}_{0} = \text{diag}(\mathbf{R}_{11},\dots,\mathbf{R}_{kk})$ is the correlation matrix under independence. The underlying assumption is that the copula of $\mathbf{X}$ is Gaussian.

Value

The second Bures-Wasserstein dependence coefficient $\mathcal{D}_{2}$ between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ .

References

De Keyser, S. & Gijbels, I. (2024). High-dimensional copula-based Wasserstein dependence. doi: https://doi.org/10.48550/arXiv.2404.07141.

Examples

q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

bwd2(R,dim)
q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

bwd2(R,dim)

bwd2asR0

Description

Given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1},...,\mathbf{X}_{k})$ with $\mathbf{X}_{i}$ a $d_{i}$ -dimensional random vector, i.e., $q = d_{1} + ... + d_{k}$ , this function simulates a sample from the asymptotic distribution of the plug-in estimator for the correlation-based Bures-Wasserstein coefficient $\mathcal{D}_{2}$ between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ given that the entire correlation matrix $\mathbf{R}$ is equal to $\mathbf{R}_{0}$ (correlation matrix under independence of $\mathbf{X}_{1},...,\mathbf{X}_{k}$ ). The argument dim should be in ascending order. This function requires importation of the python modules "numpy" and "scipy".

Usage

bwd2asR0(R, dim, M)
bwd2asR0(R, dim, M)

Arguments

`R`	The correlation matrix of $\mathbf{X}$ .
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ , in ascending order.
`M`	The sample size.

Details

A sample of size M is drawn from the asymptotic distribution of the plug-in estimator $\mathcal{D}_{2}(\widehat{\mathbf{R}}_{n})$ at $\mathbf{R}_{0} = \text{diag}(\mathbf{R}_{11}, \dots, \mathbf{R}_{kk})$ , where $\widehat{\mathbf{R}}_{n}$ is the sample matrix of normal scores rank correlations. The underlying assumption is that the copula of $\mathbf{X}$ is Gaussian.

To create a Python virtual environment with "numpy" and "scipy", run:

install_tensorflow()

reticulate::use_virtualenv("r-tensorflow", required = FALSE)

reticulate::py_install("numpy")

reticulate::py_install("scipy")

Value

A sample of size M from the asymptotic distribution of the plug-in estimator for the second Bures-Wasserstein dependence coefficient $\mathcal{D}_{2}$ under independence of $\mathbf{X}_{1},...,\mathbf{X}_{k}$ .

References

De Keyser, S. & Gijbels, I. (2024). High-dimensional copula-based Wasserstein dependence. doi: https://doi.org/10.48550/arXiv.2404.07141.

Examples


q = 5
dim = c(2,3)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

R0 = createR0(R,dim)

# Check whether scipy module is available (see details)
have_scipy = reticulate::py_module_available("scipy")

if(have_scipy){

sample = bwd2asR0(R0,dim,1000)

}

q = 5
dim = c(2,3)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

R0 = createR0(R,dim)

# Check whether scipy module is available (see details)
have_scipy = reticulate::py_module_available("scipy")

if(have_scipy){

sample = bwd2asR0(R0,dim,1000)

}

bwd2avar

Description

Usage

bwd2avar(R, dim)
bwd2avar(R, dim)

Arguments

`R`	The correlation matrix of $\mathbf{X}$ .
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ , in ascending order.

Details

The asymptotic variance of the plug-in estimator $\mathcal{D}_{2}(\widehat{\mathbf{R}}_{n})$ is computed at $\mathbf{R}$ , where $\widehat{\mathbf{R}}_{n}$ is the sample matrix of normal scores rank correlations. The underlying assumption is that the copula of $\mathbf{X}$ is Gaussian.

Value

The asymptotic variance of the plug-in estimator for the second Bures-Wasserstein dependence coefficient $\mathcal{D}_{2}$ between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ .

References

De Keyser, S. & Gijbels, I. (2024). High-dimensional copula-based Wasserstein dependence. doi: https://doi.org/10.48550/arXiv.2404.07141.

Examples

q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

bwd2avar(R,dim)
q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

bwd2avar(R,dim)

covgpenal

Description

This function computes the empirical penalized Gaussian copula covariance matrix with the Gaussian log-likelihood plus a lasso-type penalty as objective function. Model selection is done by choosing omega such that BIC is maximal.

Usage

covgpenal(
  S,
  n,
  omegas,
  derpenal = function(t, omega) {
     derSCAD(t, omega, 3.7)
 },
  nsteps = 1
)
covgpenal(
  S,
  n,
  omegas,
  derpenal = function(t, omega) {
     derSCAD(t, omega, 3.7)
 },
  nsteps = 1
)

Arguments

`S`	The sample matrix of normal scores covariances.
`n`	The sample size.
`omegas`	The candidate values for the tuning parameter in $[0,\infty)$ .
`derpenal`	The derivative of the penalty function to be used (default = scad with parameter $a = 3.7$ ).
`nsteps`	The number of weighted covariance graphical lasso iterations (default = 1).

Details

The aim is to solve/compute

$\widehat{\boldsymbol{\Sigma}}_{\text{LT},n} \in \text{arg min}_{\boldsymbol{\Sigma} > 0} \left \{ \ln \left | \boldsymbol{\Sigma} \right | + \text{tr} \left (\boldsymbol{\Sigma}^{-1} \widehat{\boldsymbol{\Sigma}}_{n} \right ) + P_{\text{LT}}\left (\boldsymbol{\Sigma},\omega_{n} \right ) \right \},$

where the penalty function $P_{\text{LT}}$ is of lasso-type:

$P_{\text{LT}} \left (\boldsymbol{\Sigma},\omega_{n} \right ) = \sum_{ij} p_{\omega_{n}} \left (\Delta_{ij} \left |\sigma_{ij} \right | \right ),$

for a certain penalty function $p_{\omega_{n}}$ with penalty parameter $\omega_{n}$ , and $\sigma_{ij}$ the $(i,j)$ 'th entry of $\boldsymbol{\Sigma}$ with $\Delta_{ij} = 1$ if $i \neq j$ and $\Delta_{ij} = 0$ if $i = j$ (in order to not shrink the variances). The matrix $\widehat{\boldsymbol{\Sigma}}_{n}$ is the matrix of sample normal scores covariances.

In case $p_{\omega_{n}}(t) = \omega_{n} t$ is the lasso penalty, the implementation for the (weighted) covariance graphical lasso is available in the R package ‘covglasso’ (see the manual for further explanations). For general penalty functions, we perform a local linear approximation to the penalty function and iteratively do (nsteps, default = 1) weighted covariance graphical lasso optimizations.

The default for the penalty function is the scad (derpenal = derivative of scad penalty), i.e.,

$p_{\omega_{n},\text{scad}}^{\prime}(t) = \omega_{n} \left [1 \left (t \leq \omega_{n} \right ) + \frac{\max \left (a \omega_{n} - t,0 \right )}{\omega_{n} (a-1)} 1 \left (t > \omega_{n} \right ) \right ],$

with $a = 3.7$ by default.

For tuning $\omega_{n}$ , we maximize (over a grid of candidate values) the BIC criterion

$\text{BIC} \left (\widehat{\boldsymbol{\Sigma}}_{\omega_{n}} \right ) = -n \left [\ln \left |\widehat{\boldsymbol{\Sigma}}_{\omega_{n}} \right | + \text{tr} \left (\widehat{\boldsymbol{\Sigma}}_{\omega_{n}}^{-1} \widehat{\boldsymbol{\Sigma}}_{n} \right ) \right ] - \ln(n) \text{df} \left (\widehat{\boldsymbol{\Sigma}}_{\omega_{n}} \right ),$

where $\widehat{\boldsymbol{\Sigma}}_{\omega_{n}}$ is the estimated candidate covariance matrix using $\omega_{n}$ and df (degrees of freedom) equals the number of non-zero entries in $\widehat{\boldsymbol{\Sigma}}_{\omega_{n}}$ , not taking the elements under the diagonal into account.

Value

A list with elements "est" containing the (lasso-type) penalized matrix of sample normal scores rank correlations (output as provided by the function “covglasso.R”), and "omega" containing the optimal tuning parameter.

References

De Keyser, S. & Gijbels, I. (2024). High-dimensional copula-based Wasserstein dependence. doi: https://doi.org/10.48550/arXiv.2404.07141.

Fop, M. (2021). covglasso: sparse covariance matrix estimation, R package version 1.0.3. url: https://CRAN.R-project.org/package=covglasso.

Wang, H. (2014). Coordinate descent algorithm for covariance graphical lasso. Statistics and Computing 24:521-529. doi: https://doi.org/10.1007/s11222-013-9385-5.

Examples

q = 10
dim = c(5,5)
n = 100

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

# Sparsity on off-diagonal blocks
R0 = createR0(R,dim)

# Sample from multivariate normal distribution
sample = mvtnorm::rmvnorm(n,rep(0,q),R0,method = "chol")

# Normal scores
scores = matrix(0,n,q)
for(j in 1:q){scores[,j] = qnorm((n/(n+1)) * ecdf(sample[,j])(sample[,j]))}

# Sample matrix of normal scores covariances
Sigma_est = cov(scores) * ((n-1)/n)

# Candidate tuning parameters
omega = seq(0.01, 0.6, length = 50)

Sigma_est_penal = covgpenal(Sigma_est,n,omega)

q = 10
dim = c(5,5)
n = 100

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

# Sparsity on off-diagonal blocks
R0 = createR0(R,dim)

# Sample from multivariate normal distribution
sample = mvtnorm::rmvnorm(n,rep(0,q),R0,method = "chol")

# Normal scores
scores = matrix(0,n,q)
for(j in 1:q){scores[,j] = qnorm((n/(n+1)) * ecdf(sample[,j])(sample[,j]))}

# Sample matrix of normal scores covariances
Sigma_est = cov(scores) * ((n-1)/n)

# Candidate tuning parameters
omega = seq(0.01, 0.6, length = 50)

Sigma_est_penal = covgpenal(Sigma_est,n,omega)

createR0

Description

Given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1},...,\mathbf{X}_{k})$ with $\mathbf{X}_{i}$ a $d_{i}$ -dimensional random vector, i.e., $q = d_{1} + ... + d_{k}$ , this function constructs the correlation matrix under independence of $\mathbf{X}_{1},...,\mathbf{X}_{k}$ , given the entire correlation matrix $\mathbf{R}$ .

Usage

createR0(R, dim)
createR0(R, dim)

Arguments

`R`	The correlation matrix of $\mathbf{X}$ .
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ .

Details

Given a correlation matrix

the matrix $\mathbf{R}_{0} = \text{diag}(\mathbf{R}_{11}, \dots, \mathbf{R}_{kk})$ , being the correlation matrix under independence of $\mathbf{X}_{1}, \dots, \mathbf{X}_{k}$ , is returned.

Value

The correlation matrix under independence of $\mathbf{X}_{1}, \dots, \mathbf{X}_{n}$ .

Examples

q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

createR0(R,dim)
q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

createR0(R,dim)

cvomega

Description

This functions selects the omega tuning parameter for ridge penalization of the empirical Gaussian copula correlation matrix via cross-validation. The objective function is the Gaussian log-likelihood, and a grid search is performed using K folds.

Usage

cvomega(sample, omegas, K)
cvomega(sample, omegas, K)

Arguments

`sample`	A sample from a $q$ -dimensional random vector $\mathbf{X}$ ( $n \times q$ matrix with observations in rows, variables in columns).
`omegas`	A grid of candidate penalty parameters in $[0,1]$ .
`K`	The number of folds to be used.

Details

The loss function is the Gaussian log-likelihood, i.e., given an estimated (penalized) Gaussian copula correlation matrix (normal scores rank correlation matrix) $\widehat{\mathbf{R}}_{n}^{(-j)}$ computed on a training set leaving out fold j, and $\widehat{\mathbf{R}}_{n}^{(j)}$ the empirical (non-penalized) Gaussian copula correlation matrix computed on test fold j, we search for the tuning parameter that minimizes

$\sum_{j = 1}^{K} \left [\ln \left ( \left | \widehat{\mathbf{R}}_{n}^{(-j)} \right | \right ) + \text{tr} \left \{\widehat{\mathbf{R}}_{n}^{(j)} \left (\widehat{\mathbf{R}}_{n}^{(-j)} \right )^{-1} \right \} \right ].$

The underlying assumption is that the copula of $\mathbf{X}$ is Gaussian.

Value

The optimal ridge penalty parameter minimizing the cross-validation error.

References

De Keyser, S. & Gijbels, I. (2024). High-dimensional copula-based Wasserstein dependence. doi: https://doi.org/10.48550/arXiv.2404.07141.

Warton, D.I. (2008). Penalized normal likelihood and ridge regularization of correlation and covariance matrices. Journal of the American Statistical Association 103(481):340-349.
doi: https://doi.org/10.1198/016214508000000021.

Examples

q = 10
n = 50

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

# Sample from multivariate normal distribution
sample = mvtnorm::rmvnorm(n,rep(0,q),R,method = "chol")

# 5-fold cross-validation with Gaussian likelihood as loss for selecting omega
omega = cvomega(sample = sample,omegas = seq(0.01,0.999,len = 50),K = 5)

R_est = estR(sample,omega = omega)
q = 10
n = 50

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

# Sample from multivariate normal distribution
sample = mvtnorm::rmvnorm(n,rep(0,q),R,method = "chol")

# 5-fold cross-validation with Gaussian likelihood as loss for selecting omega
omega = cvomega(sample = sample,omegas = seq(0.01,0.999,len = 50),K = 5)

R_est = estR(sample,omega = omega)

ellcopest

Description

This functions performs improved kernel density estimation of the generator of a meta-elliptical copula by using Liebscher's algorithm, combined with a shrinkage function.

Usage

ellcopest(
  dataU,
  Sigma_m1,
  h,
  grid,
  niter = 10,
  a,
  Kernel = "epanechnikov",
  shrink,
  verbose = 1,
  startPoint = "identity",
  prenormalization = FALSE,
  normalize = 1
)
ellcopest(
  dataU,
  Sigma_m1,
  h,
  grid,
  niter = 10,
  a,
  Kernel = "epanechnikov",
  shrink,
  verbose = 1,
  startPoint = "identity",
  prenormalization = FALSE,
  normalize = 1
)

Arguments

`dataU`	The (estimated) copula observations from a $q$ -dimensional random vector $\mathbf{X}$ ( $n \times q$ matrix with observations in rows, variables in columns).
`Sigma_m1`	The (estimated) inverse of the scale matrix of the meta-elliptical copula.
`h`	The bandwidth of the kernel.
`grid`	The grid of values on which to estimate the density generator.
`niter`	The number of iterations used in the MECIP (default = 10).
`a`	The tuning parameter to improve the performance at $0$ .
`Kernel`	The kernel used for the smoothing (default = "epanechnikov").
`shrink`	The shrinkage function to further improve the performance at $0$ and guarantee the existence of the AMISE bandwidth.
`verbose`	See the “EllDistrEst.R” function of the R package ‘ElliptCopulas’.
`startPoint`	See the “EllDistrEst.R” function of the R package ‘ElliptCopulas’.
`prenormalization`	See the “EllDistrEst.R” function of the R package ‘ElliptCopulas’.
`normalize`	A value in $\{1,2\}$ indicating the normalization procedure that is applied to the estimated generator (default = 1).

Details

The context is the one of a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1}, \dots, \mathbf{X}_{k})$ ,

with $\mathbf{X}_{i} = (X_{i1}, \dots, X_{id_{i}})$ for $i = 1, \dots, k$ , having a meta-elliptical copula. This means that there exists a generator $g_{\mathcal{R}} : (0,\infty) \rightarrow \mathbb{R}$ and a quantile function $Q$ , such that the random vector $\mathbf{Z} = (\mathbf{Z}_{1}, \dots, \mathbf{Z}_{k})$ with

$\mathbf{Z}_{i} = (Z_{i1}, \dots, Z_{id_{i}}) = \left(\left (Q \circ F_{i1} \right ) \left (X_{i1} \right ), \dots, \left (Q \circ F_{id_{i}} \right ) \left (X_{id_{i}} \right ) \right )$

for $i = 1, \dots, k$ , where $F_{ij}$ is the cdf of $X_{ij}$ , has a multivariate elliptical distribution. Denoting $\widehat{F}_{ij}(x_{ij}) = \frac{1}{n+1} \sum_{\ell = 1}^{n} 1 \left (X_{ij}^{(\ell)} \leq x_{ij} \right )$ for the (rescaled) empirical cdf of $X_{ij}$ based on a sample $X_{ij}^{(1)}, \dots, X_{ij}^{(n)}$ for $i = 1, \dots, k$ and $j = 1, \dots, d_{i}$ , and $\widehat{\mathbf{R}}$ for an estimator of the scale matrix $\mathbf{R}$ , this function estimates $g_{\mathcal{R}}$ by using the MECIP (Meta-Elliptical Copula Iterative Procedure) of Derumigny & Fermanian (2022).

This means that we start from an initial guess $\widehat{g}_{\mathcal{R},0}$ for the generator $g_{\mathcal{R}}$ , based on which we obtain an estimated sample from $\mathbf{Z}$ through the quantile function corresponding to $\widehat{g}_{\mathcal{R},0}$ . Based on this estimated sample, we then obtain an estimator $\widehat{g}_{\mathcal{R},1}$ using the function elldistrest, performing improved kernel estimation with shrinkage function. This procedure is repeated for a certain amount (niter) of iterations to obtain a final estimate for $g_{\mathcal{R}}$ .

The estimator without the shrinkage function $\alpha$ is implemented in the R package ‘ElliptCopulas’. We use this implementation and bring in the shrinkage function.

In order to make $g_{\mathcal{R}}$ identifiable, an extra normalization procedure is implemented in line with an extra constraint on $g_{\mathcal{R}}$ . When normalize = 1, this corresponds to $\mathbf{R}$ being the correlation matrix of $\mathbf{Z}$ . When normalize = 2, this corresponds to the identifiability condition of Derumigny & Fermanian (2022).

Value

The estimates for $g_{\mathcal{R}}$ at the grid points.

References

Derumigny, A., Fermanian, J.-D., Ryan, V., van der Spek, R. (2024). ElliptCopulas, R package version 0.1.4.1. url: https://CRAN.R-project.org/package=ElliptCopulas.

Derumigny, A. & Fermanian, J.-D. (2022). Identifiability and estimation of meta-elliptical copula generators. Journal of Multivariate Analysis 190:104962.
doi: https://doi.org/10.1016/j.jmva.2022.104962.

Liebscher, E. (2005). A semiparametric density estimator based on elliptical distributions. Journal of Multivariate Analysis 92(1):205-225. doi: https://doi.org/10.1016/j.jmva.2003.09.007.

Examples


q = 4

# Sample size
n = 1000

# Grid on which to evaluate the elliptical generator
grid = seq(0.005,100,by = 0.005)

# Degrees of freedom
nu = 7

# Student-t generator with 7 degrees of freedom
g_q = ((nu/(nu-2))^(q/2))*(gamma((q+nu)/2)/(((pi*nu)^(q/2))*gamma(nu/2))) *
      ((1+(grid/(nu-2)))^(-(q+nu)/2))

# Density of squared radius
R2 = function(t,q){(gamma((q+nu)/2)/(((nu-2)^(q/2))*gamma(nu/2)*gamma(q/2))) *
                   (t^((q/2)-1)) * ((1+(t/(nu-2)))^(-(q+nu)/2))}

# Sample from 4-dimensional Student-t distribution with 7 degrees of freedom
# and identity covariance matrix
sample = ElliptCopulas::EllDistrSim(n,q,diag(q),density_R2 = function(t){R2(t,q)})

# Copula pseudo-observations
pseudos = matrix(0,n,q)
for(j in 1:q){pseudos[,j] = (n/(n+1)) * ecdf(sample[,j])(sample[,j])}

# Shrinkage function
shrinkage = function(t,p){1-(1/((t^p) + 1))}

# Tuning parameter selection
opt_parameters = elliptselect(n,q,seq((3/4)-(1/q)+0.01,1-0.01,len = 200),
                                  seq(0.01,2,len = 200))

# Optimal tuning parameters
a = opt_parameters$Opta ; p = opt_parameters$Optp ; h = opt_parameters$Opth

# Estimated elliptical generator
g_est = ellcopest(dataU = pseudos,Sigma_m1 = diag(q),h = h,grid = grid,a = a,
                  shrink = function(t){shrinkage(t,p)})

plot(grid,g_est,type = "l", xlim = c(0,8))
lines(grid,g_q,col = "green")


q = 4

# Sample size
n = 1000

# Grid on which to evaluate the elliptical generator
grid = seq(0.005,100,by = 0.005)

# Degrees of freedom
nu = 7

# Student-t generator with 7 degrees of freedom
g_q = ((nu/(nu-2))^(q/2))*(gamma((q+nu)/2)/(((pi*nu)^(q/2))*gamma(nu/2))) *
      ((1+(grid/(nu-2)))^(-(q+nu)/2))

# Density of squared radius
R2 = function(t,q){(gamma((q+nu)/2)/(((nu-2)^(q/2))*gamma(nu/2)*gamma(q/2))) *
                   (t^((q/2)-1)) * ((1+(t/(nu-2)))^(-(q+nu)/2))}

# Sample from 4-dimensional Student-t distribution with 7 degrees of freedom
# and identity covariance matrix
sample = ElliptCopulas::EllDistrSim(n,q,diag(q),density_R2 = function(t){R2(t,q)})

# Copula pseudo-observations
pseudos = matrix(0,n,q)
for(j in 1:q){pseudos[,j] = (n/(n+1)) * ecdf(sample[,j])(sample[,j])}

# Shrinkage function
shrinkage = function(t,p){1-(1/((t^p) + 1))}

# Tuning parameter selection
opt_parameters = elliptselect(n,q,seq((3/4)-(1/q)+0.01,1-0.01,len = 200),
                                  seq(0.01,2,len = 200))

# Optimal tuning parameters
a = opt_parameters$Opta ; p = opt_parameters$Optp ; h = opt_parameters$Opth

# Estimated elliptical generator
g_est = ellcopest(dataU = pseudos,Sigma_m1 = diag(q),h = h,grid = grid,a = a,
                  shrink = function(t){shrinkage(t,p)})

plot(grid,g_est,type = "l", xlim = c(0,8))
lines(grid,g_q,col = "green")

elldistrest

Description

This functions performs improved kernel density estimation of the generator of an elliptical distribution by using Liebscher's algorithm, combined with a shrinkage function.

Usage

elldistrest(
  Z,
  mu = 0,
  Sigma_m1,
  grid,
  h,
  Kernel = "epanechnikov",
  a,
  shrink,
  mpfr = FALSE,
  precBits = 100,
  dopb = FALSE,
  normalize = 1
)
elldistrest(
  Z,
  mu = 0,
  Sigma_m1,
  grid,
  h,
  Kernel = "epanechnikov",
  a,
  shrink,
  mpfr = FALSE,
  precBits = 100,
  dopb = FALSE,
  normalize = 1
)

Arguments

`Z`	A sample from a $q$ -dimensional random vector $\mathbf{Z}$ ( $n \times q$ matrix with observations in rows, variables in columns).
`mu`	The (estimated) mean of $\mathbf{Z}$ (default $= 0$ ).
`Sigma_m1`	The (estimated) inverse of the scale matrix of $\mathbf{Z}$ .
`grid`	The grid of values on which to estimate the density generator.
`h`	The bandwidth of the kernel.
`Kernel`	The kernel used for the smoothing (default = "epanechnikov").
`a`	The tuning parameter to improve the performance at $0$ .
`shrink`	The shrinkage function to further improve the performance at $0$ and guarantee the existence of the AMISE bandwidth.
`mpfr`	See the “EllDistrEst.R” function of the R package ‘ElliptCopulas’.
`precBits`	See the “EllDistrEst.R” function of the R package ‘ElliptCopulas’.
`dopb`	See the “EllDistrEst.R” function of the R package ‘ElliptCopulas’.
`normalize`	A value in $\{1,2\}$ indicating the normalization procedure that is applied to the estimated generator (default = 1).

Details

The context is the one of a $q$ -dimensional random vector $\mathbf{Z}$ following an elliptical distribution with generator $g_{\mathcal{R}} : (0,\infty) \rightarrow \mathbb{R}$ and scale matrix $\mathbf{R}$ such that the density of $\mathbf{Z}$ is given by

$h(\mathbf{z}) = \left |\mathbf{R} \right |^{-1/2} g_{\mathcal{R}} \left (\mathbf{z}^{\text{T}} \mathbf{R}^{-1} \mathbf{z} \right ),$

for $\mathbf{z} \in \mathbb{R}^{q}$ . Suppose that a sample $\mathbf{Z}^{(1)}, \dots, \mathbf{Z}^{(n)}$ from $\mathbf{Z}$ is given, and let $\widehat{\mathbf{R}}$ be an estimator for the scale matrix $\mathbf{R}$ . Then, when defining

$\widehat{\mathbf{Y}}^{(\ell)} = \widehat{\mathbf{R}}^{-1/2} \mathbf{Z}^{(\ell)}$

for $\ell = 1, \dots, n$ , this function computes the estimator $\widehat{g}_{\mathcal{R}}^{\text{I}}$ for $g_{\mathcal{R}}$ given by

$\widehat{g}_{\mathcal{R}}^{\text{I}}(t) = c^{\text{I}}(t) \sum_{\ell = 1}^{n} \left \{k \left (\frac{\psi(t) - \psi \left (\left | \left |\widehat{\mathbf{Y}}^{(\ell)} \right | \right |^{2} \right )}{h_{n} \alpha \left (\psi(t) \right )} \right ) + k \left (\frac{\psi(t) + \psi \left (\left | \left |\widehat{\mathbf{Y}}^{(\ell)} \right | \right |^{2} \right )}{h_{n} \alpha \left (\psi(t) \right )} \right ) \right \},$

where $c^{\text{I}}(t) = [\Gamma(q/2)/(\pi^{q/2} n h_{n} \alpha(\psi(t)))] t^{-q/2 + 1} \psi^{\prime}(t)$ , with $k$ the kernel and $h_{n}$ the bandwidth. The function

$\psi(t) = -a + \left (a^{q/2} + t^{q/2} \right )^{2/q},$

with $a > 0$ a tuning parameter was introduced by Liebscher (2005), and the shrinkage function $\alpha(t)$ yields further estimation improvement. We suggest to take (for $q > 2$ )

$\alpha(t) = 1 - \frac{1}{t^{\delta} + 1},$

where $\delta \in (3/4 - 1/q, 1)$ is another tuning parameter. When $q = 2$ , one can just take $\alpha(t) = 1$ , and the value of $a$ does not matter.

The estimator without the shrinkage function $\alpha$ is implemented in the R package ‘ElliptCopulas’. We use this implementation and bring in the shrinkage function.

Value

The estimates for $g_{\mathcal{R}}$ at the grid points.

References

Derumigny, A., Fermanian, J.-D., Ryan, V., van der Spek, R. (2024). ElliptCopulas, R package version 0.1.4.1. url: https://CRAN.R-project.org/package=ElliptCopulas.

Liebscher, E. (2005). A semiparametric density estimator based on elliptical distributions. Journal of Multivariate Analysis 92(1):205-225. doi: https://doi.org/10.1016/j.jmva.2003.09.007.

Examples


q = 4

# Sample size
n = 1000

# Grid on which to evaluate the elliptical generator
grid = seq(0.005,100,by = 0.005)

# Degrees of freedom
nu = 7

# Student-t generator with 7 degrees of freedom
g_q = ((nu/(nu-2))^(q/2))*(gamma((q+nu)/2)/(((pi*nu)^(q/2))*gamma(nu/2))) *
      ((1+(grid/(nu-2)))^(-(q+nu)/2))

# Density of squared radius
R2 = function(t,q){(gamma((q+nu)/2)/(((nu-2)^(q/2))*gamma(nu/2)*gamma(q/2))) *
                   (t^((q/2)-1)) * ((1+(t/(nu-2)))^(-(q+nu)/2))}

# Sample from 4-dimensional Student-t distribution with 7 degrees of freedom
# and identity covariance matrix
sample = ElliptCopulas::EllDistrSim(n,q,diag(q),density_R2 = function(t){R2(t,q)})

# Shrinkage function
shrinkage = function(t,p){1-(1/((t^p) + 1))}

# Tuning parameter selection
opt_parameters = elliptselect(n,q,seq((3/4)-(1/q)+0.01,1-0.01,len = 200),
                                  seq(0.01,2,len = 200))

# Optimal tuning parameters
a = opt_parameters$Opta ; p = opt_parameters$Optp ; h = opt_parameters$Opth

# Estimated elliptical generator
g_est = elldistrest(Z = sample, Sigma_m1 = diag(q), grid = grid, h = h, a = a,
                    shrink = function(t){shrinkage(t,p)})

plot(grid,g_est,type = "l", xlim = c(0,8))
lines(grid,g_q,col = "green")


q = 4

# Sample size
n = 1000

# Grid on which to evaluate the elliptical generator
grid = seq(0.005,100,by = 0.005)

# Degrees of freedom
nu = 7

# Student-t generator with 7 degrees of freedom
g_q = ((nu/(nu-2))^(q/2))*(gamma((q+nu)/2)/(((pi*nu)^(q/2))*gamma(nu/2))) *
      ((1+(grid/(nu-2)))^(-(q+nu)/2))

# Density of squared radius
R2 = function(t,q){(gamma((q+nu)/2)/(((nu-2)^(q/2))*gamma(nu/2)*gamma(q/2))) *
                   (t^((q/2)-1)) * ((1+(t/(nu-2)))^(-(q+nu)/2))}

# Sample from 4-dimensional Student-t distribution with 7 degrees of freedom
# and identity covariance matrix
sample = ElliptCopulas::EllDistrSim(n,q,diag(q),density_R2 = function(t){R2(t,q)})

# Shrinkage function
shrinkage = function(t,p){1-(1/((t^p) + 1))}

# Tuning parameter selection
opt_parameters = elliptselect(n,q,seq((3/4)-(1/q)+0.01,1-0.01,len = 200),
                                  seq(0.01,2,len = 200))

# Optimal tuning parameters
a = opt_parameters$Opta ; p = opt_parameters$Optp ; h = opt_parameters$Opth

# Estimated elliptical generator
g_est = elldistrest(Z = sample, Sigma_m1 = diag(q), grid = grid, h = h, a = a,
                    shrink = function(t){shrinkage(t,p)})

plot(grid,g_est,type = "l", xlim = c(0,8))
lines(grid,g_q,col = "green")

elliptselect

Description

This functions selects optimal tuning parameters for improved kernel estimation of the generator of an elliptical distribution.

Usage

elliptselect(n, q, pseq, aseq)
elliptselect(n, q, pseq, aseq)

Arguments

`n`	The sample size.
`q`	The total dimension.
`pseq`	Candidate values for the $\delta$ parameter of the shrinkage function.
`aseq`	Candidate values for the $a$ parameter of the Liebscher function.

Details

When using the function elldistrest for estimating an elliptical generator $g_{\mathcal{R}}$ based on a kernel $k$ with bandwidth $h_{n}$ , the function

$\psi(t) = -a + \left (a^{q/2} + t^{q/2} \right )^{2/q},$

and the shrinkage function (for $q > 3$ )

$\alpha(t) = 1 - \frac{1}{t^{\delta} + 1},$

this function selects $h_{n}, \delta$ and $a$ in the following way.

Use the normal generator $g_{\mathcal{R}}(t) = e^{-t/2}/(2 \pi)^{q/2}$ as reference generator, and define

$\Psi(t) = \frac{\pi^{q/2}}{\Gamma(q/2)} \left (\psi^{-1}(t) \right )^{\prime} \left (\psi^{-1}(t) \right )^{q/2 - 1} g_{\mathcal{R}} \left (\psi^{-1}(t) \right ),$

as well as

$h_{n}^{\text{opt}} = \left \{\frac{\left (\int_{-1}^{1} k^{2}(t) dt \right ) \left (\int_{0}^{\infty} \alpha(t)^{-1} \Psi(t) dt \right )}{\left (\int_{-1}^{1} t^{2} k(t) dt \right )^{2} \left (\int_{0}^{\infty} \left (\alpha(t)^{2} \Psi^{\prime \prime}(t) \right )^{2} dt \right )} \right \}^{1/5} n^{-1/5}.$

When $q = 2$ , take $\alpha(t) = 1$ (there is no need for shrinkage), and take $h_{n}^{\text{opt}}$ . The value of $a$ does not matter.

When $q > 2$ , specify a grid of candidate $\delta$ -values in $(3/4 - 1/q,1)$ and a grid of $a$ -values in $(0, \infty)$ . For each of these candidate values, compute the corresponding optimal (AMISE) bandwidth $h_{n}^{\text{opt}}$ . Take the combination of parameters that minimizes (a numerical approximation of) the (normal reference) AMISE given in equation (20) of De Keyser & Gijbels (2024).

Value

A list with elements "Opta" containing the optimal $a$ , "Optp" containing the optimal $\delta$ , and "Opth" containing the optimal $h_{n}$ .

References

Examples


q = 4
n = 1000
opt_parameters = elliptselect(n,q,seq((3/4)-(1/q)+0.01,1-0.01,len = 200),
                                  seq(0.01,2,len = 200))

q = 4
n = 1000
opt_parameters = elliptselect(n,q,seq((3/4)-(1/q)+0.01,1-0.01,len = 200),
                                  seq(0.01,2,len = 200))

estphi

Description

Given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1},...,\mathbf{X}_{k})$ with $\mathbf{X}_{i}$ a $d_{i}$ -dimensional random vector, i.e., $q = d_{1} + ... + d_{k}$ , this function estimates the $\Phi$ -dependence between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ by estimating the joint and marginal copula densities.

Usage

estphi(sample, dim, est_method, phi)
estphi(sample, dim, est_method, phi)

Arguments

`sample`	A sample from a $q$ -dimensional random vector $\mathbf{X}$ ( $n \times q$ matrix with observations in rows, variables in columns).
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ .
`est_method`	The method used for estimating the $\Phi$ -dependence.
`phi`	The function $\Phi$ .

Details

When $\mathbf{X}$ has copula density $c$ with marginal copula densities $c_{i}$ of $\mathbf{X}_{i}$ for $i = 1, \dots, k$ , the $\Phi$ -dependence between $\mathbf{X}_{1}, \dots, \mathbf{X}_{k}$ equals

$\mathcal{D}_{\Phi} \left (\mathbf{X}_{1}, \dots, \mathbf{X}_{k} \right ) = \mathbb{E} \left \{ \frac{\prod_{i = 1}^{k} c_{i}(\mathbf{U}_{i})}{c \left ( \mathbf{U} \right )} \Phi \left (\frac{c(\mathbf{U})}{\prod_{i = 1}^{k}c_{i}(\mathbf{U}_{i})} \right ) \right \},$

for a certain continuous, convex function $\Phi : (0,\infty) \rightarrow \mathbb{R}$ , and with $\mathbf{U} = (\mathbf{U}_{1}, \dots, \mathbf{U}_{k}) \sim c$ .

This functions allows to estimate $\mathcal{D}_{\Phi}$ in several ways (options for est_method)

list("hac", type = type, M = M) for parametric estimation by fitting a hierarchical Archimedean copula (hac) via pseudo-maximum likelihood estimation, using a generator of type = type and a simulated Monte Carlo sample of size $M$ in order to approximate the expectation, see also the functions mlehac and phihac,
list("nphac", estimator = estimator, type = type) for fully non-parametric estimation using the beta kernel estimator or Gaussian transformation kernel estimator using a fitted hac (via pseudo-maximum likelihood estimation) of type = type to find locally optimal bandwidths, see also the function phinp,
list("np", estimator = estimator, bw_method = bw_method) for fully non-parametric estimation using the beta kernel estimator or Gaussian transformation kernel estimator, see phinp for different bw_method arguments (either 1 or 2, for performing local bandwidth selection),
list("ellip", grid = grid) for semi-parametric estimation through meta-elliptical copulas, with bandwidths determined by the elliptselect function, see also the function phiellip.

Value

The estimated $\Phi$ -dependence between $\mathbf{X}_{1}, \dots, \mathbf{X}_{k}$ .

References

De Keyser, S. & Gijbels, I. (2024). Parametric dependence between random vectors via copula-based divergence measures. Journal of Multivariate Analysis 203:105336.
doi: https://doi.org/10.1016/j.jmva.2024.105336.

Examples



# Hierarchical Archimedean copula setting
q = 4
dim = c(2,2)

# Sample size
n = 1000

# Four dimensional hierarchical Gumbel copula
# with parameters (theta_0,theta_1,theta_2) = (2,3,4)
hac = gethac(dim,c(2,3,4),type = 1)

# Sample
sample =  suppressWarnings(HAC::rHAC(n,hac))

# Several estimators for the mutual information between two random vectors of size 2

est_phi_1 = estphi(sample,dim,list("hac",type = 1,M = 10000),function(t){t * log(t)})
est_phi_2 = estphi(sample,dim,list("nphac",estimator = "beta",type = 1),
                                   function(t){t * log(t)})
est_phi_3 = estphi(sample,dim,list("nphac",estimator = "trans",type = 1),
                                   function(t){t * log(t)})
est_phi_4 = estphi(sample,dim,list("np",estimator = "beta",bw_method = 1),
                                   function(t){t * log(t)})
est_phi_5 = estphi(sample,dim,list("np",estimator = "trans",bw_method = 1),
                                   function(t){t * log(t)})
est_phi_6 = estphi(sample,dim,list("np",estimator = "beta",bw_method = 2),
                                   function(t){t * log(t)})
est_phi_7 = estphi(sample,dim,list("np",estimator = "trans",bw_method = 2),
                                   function(t){t * log(t)})

true_phi = phihac(hac,dim,10000,function(t){t * log(t)})

# Gaussian copula setting

q = 4
dim = c(2,2)

# Sample size
n = 1000

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

# Sample from 4-dimensional normal distribution
sample = mvtnorm::rmvnorm(n,rep(0,q),R,method = "chol")

# Estimate mutual information via MECIP procedure
est_phi = estphi(sample,dim,list("ellip",grid = seq(0.005,100,by = 0.005)),
                                 function(t){t * log(t)})

true_phi = minormal(R,dim)


# Hierarchical Archimedean copula setting
q = 4
dim = c(2,2)

# Sample size
n = 1000

# Four dimensional hierarchical Gumbel copula
# with parameters (theta_0,theta_1,theta_2) = (2,3,4)
hac = gethac(dim,c(2,3,4),type = 1)

# Sample
sample =  suppressWarnings(HAC::rHAC(n,hac))

# Several estimators for the mutual information between two random vectors of size 2

est_phi_1 = estphi(sample,dim,list("hac",type = 1,M = 10000),function(t){t * log(t)})
est_phi_2 = estphi(sample,dim,list("nphac",estimator = "beta",type = 1),
                                   function(t){t * log(t)})
est_phi_3 = estphi(sample,dim,list("nphac",estimator = "trans",type = 1),
                                   function(t){t * log(t)})
est_phi_4 = estphi(sample,dim,list("np",estimator = "beta",bw_method = 1),
                                   function(t){t * log(t)})
est_phi_5 = estphi(sample,dim,list("np",estimator = "trans",bw_method = 1),
                                   function(t){t * log(t)})
est_phi_6 = estphi(sample,dim,list("np",estimator = "beta",bw_method = 2),
                                   function(t){t * log(t)})
est_phi_7 = estphi(sample,dim,list("np",estimator = "trans",bw_method = 2),
                                   function(t){t * log(t)})

true_phi = phihac(hac,dim,10000,function(t){t * log(t)})

# Gaussian copula setting

q = 4
dim = c(2,2)

# Sample size
n = 1000

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

# Sample from 4-dimensional normal distribution
sample = mvtnorm::rmvnorm(n,rep(0,q),R,method = "chol")

# Estimate mutual information via MECIP procedure
est_phi = estphi(sample,dim,list("ellip",grid = seq(0.005,100,by = 0.005)),
                                 function(t){t * log(t)})

true_phi = minormal(R,dim)

estR

Description

This function computes the sample $Q$ -scores rank correlation matrix. A ridge penalization is possible.

Usage

estR(
  sample,
  omega = 1,
  Q = function(t) {
     stats::qnorm(t)
 }
)
estR(
  sample,
  omega = 1,
  Q = function(t) {
     stats::qnorm(t)
 }
)

Arguments

`sample`	A sample from a $q$ -dimensional random vector $\mathbf{X}$ ( $n \times q$ matrix with observations in rows, variables in columns).
`omega`	The penalty parameter for ridge penalization (default = 1, meaning no penalization).
`Q`	The quantile function to be applied to the copula pseudo-observations (default = qnorm()).

Details

Given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1},...,\mathbf{X}_{k})$ with $\mathbf{X}_{i} = (X_{i1}, \dots, X_{id_{i}})$ a $d_{i}$ dimensional random vector, i.e., $q = d_{1} + ... + d_{k}$ , the sample $Q$ -scores rank correlation matrix is given as

$\widehat{\mathbf{R}}_{n} = \begin{pmatrix} \widehat{\mathbf{R}}_{11} & \widehat{\mathbf{R}}_{12} & \cdots & \widehat{\mathbf{R}}_{1k} \\ \widehat{\mathbf{R}}_{12}^{\text{T}} & \widehat{\mathbf{R}}_{22} & \cdots & \widehat{\mathbf{R}}_{2k} \\ \vdots & \vdots & \ddots & \vdots \\ \widehat{\mathbf{R}}_{1k}^{\text{T}} & \widehat{\mathbf{R}}_{2k}^{\text{T}} & \cdots & \widehat{\mathbf{R}}_{kk} \end{pmatrix} \hspace{0.2cm} \text{with} \hspace{0.2cm} \left (\widehat{\mathbf{R}}_{im} \right )_{jt} = \widehat{\rho}_{ij,mt} = \frac{\frac{1}{n} \sum_{\ell = 1}^{n} \widehat{Z}_{ij}^{(\ell)} \widehat{Z}_{mt}^{(\ell)}}{\frac{1}{n} \sum_{\ell = 1}^{n} \left [Q \left (\frac{\ell}{n+1} \right ) \right ]^{2}},$

for $i,m = 1, \dots, k$ , $j = 1, \dots, d_{i}$ , and $t = 1, \dots, d_{m}$ , based on the observed $Q$ -scores

$\widehat{Z}_{ij}^{(\ell)} = Q \left (\frac{n}{n+1} \widehat{F}_{ij} \left (X_{ij}^{(\ell)} \right )\right ) = Q \left (\frac{1}{n+1} \sum_{t = 1}^{n} 1 \left \{X_{ij}^{(t)} \leq X_{ij}^{(\ell)} \right \} \right ),$

for $\ell = 1, \dots, n$ , where $\widehat{F}_{ij}$ is the empirical cdf of the sample $X_{ij}^{(1)},\dots,X_{ij}^{(n)}$ for $i = 1, \dots, k$ and $j = 1, \dots, d_{i}$ . The underlying assumption is that the copula of $\mathbf{X}$ is meta-elliptical. The default for $Q$ is the standard normal quantile function (corresponding to the assumption of a Gaussian copula). Ridge penalization (especially in the Gaussian copula setting) with penalty parameter omega = $\omega$ boils down to computing

$\omega \widehat{\mathbf{R}}_{n} + (1-\omega) \mathbf{I}_{q},$

where $\mathbf{I}_{q}$ stands for the identity matrix.

Value

The (ridge penalized) sample $Q$ -scores rank correlation matrix.

References

De Keyser, S. & Gijbels, I. (2024). Some new tests for independence among continuous random vectors.

Examples


# Multivariate normal copula setting

q = 10
n = 50

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

# Sample from multivariate normal distribution
sample = mvtnorm::rmvnorm(n,rep(0,q),R,method = "chol")

# 5-fold cross-validation with Gaussian likelihood as loss for selecting omega
omega = cvomega(sample = sample,omegas = seq(0.01,0.999,len = 50),K = 5)

R_est = estR(sample,omega = omega)

# Multivariate Student-t copula setting

q = 10
n = 500

# Degrees of freedom
nu = 7

# Density of R^2, with R the radius of the elliptical distribution
# Identifiability contraint is that R is the correlation matrix
R2 = function(t,q){(gamma((q+nu)/2)/(((nu-2)^(q/2)) * gamma(nu/2) * gamma(q/2))) *
                   (t^((q/2)-1)) * ((1+(t/(nu-2)))^(-(q+nu)/2))}

# Univariate quantile function, with unit variance
Q = function(t){extraDistr::qlst(t,nu,0,sqrt((nu-2)/nu))}

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

# Sample from multivariate Student-t distribution
# with correlation matrix R and nu degrees of freedom
sample = ElliptCopulas::EllDistrSim(n,q,t(chol(R)),density_R2 = function(t){R2(t,q)})

R_est = estR(sample,Q = Q)
# Multivariate normal copula setting

q = 10
n = 50

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

# Sample from multivariate normal distribution
sample = mvtnorm::rmvnorm(n,rep(0,q),R,method = "chol")

# 5-fold cross-validation with Gaussian likelihood as loss for selecting omega
omega = cvomega(sample = sample,omegas = seq(0.01,0.999,len = 50),K = 5)

R_est = estR(sample,omega = omega)

# Multivariate Student-t copula setting

q = 10
n = 500

# Degrees of freedom
nu = 7

# Density of R^2, with R the radius of the elliptical distribution
# Identifiability contraint is that R is the correlation matrix
R2 = function(t,q){(gamma((q+nu)/2)/(((nu-2)^(q/2)) * gamma(nu/2) * gamma(q/2))) *
                   (t^((q/2)-1)) * ((1+(t/(nu-2)))^(-(q+nu)/2))}

# Univariate quantile function, with unit variance
Q = function(t){extraDistr::qlst(t,nu,0,sqrt((nu-2)/nu))}

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

# Sample from multivariate Student-t distribution
# with correlation matrix R and nu degrees of freedom
sample = ElliptCopulas::EllDistrSim(n,q,t(chol(R)),density_R2 = function(t){R2(t,q)})

R_est = estR(sample,Q = Q)

gethac

Description

Given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1},...,\mathbf{X}_{k})$ with $\mathbf{X}_{i}$ a $d_{i}$ -dimensional random vector, i.e., $q = d_{1} + ... + d_{k}$ , this function construct a hac object (hierarchical Archimedean copula) with two nesting levels given the specified dimensions and parameters of the root and $k$ child copulas.

Usage

gethac(dim, thetas, type)
gethac(dim, thetas, type)

Arguments

`dim`	The vector of dimensions $(d_{1},...,d_{k})$ .
`thetas`	The parameters $(\theta_{0}, \theta_{1}, \dots, \theta_{k})$ .
`type`	The type of Archimedean copula.

Details

A hierarchical (or nested) Archimedean copula $C$ with two nesting levels and $k$ child copulas is given by

$C(\mathbf{u}) = C_{0} \left (C_{1}(\mathbf{u}_{1}), \dots, C_{k}(\mathbf{u}_{k}) \right ),$

where $\mathbf{u} = (\mathbf{u}_{1}, \dots, \mathbf{u}_{k}) \in \mathbb{R}^{q}$ with $\mathbf{u}_{i} \in \mathbb{R}^{d_{i}}$ for $i = 1, \dots, k$ . The ( $k$ -dimensional) copula $C_{0}$ is called the root copula, and the ( $d_{i}$ -dimensional) copulas $C_{i}$ are the child copulas.

They all belong to the class of Archimedean copulas, and we denote $\theta_{i}$ for the parameter of $C_{i}$ for $i = 0,1,\dots,k$ . A sufficient condition to guarantee that $C$ indeed is a copula, is that $C_{0},C_{1}, \dots, C_{k}$ are all a particular member of this class of Archimedean copulas (e.g., Clayton), and such that $\theta_{0} \leq \theta_{i}$ for $i = 1, \dots, k$ (sufficient nesting condition).

When a certain child copula $C_{i}$ is one dimensional ( $\mathbf{X}_{i}$ is one dimensional), $\theta_{i}$ can be any number. It must hold that length(thetas) $= k + 1$ .

Many functions for working with nested Archimedean copulas are developed in the R package ‘HAC’, and the function gethac utilizes these functions to quickly construct a hac object that is useful for modelling the dependence between $\mathbf{X}_{1}, \dots, \mathbf{X}_{k}$ . See also the R package ‘HAC’ for the different possibilities of type (specified by a number in $\{1,\dots,10\}$ ).

Value

A hac object with two nesting levels and $k$ child copulas.

References

Okhrin, O., Ristig, A. & Chen, G. (2024). HAC: estimation, simulation and visualization of hierarchical Archimedean copulae (HAC), R package version 1.1-1.
url: https://CRAN.R-project.org/package=HAC.

Examples

dim = c(3,5,1,2)
thetas = c(2,2,3,1,4)

# 11 dimensional nested Gumbel copula with
# (theta_0,theta_1,theta_2,theta_3,theta_4) = (2,2,3,1,4),
# where the value of theta_3 could be anything,
# because the third random vector is one dimensional

HAC = gethac(dim,thetas,type = 1)

dim = c(3,5,1,2)
thetas = c(2,2,3,1,4)

# 11 dimensional nested Gumbel copula with
# (theta_0,theta_1,theta_2,theta_3,theta_4) = (2,2,3,1,4),
# where the value of theta_3 could be anything,
# because the third random vector is one dimensional

HAC = gethac(dim,thetas,type = 1)

grouplasso

Description

Given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1},...,\mathbf{X}_{k})$ with $\mathbf{X}_{i}$ a $d_{i}$ -dimensional random vector, i.e., $q = d_{1} + ... + d_{k}$ , this function computes the empirical penalized Gaussian copula covariance matrix with the Gaussian log-likelihood plus the grouped lasso penalty as objective function, where the groups are the diagonal and off-diagonal blocks corresponding to the different random vectors. Model selection is done by choosing omega such that BIC is maximal.

Usage

grouplasso(Sigma, S, n, omegas, dim, step.size = 100, trace = 0)
grouplasso(Sigma, S, n, omegas, dim, step.size = 100, trace = 0)

Arguments

`Sigma`	An initial guess for the covariance matrix (typically equal to S).
`S`	The sample matrix of normal scores covariances.
`n`	The sample size.
`omegas`	The candidate values for the tuning parameter in $[0,\infty)$ .
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ .
`step.size`	The step size used in the generalized gradient descent, affects the speed of the algorithm (default = 100).
`trace`	Controls how verbose output should be (default = 0, meaning no verbose output).

Details

Given a covariance matrix

$\boldsymbol{\Sigma} = \begin{pmatrix} \boldsymbol{\Sigma}_{11} & \boldsymbol{\Sigma}_{12} & \cdots & \boldsymbol{\Sigma}_{1k} \\ \boldsymbol{\Sigma}_{12}^{\text{T}} & \boldsymbol{\Sigma}_{22} & \cdots & \boldsymbol{\Sigma}_{2k} \\ \vdots & \vdots & \ddots & \vdots \\ \boldsymbol{\Sigma}_{1k}^{\text{T}} & \boldsymbol{\Sigma}_{2k}^{\text{T}} & \cdots & \boldsymbol{\Sigma}_{kk} \end{pmatrix},$

the aim is to solve/compute

$\widehat{\boldsymbol{\Sigma}}_{\text{GLT},n} \in \text{arg min}_{\boldsymbol{\Sigma} > 0} \left \{ \ln \left | \boldsymbol{\Sigma} \right | + \text{tr} \left (\boldsymbol{\Sigma}^{-1} \widehat{\boldsymbol{\Sigma}}_{n} \right ) + P_{\text{GLT}}\left (\boldsymbol{\Sigma},\omega_{n} \right ) \right \},$

where the penalty function $P_{\text{GLT}}$ is of group lasso-type:

$P_{\text{GLT}} \left (\boldsymbol{\Sigma},\omega_{n} \right ) = 2 \sum_{i,j = 1, j > i}^{k} p_{\omega_{n}} \left (\sqrt{d_{i}d_{j}} \left | \left |\boldsymbol{\Sigma}_{ij} \right | \right |_{\text{F}} \right ) + \sum_{i = 1}^{k} p_{\omega_{n}} \left (\sqrt{d_{i}(d_{i}-1)} \left | \left | \boldsymbol{\Delta}_{i} * \boldsymbol{\Sigma}_{ii} \right | \right |_{\text{F}} \right ),$

for a certain penalty function $p_{\omega_{n}}$ with penalty parameter $\omega_{n}$ , and $\boldsymbol{\Delta}_{i} \in \mathbb{R}^{d_{i} \times d_{i}}$ a matrix with ones as off-diagonal elements and zeroes on the diagonal (in order to avoid shrinking the variances, the operator $*$ stands for elementwise multiplication).

For now, the only possibility in this function for $p_{\omega_{n}}$ is the lasso penalty $p_{\omega_{n}}(t) = \omega_{n} t$ . For other penalties (e.g., scad), one can do a local linear approximation to the penalty function and iteratively perform weighted group lasso optimizations (similar to what is done in the function covgpenal).

Regarding the implementation, we used the code available in the R package ‘spcov’ (see the manual for further explanations), but altered it to the context of a group-lasso penalty.

For tuning $\omega_{n}$ , we maximize (over a grid of candidate values) the BIC criterion

where $\widehat{\boldsymbol{\Sigma}}_{\omega_{n}}$ is the estimated candidate covariance matrix using $\omega_{n}$ and df (degrees of freedom) equals

$\hspace{-3cm} \text{df} \left (\widehat{\boldsymbol{\Sigma}}_{\omega_{n}} \right ) = \sum_{i,j = 1, j > i}^{k} 1 \left (\left | \left | \widehat{\boldsymbol{\Sigma}}_{\omega_{n},ij} \right | \right |_{\text{F}} > 0 \right ) \left (1 + \frac{\left | \left | \widehat{\boldsymbol{\Sigma}}_{\omega_{n},ij} \right | \right |_{\text{F}}}{\left | \left | \widehat{\boldsymbol{\Sigma}}_{n,ij} \right | \right |_{\text{F}}} \left (d_{i}d_{j} - 1 \right ) \right )$

$\hspace{2cm} + \sum_{i = 1}^{k} 1 \left (\left | \left |\boldsymbol{\Delta}_{i} * \widehat{\boldsymbol{\Sigma}}_{\omega_{n},ii} \right | \right |_{\text{F}} > 0 \right ) \left (1 + \frac{\left | \left |\boldsymbol{\Delta}_{i} * \widehat{\boldsymbol{\Sigma}}_{\omega_{n},ii} \right | \right |_{\text{F}}}{\left | \left |\boldsymbol{\Delta}_{i} * \widehat{\boldsymbol{\Sigma}}_{n,ii} \right | \right |_{\text{F}}} \left (\frac{d_{i} \left ( d_{i} - 1 \right )}{2} - 1 \right ) \right ) + q,$

with $\widehat{\boldsymbol{\Sigma}}_{\omega_{n},ij}$ the $(i,j)$ 'th block of $\widehat{\boldsymbol{\Sigma}}_{\omega_{n}}$ , similarly for $\widehat{\boldsymbol{\Sigma}}_{n,ij}$ .

Value

A list with elements "est" containing the (group lasso) penalized matrix of sample normal scores rank correlations (output as provided by the function “spcov.R”), and "omega" containing the optimal tuning parameter.

References

De Keyser, S. & Gijbels, I. (2024). High-dimensional copula-based Wasserstein dependence. doi: https://doi.org/10.48550/arXiv.2404.07141.

Bien, J. & Tibshirani, R. (2022). spcov: sparse estimation of a covariance matrix, R package version 1.3. url: https://CRAN.R-project.org/package=spcov.

Bien, J. & Tibshirani, R. (2011). Sparse Estimation of a Covariance Matrix. Biometrika 98(4):807-820. doi: https://doi.org/10.1093/biomet/asr054.

Examples


q = 10
dim = c(5,5)
n = 100

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

# Sparsity on off-diagonal blocks
R0 = createR0(R,dim)

# Sample from multivariate normal distribution
sample = mvtnorm::rmvnorm(n,rep(0,q),R0,method = "chol")

# Normal scores
scores = matrix(0,n,q)
for(j in 1:q){scores[,j] = qnorm((n/(n+1)) * ecdf(sample[,j])(sample[,j]))}

# Sample matrix of normal scores covariances
Sigma_est = cov(scores) * ((n-1)/n)

# Candidate tuning parameters
omega = seq(0.01, 0.6, length = 50)

Sigma_est_penal = grouplasso(Sigma_est, Sigma_est, n, omega, dim)

q = 10
dim = c(5,5)
n = 100

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

# Sparsity on off-diagonal blocks
R0 = createR0(R,dim)

# Sample from multivariate normal distribution
sample = mvtnorm::rmvnorm(n,rep(0,q),R0,method = "chol")

# Normal scores
scores = matrix(0,n,q)
for(j in 1:q){scores[,j] = qnorm((n/(n+1)) * ecdf(sample[,j])(sample[,j]))}

# Sample matrix of normal scores covariances
Sigma_est = cov(scores) * ((n-1)/n)

# Candidate tuning parameters
omega = seq(0.01, 0.6, length = 50)

Sigma_est_penal = grouplasso(Sigma_est, Sigma_est, n, omega, dim)

hamse

Description

This function performs local bandwidth selection based on the amse (asymptotic mean squared error) for the beta kernel or Gaussian transformation kernel copula density estimator.

Usage

hamse(input, cop = NULL, pseudos = NULL, n, estimator, bw_method)
hamse(input, cop = NULL, pseudos = NULL, n, estimator, bw_method)

Arguments

`input`	The copula argument at which the optimal local bandwidth is to be computed.
`cop`	A fitted reference hac object, in case bw_method = 0 (default = NULL).
`pseudos`	The (estimated) copula observations from a $q$ -dimensional random vector $\mathbf{X}$ ( $n \times q$ matrix with observations in rows, variables in columns), in case bw_method = 1 (default = NULL).
`n`	The sample size.
`estimator`	Either "beta" or "trans" for the beta kernel or the Gaussian transformation kernel copula density estimator.
`bw_method`	A number in $\{0,1\}$ specifying the method used for computing the bandwidth.

Details

When estimator = "beta", this function computes, at a certain input, a numerical approximation of the optimal local bandwidth (for the beta kernel copula density estimator) in terms of the amse (asymptotic mean squared error) given in equation (27) of De Keyser & Gijbels (2024). When estimator = "trans" (for the Gaussian transformation kernel copula density estimator), this optimal bandwidth is given at the end of Section 5.2 in De Keyser & Gijbels (2024).

Of course, these optimal bandwidths depend upon the true unknown copula. If bw_method = 0, then the given fitted (e.g., via MLE using mlehac) hac object (hierarchical Archimedean copula) cop is used as reference copula. If bw_method = 1, then a non-parametric (beta or Gaussian transformation) kernel copula density estimator based on the pseudos as pivot is used. This pivot is computed using the big O bandwidth (i.e., $n^{-2/(q+4)}$ in case of the beta estimator, and $n^{-1/(q+4)}$ for the transformation estimator, with $q$ the total dimension).

Value

The optimal local bandwidth (in terms of amse).

References

Examples

q = 4
dim = c(2,2)

# Sample size
n = 1000

# Four dimensional hierarchical Gumbel copula
# with parameters (theta_0,theta_1,theta_2) = (2,3,4)
HAC = gethac(dim,c(2,3,4),type = 1)

# Sample
sample = suppressWarnings(HAC::rHAC(n,HAC))

# Copula pseudo-observations
pseudos = matrix(0,n,q)
for(j in 1:q){pseudos[,j] = (n/(n+1)) * ecdf(sample[,j])(sample[,j])}

# Maximum pseudo-likelihood estimator to be used
# as reference copula for bw_method = 0
est_cop = mlehac(sample,dim,1,c(2,3,4))

h_1 = hamse(rep(0.5,q),cop = est_cop,n = n,estimator = "beta",bw_method = 0)
h_2 = hamse(rep(0.5,q),cop = est_cop,n = n,estimator = "trans",bw_method = 0)
h_3 = hamse(rep(0.5,q),pseudos = pseudos,n = n,estimator = "beta",bw_method = 1)
h_4 = hamse(rep(0.5,q),pseudos = pseudos,n = n,estimator = "trans",bw_method = 1)

est_dens_1 = betakernelestimator(rep(0.5,q),h_1,pseudos)
est_dens_2 = transformationestimator(rep(0.5,q),h_2,pseudos)
est_dens_3 = betakernelestimator(rep(0.5,q),h_3,pseudos)
est_dens_4 = transformationestimator(rep(0.5,q),h_4,pseudos)

true = HAC::dHAC(c("X1" = 0.5, "X2" = 0.5, "X3" = 0.5, "X4" = 0.5), HAC)

q = 4
dim = c(2,2)

# Sample size
n = 1000

# Four dimensional hierarchical Gumbel copula
# with parameters (theta_0,theta_1,theta_2) = (2,3,4)
HAC = gethac(dim,c(2,3,4),type = 1)

# Sample
sample = suppressWarnings(HAC::rHAC(n,HAC))

# Copula pseudo-observations
pseudos = matrix(0,n,q)
for(j in 1:q){pseudos[,j] = (n/(n+1)) * ecdf(sample[,j])(sample[,j])}

# Maximum pseudo-likelihood estimator to be used
# as reference copula for bw_method = 0
est_cop = mlehac(sample,dim,1,c(2,3,4))

h_1 = hamse(rep(0.5,q),cop = est_cop,n = n,estimator = "beta",bw_method = 0)
h_2 = hamse(rep(0.5,q),cop = est_cop,n = n,estimator = "trans",bw_method = 0)
h_3 = hamse(rep(0.5,q),pseudos = pseudos,n = n,estimator = "beta",bw_method = 1)
h_4 = hamse(rep(0.5,q),pseudos = pseudos,n = n,estimator = "trans",bw_method = 1)

est_dens_1 = betakernelestimator(rep(0.5,q),h_1,pseudos)
est_dens_2 = transformationestimator(rep(0.5,q),h_2,pseudos)
est_dens_3 = betakernelestimator(rep(0.5,q),h_3,pseudos)
est_dens_4 = transformationestimator(rep(0.5,q),h_4,pseudos)

true = HAC::dHAC(c("X1" = 0.5, "X2" = 0.5, "X3" = 0.5, "X4" = 0.5), HAC)

Helhac

Description

This function computes the Hellinger distance between all the child copulas of a hac object obtained by the function gethac, i.e., given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X_{1}},...,\mathbf{X}_{k})$ with $\mathbf{X}_{i}$ a $d_{i}$ -dimensional random vector, i.e., $q = d_{1} + ... + d_{k}$ , where $\mathbf{X}_{1},...,\mathbf{X}_{k}$ are connected via a hierarchical Archimedean copula with two nesting levels, Helhac computes the Hellinger distance between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ .

Usage

Helhac(cop, dim, M)
Helhac(cop, dim, M)

Arguments

`cop`	A hac object as provided by the function `gethac`.
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ .
`M`	The size of the Monte Carlo sample used for approximating the integral of the Hellinger distance.

Details

$\mathcal{D}_{\Phi} \left (\mathbf{X}_{1}, \dots, \mathbf{X}_{k} \right ) = \int_{[0,1]^{q}} \prod_{i = 1}^{k} c_{i}(\mathbf{u}_{i}) \Phi \left (\frac{c(\mathbf{u})}{\prod_{i = 1}^{k}c_{i}(\mathbf{u}_{i})} \right ),$

for a certain continuous, convex function $\Phi : (0,\infty) \rightarrow \mathbb{R}$ . The Hellinger distance corresponds to $\Phi(t) = (\sqrt{t}-1)^{2}$ , and $\mathcal{D}_{(\sqrt{t}-1)^{2}}$ could be approximated by $\widehat{\mathcal{D}}_{(\sqrt{t}-1)^{2}}$ as implemented in the function phihac. Yet, for this specific choice of $\Phi$ , it is better to first simplify $\mathcal{D}_{(\sqrt{t}-1)^{2}}$ to

$\mathcal{D}_{(\sqrt{t}-1)^{2}} \left (\mathbf{X}_{1}, \dots, \mathbf{X}_{k} \right ) = 2 - 2 \int_{[0,1]^{q}} \sqrt{c(\mathbf{u}) \prod_{i = 1}^{k} c_{i}(\mathbf{u}_{i})} d \mathbf{u},$

and then, by drawing a sample of size $M$ from $c$ , say $\mathbf{U}^{(1)}, \dots, \mathbf{U}^{(M)}$ , with $\mathbf{U}^{(\ell)} = (\mathbf{U}_{1}^{(\ell)}, \dots, \mathbf{U}_{k}^{(\ell)})$ , approximate it by

$\widetilde{D}_{(\sqrt{t}-1)^{2}} = 2 - \frac{2}{M} \sum_{\ell = 1}^{M} \sqrt{\frac{\prod_{i = 1}^{k} c_{i} \left (\mathbf{U}_{i}^{(\ell)} \right )}{c \left ( \mathbf{U}^{(\ell)} \right )}}.$

The function Helhac computes $\widetilde{\mathcal{D}}_{(\sqrt{t}-1)^{2}}$ when $c$ is a hierarchical Archimedean copula with two nesting levels, as produced by the function gethac.

Value

The Hellinger distance between $\mathbf{X}_{1}, \dots, \mathbf{X}_{k}$ (i.e., between all the child copulas of the hac object).

References

Examples


dim = c(2,2)
thetas = c(2,3,4)

# 4 dimensional nested Gumbel copula with (theta_0,theta_1,theta_2) = (2,3,4)
HAC = gethac(dim,thetas,type = 1)

# Hellinger distance based on Monte Carlo sample of size 10000
Hel = Helhac(HAC,dim,10000)


dim = c(2,2)
thetas = c(2,3,4)

# 4 dimensional nested Gumbel copula with (theta_0,theta_1,theta_2) = (2,3,4)
HAC = gethac(dim,thetas,type = 1)

# Hellinger distance based on Monte Carlo sample of size 10000
Hel = Helhac(HAC,dim,10000)

Helnormal

Description

Given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1},...,\mathbf{X}_{k})$ with $\mathbf{X}_{i}$ a $d_{i}$ -dimensional random vector, i.e., $q = d_{1} + ... + d_{k}$ , this function computes the correlation-based Hellinger distance between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ given the entire correlation matrix $\mathbf{R}$ .

Usage

Helnormal(R, dim)
Helnormal(R, dim)

Arguments

`R`	The correlation matrix of $\mathbf{X}$ .
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ .

Details

Given a correlation matrix

the Hellinger distance equals

$\mathcal{D}_{(\sqrt{t}-1)^{2}}^{\mathcal{N}}(\mathbf{R}) = 2 - 2 \frac{2^{q/2} |\mathbf{R}|^{1/4}}{\left |\mathbf{I}_{q} + \mathbf{R}_{0}^{-1} \mathbf{R} \right |^{1/2} \prod_{i = 1}^{k} \left | \mathbf{R}_{ii} \right |^{1/4}},$

where $\mathbf{I}_{q}$ denotes the identity matrix, and $\mathbf{R}_{0} = \text{diag}(\mathbf{R}_{11},\dots,\mathbf{R}_{kk})$ is the correlation matrix under independence of $\mathbf{X}_{1}, \dots, \mathbf{X}_{k}$ . The underlying assumption is that the copula of $\mathbf{X}$ is Gaussian.

Value

The correlation-based Hellinger distance between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ .

References

Examples

q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

Helnormal(R,dim)
q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

Helnormal(R,dim)

Helnormalavar

Description

Usage

Helnormalavar(R, dim)
Helnormalavar(R, dim)

Arguments

`R`	The correlation matrix of $\mathbf{X}$ .
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ .

Details

The asymptotic variance of the plug-in estimator $\mathcal{D}_{(\sqrt{t}-1)^{2}}(\widehat{\mathbf{R}}_{n})$ is computed at $\mathbf{R}$ , where $\widehat{\mathbf{R}}_{n}$ is the sample matrix of normal scores rank correlations. The underlying assumption is that the copula of $\mathbf{X}$ is Gaussian.

Value

The asymptotic variance of the correlation-based Hellinger distance between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ .

References

Examples

q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

Helnormalavar(R,dim)
q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

Helnormalavar(R,dim)

Icluster

Description

This function clusters the columns (variables) of a dataset via agglomerative hierarchical variable clustering using estimated multivariate similarities (dependence coefficients) between random vectors.

Usage

Icluster(
  data,
  est_method,
  max_dim = Inf,
  norm = NULL,
  link = "average",
  trace = 1
)
Icluster(
  data,
  est_method,
  max_dim = Inf,
  norm = NULL,
  link = "average",
  trace = 1
)

Arguments

`data`	The dataset ( $n \times q$ matrix with observations in rows, variables in columns) whose columns need to be clustered.
`est_method`	The method for estimating the similarity between two clusters of variables.
`max_dim`	The maximum dimension of the random vectors for which no link function is used when computing the similarity (default = Inf).
`norm`	A possible normalization function applied to the dependence measure (default = NULL, meaning no normalization).
`link`	The link function to be used when max_dim is exceeded (default = "average").
`trace`	Controls how verbose output should be (default = 1, showing the progress).

Details

Suppose that the $q$ variables (of which we have $n$ observations in data) are $\mathcal{S} = \{X_{1}, \dots, X_{q}\}$ . Then, most important in hierarchical variable clustering, is computing the similarity

$\mathcal{D}(\mathbb{X},\mathbb{Y})$

between two disjoint subsets of variables $\mathbb{X}, \mathbb{Y} \subset \mathcal{S}$ . In particular, the main algorithm is as follows:

Each object $\{X_{i}\}$ forms a separate cluster, i.e., $\aleph_{1} = \{\{X_{1}\},\dots,\{X_{q}\}\}$ is the initial feature partition.

For $i = 1,2,\dots,q-1$ :

For each pair of disjoint clusters $\mathbb{X},\mathbb{Y} \in \aleph_{i}$ , compute the similarity $\mathcal{D}(\mathbb{X},\mathbb{Y})$ .
Define $\aleph_{i+1} = (\aleph_{i} \setminus \{\widetilde{\mathbb{X}},\widetilde{\mathbb{Y}}\}) \cup \{\widetilde{\mathbb{X}} \cup \widetilde{\mathbb{Y}} \}$ , where $\widetilde{\mathbb{X}},\widetilde{\mathbb{Y}}$ are the clusters having maximal similarity according to the previous step.
The algorithm stops with $\aleph_{q} = \{\{X_{1},\dots,X_{q}\}\}$ .

We call $\{\aleph_{1}, \dots, \aleph_{q}\}$ the hierarchy constructed throughout the algorithm, and define, for $i \in \{1, \dots, q\}$ , $\text{Adiam}(\aleph_{i}) = |\aleph_{i}|^{-1} \sum_{\mathbb{X} \in \aleph_{i}} \text{diam}(\mathbb{X})$ , with

$\text{diam}(\mathbb{X}) = \begin{cases} \underset{\{X,Y\} \subset \mathbb{X} }{\min} \mathcal{D}(X,Y) & \mbox{if } |\mathbb{X}| > 1 \\ 1 & \mbox{if } |\mathbb{X}| = 1, \end{cases}$

and $\text{Msplit}(\aleph_{i}) = \max_{\mathbb{X} \in \aleph_{i}} \text{split}(\mathbb{X})$ , with

$\text{split}(\mathbb{X}) = \underset{Y \in \aleph_{i} \setminus \mathbb{X}}{\underset{X \in \mathbb{X}}{\max}} \mathcal{D}(X,Y) \hspace{0.2cm} \text{for} \hspace{0.2cm} \{\mathbb{X}\} \neq \aleph_{i}.$

Adiam stands for the average diameter of a partition (measuring the homogeneity, which we want to be large), while Msplit stands for the maximum split of a partition (measuring the non-separation, which we want to be small).

For measuring the similarity $\mathcal{D}(\mathbb{X},\mathbb{Y})$ , we approach $\mathbb{X}$ and $\mathbb{Y}$ as being two random vectors (let's say of dimensions $d_{1}$ and $d_{2}$ respectively). For $\mathcal{D}$ , we take an estimated dependence measure between (two) random vectors. The following options are possible:

list("phi", "mi", "Gauss", omegas = omegas) for the estimated Gaussian copula mutual information. Use omegas = 1 for no penalty, or a sequence of omegas for a ridge penalty tuned via 5-fold cross-validation, see also the functions minormal, estR, and cvomega,
list("phi", "Hel", "Gauss", omegas = omegas) for the estimated Gaussian copula Hellinger distance. Use omegas = 1 for no penalty, or a sequence of omegas for a ridge penalty tuned via 5-fold cross-validation, see also the functions Helnormal, estR, and cvomega,
list("phi", phi(t), "hac", type = type, M = M) for general $\Phi$ -dependence with specified function phi(t) = $\Phi(t)$ , estimated by fitting (via pseudo maximum likelihood estimation) a hierarchical Archimedean copula of given type = type, and computed based on a Monte Carlo sample of size $M$ in order to approximate the expectation, see also the functions mlehac, phihac and estphi,
list("phi", phi(t), "nphac", estimator = estimator, type = type) for general $\Phi$ -dependence with specified function phi(t) = $\Phi(t)$ , estimated via non-parametric beta kernel estimation or Gaussian transformation kernel estimation, and local bandwidth selection, by using a fitted (via pseudo maximum likelihood) hierarchical Archimedean copula as reference copula, see also the functions phinp and estphi,
list("phi", phi(t), "np", estimator = estimator, bw_method = bw_method) for general
$\Phi$ -dependence with specified function phi(t) = $\Phi(t)$ , estimated via non-parametric beta kernel estimation or Gaussian transformation kernel estimation, and local bandwidth selection, either by using a non-parametric kernel estimator as reference copula if bw_method = 1, or by using a big O bandwidth rule if bw_method = 2, see also the functions phinp and estphi,
list("phi", phi(t), "ellip", grid = grid) for general $\Phi$ -dependence with specified function phi(t) = $\Phi(t)$ , estimated via the improved MECIP procedure on the specified grid, and parameter selection done via the function elliptselect using the Gaussian generator as reference generator, see also the functions phiellip and estphi,
list("ot", coef = coef, omegas = omegas) for Gaussian copula Bures-Wasserstein dependence measures, either coefficient $\mathcal{D}_{1}$ (coef = 1) or coefficient $\mathcal{D}_{2}$ (coef = 2). Use omegas = 1 for no penalty, or a sequence of omegas for a ridge penalty tuned via 5-fold cross-validation, see also the functions bwd1, bwd2, estR, and cvomega.

When $d_{1} + d_{2} >$ max_dim, the specified link function (say $L$ ) is used for computing the similarity between $\mathbb{X}$ and $\mathbb{Y}$ , i.e.,

$\mathcal{D} \left ( \mathbb{X}, \mathbb{Y} \right ) = L \left (\left \{\mathcal{D}(X,Y) : X \in \mathbb{X}, Y \in \mathbb{Y} \right \} \right ),$

which by default is the average of all inter-pairwise similarities. Other options are "single" for the minimum, and "complete" for the maximum.

The function norm (say $N$ ) is a possible normalization applied to the similarity measure, i.e., instead of computing $\mathcal{D}$ (using the method specified by est_method), the similarity becomes $N \circ \mathcal{D}$ . The default is $N(t) = t$ , meaning that no normalization is applied.

Value

A list with elements "hierarchy" containing the hierarchy constructed throughout the algorithm (a hash object), "all" containing all similarities that were computed throughout the algorithm (a hash object), "diam" containing the average diameters of all partitions created throughout the algorithm (a vector), and "split" containing the maximum splits of all partitions created throughout the algorithm (a vector).

References

De Keyser, S. & Gijbels, I. (2024). High-dimensional copula-based Wasserstein dependence. doi: https://doi.org/10.48550/arXiv.2404.07141.

Examples


q = 20

# We will impose a clustering
# {{X1,X2},{X3,X4,X5},{X6,X7,X8},{X9,X10,X11,X12,X13},{X14,X15,X16,X17,X18,X19,X20}}
dim = c(2,3,3,5,7)

# Sample size
n = 200

# Twenty dimensional hierarchical Gumbel copula with parameters
# (theta_0,theta_1,theta_2,theta_3,theta_4,theta_5) = (2,3,4,5,6,7)
hac = gethac(dim,c(2,3,4,5,6,7),type = 1)

# So, strongest cluster is {X14,X15,X16,X17,X18,X19,X20}, then {X9,X10,X11,X12,X13},
# then {X6,X7,X8}, then {X3,X4,X5}, and finally {X1,X2}

# Sample
sample =  suppressWarnings(HAC::rHAC(n,hac))

# Cluster using different methods

# Gaussian copula based methods

Clustering1 =  Icluster(data = sample,
                        est_method = list("phi", "mi", "Gauss", omegas = 1))

# 5-cluster partition
Clustering1$hierarchy$Aleph_16

Clustering2 =  Icluster(data = sample,
                        est_method = list("phi", "mi", "Gauss",
                                          omegas = seq(0.01,0.999,len = 50)))

# 5-cluster partition
Clustering2$hierarchy$Aleph_16

Clustering3 =  Icluster(data = sample,
                        est_method = list("phi", "mi", "Gauss", omegas = 1),
                        max_dim = 2)

# 5-cluster partition
Clustering3$hierarchy$Aleph_16

Clustering4 =  Icluster(data = sample,
                        est_method = list("phi", "Hel", "Gauss", omegas = 1))

# 5-cluster partition
Clustering4$hierarchy$Aleph_16

Clustering5 =  Icluster(data = sample,
                        est_method = list("ot", coef = 1, omegas = 1))

# 5-cluster partition
Clustering5$hierarchy$Aleph_16

Clustering6 =  Icluster(data = sample,
                        est_method = list("ot", coef = 2, omegas = 1))

# 5-cluster partition
Clustering6$hierarchy$Aleph_16

Clustering7 =  Icluster(data = sample,
                        est_method = list("ot", coef = 2, omegas = 1), max_dim = 4)

# 5-cluster partition
Clustering7$hierarchy$Aleph_16

# Parametric hierarchical Archimedean copula approach

Clustering8 = Icluster(data = sample,
                       est_method = list("phi", function(t){t * log(t)}, "hac",
                                         type = 1, M = 1000), max_dim = 4)

# 5-cluster partition
Clustering8$hierarchy$Aleph_16

Clustering9 = Icluster(data = sample,
                       est_method = list("phi", function(t){(sqrt(t)-1)^2}, "hac",
                                         type = 1, M = 1000), max_dim = 2)

# 5-cluster partition
Clustering9$hierarchy$Aleph_16

# Non-parametric approaches

Clustering10 = Icluster(data = sample,
                        est_method = list("phi", function(t){t * log(t)}, "nphac",
                                       estimator = "beta", type = 1), max_dim = 3)

# 5-cluster partition
Clustering10$hierarchy$Aleph_16

Clustering11 = Icluster(data = sample,
                        est_method = list("phi", function(t){t * log(t)}, "nphac",
                                     estimator = "trans", type = 1), max_dim = 3)

# 5-cluster partition
Clustering11$hierarchy$Aleph_16

Clustering12 = Icluster(data = sample,
                        est_method = list("phi", function(t){t * log(t)}, "np",
                                     estimator = "beta", bw_method = 1), max_dim = 3)

# 5-cluster partition
Clustering12$hierarchy$Aleph_16

Clustering13 = Icluster(data = sample,
                        est_method = list("phi", function(t){t * log(t)}, "np",
                                     estimator = "trans", bw_method = 2), max_dim = 3)

# 5-cluster partition
Clustering13$hierarchy$Aleph_16

Clustering14 = Icluster(data = sample,
                        est_method = list("phi", function(t){(sqrt(t)-1)^2}, "np",
                                      estimator = "trans", bw_method = 1), max_dim = 2)

# 5-cluster partition
Clustering14$hierarchy$Aleph_16

# Semi-parametric meta-elliptical copula approach
# Uncomment to run (takes a long time)

# Clustering15 = Icluster(data = sample,
#                        est_method = list("phi", function(t){t * log(t)}, "ellip",
#                                     grid = seq(0.005,100,by = 0.005)), max_dim = 2)

# 5-cluster partition
# Clustering15$hierarchy$Aleph_16



q = 20

# We will impose a clustering
# {{X1,X2},{X3,X4,X5},{X6,X7,X8},{X9,X10,X11,X12,X13},{X14,X15,X16,X17,X18,X19,X20}}
dim = c(2,3,3,5,7)

# Sample size
n = 200

# Twenty dimensional hierarchical Gumbel copula with parameters
# (theta_0,theta_1,theta_2,theta_3,theta_4,theta_5) = (2,3,4,5,6,7)
hac = gethac(dim,c(2,3,4,5,6,7),type = 1)

# So, strongest cluster is {X14,X15,X16,X17,X18,X19,X20}, then {X9,X10,X11,X12,X13},
# then {X6,X7,X8}, then {X3,X4,X5}, and finally {X1,X2}

# Sample
sample =  suppressWarnings(HAC::rHAC(n,hac))

# Cluster using different methods

# Gaussian copula based methods

Clustering1 =  Icluster(data = sample,
                        est_method = list("phi", "mi", "Gauss", omegas = 1))

# 5-cluster partition
Clustering1$hierarchy$Aleph_16

Clustering2 =  Icluster(data = sample,
                        est_method = list("phi", "mi", "Gauss",
                                          omegas = seq(0.01,0.999,len = 50)))

# 5-cluster partition
Clustering2$hierarchy$Aleph_16

Clustering3 =  Icluster(data = sample,
                        est_method = list("phi", "mi", "Gauss", omegas = 1),
                        max_dim = 2)

# 5-cluster partition
Clustering3$hierarchy$Aleph_16

Clustering4 =  Icluster(data = sample,
                        est_method = list("phi", "Hel", "Gauss", omegas = 1))

# 5-cluster partition
Clustering4$hierarchy$Aleph_16

Clustering5 =  Icluster(data = sample,
                        est_method = list("ot", coef = 1, omegas = 1))

# 5-cluster partition
Clustering5$hierarchy$Aleph_16

Clustering6 =  Icluster(data = sample,
                        est_method = list("ot", coef = 2, omegas = 1))

# 5-cluster partition
Clustering6$hierarchy$Aleph_16

Clustering7 =  Icluster(data = sample,
                        est_method = list("ot", coef = 2, omegas = 1), max_dim = 4)

# 5-cluster partition
Clustering7$hierarchy$Aleph_16

# Parametric hierarchical Archimedean copula approach

Clustering8 = Icluster(data = sample,
                       est_method = list("phi", function(t){t * log(t)}, "hac",
                                         type = 1, M = 1000), max_dim = 4)

# 5-cluster partition
Clustering8$hierarchy$Aleph_16

Clustering9 = Icluster(data = sample,
                       est_method = list("phi", function(t){(sqrt(t)-1)^2}, "hac",
                                         type = 1, M = 1000), max_dim = 2)

# 5-cluster partition
Clustering9$hierarchy$Aleph_16

# Non-parametric approaches

Clustering10 = Icluster(data = sample,
                        est_method = list("phi", function(t){t * log(t)}, "nphac",
                                       estimator = "beta", type = 1), max_dim = 3)

# 5-cluster partition
Clustering10$hierarchy$Aleph_16

Clustering11 = Icluster(data = sample,
                        est_method = list("phi", function(t){t * log(t)}, "nphac",
                                     estimator = "trans", type = 1), max_dim = 3)

# 5-cluster partition
Clustering11$hierarchy$Aleph_16

Clustering12 = Icluster(data = sample,
                        est_method = list("phi", function(t){t * log(t)}, "np",
                                     estimator = "beta", bw_method = 1), max_dim = 3)

# 5-cluster partition
Clustering12$hierarchy$Aleph_16

Clustering13 = Icluster(data = sample,
                        est_method = list("phi", function(t){t * log(t)}, "np",
                                     estimator = "trans", bw_method = 2), max_dim = 3)

# 5-cluster partition
Clustering13$hierarchy$Aleph_16

Clustering14 = Icluster(data = sample,
                        est_method = list("phi", function(t){(sqrt(t)-1)^2}, "np",
                                      estimator = "trans", bw_method = 1), max_dim = 2)

# 5-cluster partition
Clustering14$hierarchy$Aleph_16

# Semi-parametric meta-elliptical copula approach
# Uncomment to run (takes a long time)

# Clustering15 = Icluster(data = sample,
#                        est_method = list("phi", function(t){t * log(t)}, "ellip",
#                                     grid = seq(0.005,100,by = 0.005)), max_dim = 2)

# 5-cluster partition
# Clustering15$hierarchy$Aleph_16

install_tensorflow

Description

This function installs a python virtual environment.

Usage

install_tensorflow(envname = "r-tensorflow")
install_tensorflow(envname = "r-tensorflow")

Arguments

envname

Name of the environment.

Value

No return value, used for creating a python virtual environment.

minormal

Description

Given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1},...,\mathbf{X}_{k})$ with $\mathbf{X}_{i}$ a $d_{i}$ -dimensional random vector, i.e., $q = d_{1} + ... + d_{k}$ , this function computes the correlation-based mutual information between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ given the entire correlation matrix $\mathbf{R}$ .

Usage

minormal(R, dim)
minormal(R, dim)

Arguments

`R`	The correlation matrix of $\mathbf{X}$ .
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ .

Details

Given a correlation matrix

the mutual information equals

$\mathcal{D}_{t \ln(t)}^{\mathcal{N}}(\mathbf{R}) = - \frac{1}{2} \ln \left (\frac{|\mathbf{R}|}{\prod_{i = 1}^{k} \left |\mathbf{R}_{ii} \right |} \right ).$

The underlying assumption is that the copula of $\mathbf{X}$ is Gaussian.

Value

The correlation-based mutual information between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ .

References

Examples

q = 10
dim = c(1,2,3,4)
# AR(1) correlation matrix with correlation 0.5

R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

minormal(R,dim)
q = 10
dim = c(1,2,3,4)
# AR(1) correlation matrix with correlation 0.5

R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

minormal(R,dim)

minormalavar

Description

Usage

minormalavar(R, dim)
minormalavar(R, dim)

Arguments

`R`	The correlation matrix of $\mathbf{X}$ .
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ .

Details

The asymptotic variance of the plug-in estimator $\mathcal{D}_{t \ln(t)}(\widehat{\mathbf{R}}_{n})$ is computed at $\mathbf{R}$ , where $\widehat{\mathbf{R}}_{n}$ is the sample matrix of normal scores rank correlations. The underlying assumption is that the copula of $\mathbf{X}$ is Gaussian.

Value

The asymptotic variance of the correlation-based mutual information between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ .

References

Examples

q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

minormalavar(R,dim)
q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

minormalavar(R,dim)

miStudent

Description

Given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1},...,\mathbf{X}_{k})$ with $\mathbf{X}_{i}$ a $d_{i}$ -dimensional random vector, i.e., $q = d_{1} + ... + d_{k}$ , this function computes the Student-t mutual information between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ given the entire correlation matrix $\mathbf{R}$ and the degrees of freedom nu.

Usage

miStudent(R, dim, nu)
miStudent(R, dim, nu)

Arguments

`R`	The correlation matrix of $\mathbf{X}$ .
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ .
`nu`	The degrees of freedom.

Details

Given a correlation matrix

and a certain amount of degrees of freedom $\nu > 0$ , the Student-t mutual information equals

$\mathcal{D}_{t \ln(t)}^{\text{S}}(\mathbf{R},\nu) = - \frac{1}{2} \ln \left (\frac{|\mathbf{R}|}{\prod_{i = 1}^{k} \left |\mathbf{R}_{ii} \right |} \right ) + K(\nu),$

where

$\hspace{-2cm} K(\nu) = \ln \left (\frac{\Gamma((q+\nu)/2) \Gamma(\nu/2)^{k-1}}{\prod_{i = 1}^{k} \Gamma((d_{i} + \nu)/2)} \right ) + \sum_{i = 1}^{k} \left [\frac{d_{i} + \nu}{2} \psi((d_{i} + \nu)/2) \right ]$

$\hspace{5.4cm} - \frac{q + \nu}{2} \psi((q + \nu)/2) - \frac{\nu}{2}(k-1)\psi(\nu/2),$

with $\Gamma$ the gamma function and $\psi$ the digamma function. The underlying assumption is that the copula of $\mathbf{X}$ is Student-t.

Value

The Student-t mutual information between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ .

References

Examples

q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

# Degrees of freedom
nu = 7

miStudent(R,dim,nu)
q = 10
dim = c(1,2,3,4)

# AR(1) correlation matrix with correlation 0.5
R = 0.5^(abs(matrix(1:q-1,nrow = q, ncol = q, byrow = TRUE) - (1:q-1)))

# Degrees of freedom
nu = 7

miStudent(R,dim,nu)

mlehac

Description

Given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1},...,\mathbf{X}_{k})$ with $\mathbf{X}_{i}$ a $d_{i}$ -dimensional random vector, i.e., $q = d_{1} + ... + d_{k}$ , this function performs maximum pseudo-likelihood estimation for the parameters of a hierarchical Archimedean copula with two nesting levels of a specific type, used for modelling the dependence between $\mathbf{X}_{1}, \dots, \mathbf{X}_{k}$ .

Usage

mlehac(sample, dim, type, start_val = NULL)
mlehac(sample, dim, type, start_val = NULL)

Arguments

`sample`	A sample from a $q$ -dimensional random vector $\mathbf{X}$ ( $n \times q$ matrix with observations in rows, variables in columns).
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ .
`type`	The type of Archimedean copula.
`start_val`	The starting values for the parameters $(\theta_{0},\theta_{1},...,\theta_{k})$ of the hierarchical Archimedean copula.

Details

Under the assumption that $\mathbf{X} = (\mathbf{X}_{1}, \dots, \mathbf{X}_{k})$ has a hierarchical Archimedean copula with two nesting levels, i.e.,

$C(\mathbf{u}) = C_{0} \left (C_{1}(\mathbf{u}_{1}), \dots, C_{k}(\mathbf{u}_{k}) \right ),$

where $\mathbf{u} = (\mathbf{u}_{1}, \dots, \mathbf{u}_{k}) \in \mathbb{R}^{q}$ with $\mathbf{u}_{i} \in \mathbb{R}^{d_{i}}$ for $i = 1, \dots, k$ , and with $\theta_{i}$ the parameter of $C_{i}$ for $i = 0,1, \dots, k$ (see the function gethac), this functions performs maximum pseudo-likelihood estimation for $\boldsymbol{\theta}_{C} = (\theta_{0}, \theta_{1}, \dots, \theta_{k})$ . This means that for $\widehat{F}_{ij}(x_{ij}) = \frac{1}{n+1} \sum_{\ell = 1}^{n} 1 \left (X_{ij}^{(\ell)} \leq x_{ij} \right )$ the (rescaled) empirical cdf of $X_{ij}$ based on a sample $X_{ij}^{(1)}, \dots, X_{ij}^{(n)}$ for $i = 1, \dots, k$ and $j = 1, \dots, d_{i}$ (recall that $\mathbf{X}_{i} = (X_{i1}, \dots, X_{id_{i}})$ ), we look for

$\widehat{\boldsymbol{\theta}}_{C,n}^{\text{NP}} = \text{arg max}_{\boldsymbol{\theta}_{C}} \sum_{\ell = 1}^{n} \ln \left \{c \left ( \widehat{F}_{11} \left (X_{11}^{(\ell)} \right ), \dots, \widehat{F}_{kd_{k}} \left (X_{kd_{k}}^{(\ell)} \right ) ; \boldsymbol{\theta}_{C} \right ) \right \},$

where $c( \cdot ; \boldsymbol{\theta}_{C})$ is the copula density of the hierarchical Archimedean copula.

We assume that $C_{i}$ belongs to the same family of Archimedean copulas (e.g., Clayton) for $i = 0, \dots, k$ , and make use of the R package ‘HAC’.

In case the starting values (start_val) are not specified, the starting value for $\theta_{0}$ is put equal to 1.9 and the starting values for $\theta_{i}$ with $i \in \{1, \dots, k \}$ are determined by performing maximum pseudo-likelihood estimation to the $d_{i}$ -dimensional marginals with starting value $2$ .

Value

The maximum pseudo-likelihood estimates for $(\theta_{0},\theta_{1}, \dots, \theta_{k})$ .

References

Examples

dim = c(2,2)
thetas = c(2,3,4)

# Sample size
n = 1000

# 4 dimensional nested Gumbel copula with (theta_0,theta_1,theta_2) = (2,3,4)
HAC = gethac(dim,thetas,type = 1)

# Sample
sample = suppressWarnings(HAC::rHAC(n,HAC))

# Maximum pseudo-likelihood estimator with starting values equal to thetas
HAC_est_1 = mlehac(sample,dim,1,thetas)

# Maximum pseudo-likelihood estimator with starting values
# theta_0 = 1.9, and theta_1, theta_2 determined by maximum
# pseudo-likelihood estimation for marginal child copulas

HAC_est_2 = mlehac(sample,dim,1)


dim = c(2,2)
thetas = c(2,3,4)

# Sample size
n = 1000

# 4 dimensional nested Gumbel copula with (theta_0,theta_1,theta_2) = (2,3,4)
HAC = gethac(dim,thetas,type = 1)

# Sample
sample = suppressWarnings(HAC::rHAC(n,HAC))

# Maximum pseudo-likelihood estimator with starting values equal to thetas
HAC_est_1 = mlehac(sample,dim,1,thetas)

# Maximum pseudo-likelihood estimator with starting values
# theta_0 = 1.9, and theta_1, theta_2 determined by maximum
# pseudo-likelihood estimation for marginal child copulas

HAC_est_2 = mlehac(sample,dim,1)

otsort

Description

Usage

otsort(sample, dim)
otsort(sample, dim)

Arguments

`sample`	A sample from a $q$ -dimensional random vector $\mathbf{X}$ ( $n \times q$ matrix with observations in rows, variables in columns).
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ , in order as given in sample.

Details

The columns of sample are rearranged such that the data corresponding to the random vector $\mathbf{X}_{i}$ having the smallest dimension $d_{i}$ comes first, then the random vector with second smallest dimension, and so on.

Value

A list with elements "sample" containing the ordered sample, and "dim" containing the ordered dimensions.

Examples

q = 10
n = 50
dim = c(2,3,1,4)

# Sample from multivariate normal distribution
sample = mvtnorm::rmvnorm(n,rep(0,q),diag(q), method = "chol")

ordered = otsort(sample,dim)
q = 10
n = 50
dim = c(2,3,1,4)

# Sample from multivariate normal distribution
sample = mvtnorm::rmvnorm(n,rep(0,q),diag(q), method = "chol")

ordered = otsort(sample,dim)

phiellip

Description

Given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1},...,\mathbf{X}_{k})$ with $\mathbf{X}_{i}$ a $d_{i}$ -dimensional random vector, i.e., $q = d_{1} + ... + d_{k}$ , this function estimates the $\Phi$ -dependence between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ by estimating the joint and marginal meta-elliptical copula generators via the MECIP.

Usage

phiellip(sample, dim, phi, grid, params, normalize = 1)
phiellip(sample, dim, phi, grid, params, normalize = 1)

Arguments

`sample`	A sample from a $q$ -dimensional random vector $\mathbf{X}$ ( $n \times q$ matrix with observations in rows, variables in columns).
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ .
`phi`	The function $\Phi$ .
`grid`	The grid of values on which to estimate the density generators.
`params`	The tuning parameters to be used when estimating the density generators.
`normalize`	A value in $\{1,2\}$ indicating the normalization procedure that is applied to the estimated generator (default = 1).

Details

When $\mathbf{X} = (\mathbf{X}_{1}, \dots, \mathbf{X}_{k})$ has a meta-elliptical copula with generator $g_{\mathcal{R}}$ , marginal generators $g_{\mathcal{R}_{i}}$ of $\mathbf{X}_{i}$ for $i = 1, \dots, k$ , and scale matrix

the $\Phi$ -dependence between $\mathbf{X}_{1}, \dots, \mathbf{X}_{k}$ equals

$\mathcal{D}_{\Phi}\left (\mathbf{X}_{1}, \dots, \mathbf{X}_{k} \right ) = \mathbb{E} \left \{\frac{\prod_{i = 1}^{k} g_{\mathcal{R}_{i}}\left (\mathbf{Z}_{i}^{\text{T}} \mathbf{R}_{ii}^{-1} \mathbf{Z}_{i} \right ) \left | \mathbf{R} \right |^{1/2}}{g_{\mathcal{R}}\left (\mathbf{Z}^{\text{T}} \mathbf{R}^{-1} \mathbf{Z} \right ) \prod_{i = 1}^{k} \left | \mathbf{R}_{ii} \right |^{1/2}} \Phi \left (\frac{g_{\mathcal{R}} \left (\mathbf{Z}^{\text{T}} \mathbf{R}^{-1} \mathbf{Z} \right ) \prod_{i = 1}^{k} \left |\mathbf{R}_{ii} \right |^{1/2}}{\prod_{i = 1}^{k} g_{\mathcal{R}_{i}} \left (\mathbf{Z}_{i}^{\text{T}}\mathbf{R}_{ii}^{-1} \mathbf{Z}_{i} \right ) \left |\mathbf{R} \right |^{1/2} } \right )\right \},$

where (recall that $\mathbf{X}_{i} = (X_{i1}, \dots, X_{id_{i}})$ for $i = 1, \dots, k$ )

$\mathbf{Z}_{i} = (Z_{i1}, \dots, Z_{id_{i}}) = \left(\left (Q \circ F_{i1} \right ) \left (X_{i1} \right ), \dots, \left (Q \circ F_{id_{i}} \right ) \left (X_{id_{i}} \right ) \right ),$

and $\mathbf{Z} = (\mathbf{Z}_{1}, \dots, \mathbf{Z}_{k})$ , with $Q$ the quantile function corresponding to $g_{\mathcal{R}}$ .

The expectation $\mathbb{E}$ is replaced by the empirical mean using the estimated sample $\widehat{\mathbf{Z}}^{(1)}, \dots, \widehat{\mathbf{Z}}^{(n)}$ with $\widehat{\mathbf{Z}}^{(\ell)} = (\widehat{\mathbf{Z}}_{1}^{(\ell)}, \dots, \widehat{\mathbf{Z}}_{k}^{(\ell)})$ for $\ell = 1, \dots, n$ , where

$\widehat{\mathbf{Z}}_{i}^{(\ell)} = \left (\widehat{Z}_{i1}^{(\ell)}, \dots, \widehat{Z}_{id_{i}}^{(\ell)} \right ) = \left ( \left (\widehat{Q} \circ \widehat{F}_{i1} \right ) \left (X_{i1}^{(\ell)} \right ), \dots, \left (\widehat{Q} \circ \widehat{F}_{id_{i}} \right ) \left (X_{id_{i}}^{(\ell)} \right ) \right ),$

for $i = 1, \dots, k$ . Here, $\widehat{Q}$ will be the quantile function corresponding to the final estimator for $g_{\mathcal{R}}$ , and

$\widehat{F}_{ij}(x_{ij}) = \frac{1}{n+1} \sum_{\ell = 1}^{n} 1 \left (X_{ij}^{(\ell)} \leq x_{ij} \right )$

is the (rescaled) empirical cdf of $X_{ij}$ based on a sample $X_{ij}^{(1)}, \dots, X_{ij}^{(n)}$ for $i = 1, \dots, k$ and $j = 1, \dots, d_{i}$ .

The estimation of $\mathbf{R}$ is done via its relation with the Kendall's tau matrix, see the function “KTMatrixEst.R” in the R package ‘ElliptCopulas’ of Derumigny et al. (2024).

For estimating $g_{\mathcal{R}}$ and $g_{\mathcal{R}_{i}}$ for $i = 1, \dots, k$ , the function ellcopest is used. This function requires certain tuning parameters (a bandwidth $h$ , a parameter $a$ , and a parameter $\delta$ for the shrinkage function). Suppose that there are $m$ marginal random vectors (among $\mathbf{X}_{1}, \dots, \mathbf{X}_{k}$ ) that are of dimension strictly larger than one. Then, all tuning parameters should be given as

$\text{params} = \text{list}(\text{"h"} = (h,h_{1},\dots,h_{m}), \text{"a"} = (a,a_{1}, \dots, a_{m}), \text{"p"} = (\delta, \delta_{1}, \dots, \delta_{m})),$

i.e., $(h,a,\delta)$ will be used for estimating $g_{\mathcal{R}}$ , and $(h_{i},a_{i},\delta_{i})$ will be used for estimating $g_{\mathcal{R}_{i}}$ for $i = 1, \dots, k$ .

When $d_{i} = 1$ for a certain $i \in \{1, \dots, k \}$ , the function “Convert_gd_To_g1.R” from the R package ‘ElliptCopulas’ is used to estimate $g_{\mathcal{R}_{i}}$ .

Value

The estimated $\Phi$ -dependence between $\mathbf{X}_{1}, \dots, \mathbf{X}_{k}$ .

References

Derumigny, A., Fermanian, J.-D., Ryan, V., van der Spek, R. (2024). ElliptCopulas, R package version 0.1.4.1. url: https://CRAN.R-project.org/package=ElliptCopulas.

Examples


q = 4
dim = c(2,2)

# Sample size
n = 1000

# Grid on which to evaluate the elliptical generator
grid = seq(0.005,100,by = 0.005)

# Degrees of freedom
nu = 7

# Student-t generator with 7 degrees of freedom
g_q = ((nu/(nu-2))^(q/2))*(gamma((q+nu)/2)/(((pi*nu)^(q/2))*gamma(nu/2))) *
                          ((1+(grid/(nu-2)))^(-(q+nu)/2))

# Density of squared radius
R2 = function(t,q){(gamma((q+nu)/2)/(((nu-2)^(q/2))*gamma(nu/2)*gamma(q/2))) *
                   (t^((q/2)-1)) * ((1+(t/(nu-2)))^(-(q+nu)/2))}

# Sample from 4-dimensional Student-t distribution with 7 degrees of freedom
# and identity covariance matrix
sample = ElliptCopulas::EllDistrSim(n,q,diag(q),density_R2 = function(t){R2(t,q)})

# Tuning parameter selection for g_R
opt_parameters_joint = elliptselect(n,q,seq((3/4)-(1/q)+0.01,1-0.01,len = 200),
                                        seq(0.01,2,len = 200))

# Optimal tuning parameters for g_R
a = opt_parameters_joint$Opta ; p = opt_parameters_joint$Optp ;
                                h = opt_parameters_joint$Opth

# Tuning parameter selection for g_R_1 (same for g_R_2)
opt_parameters_marg = elliptselect(n,2,seq((3/4)-(1/2)+0.01,1-0.01,len = 200),
                                       seq(0.01,2,len = 200))

# Optimal tuning parameters for g_R_1 (same for g_R_2)
a1 = opt_parameters_marg$Opta ; p1 = opt_parameters_marg$Optp ;
                                h1 = opt_parameters_marg$Opth

a2 = a1 ; p2 = p1 ; h2 = h1
params = list("h" = c(h,h1,h2), "a" = c(a,a1,a2), "p" = c(p,p1,p2))

# Mutual information between two random vectors of size 2
est_phi = phiellip(sample, dim, function(t){t * log(t)}, grid, params)


q = 4
dim = c(2,2)

# Sample size
n = 1000

# Grid on which to evaluate the elliptical generator
grid = seq(0.005,100,by = 0.005)

# Degrees of freedom
nu = 7

# Student-t generator with 7 degrees of freedom
g_q = ((nu/(nu-2))^(q/2))*(gamma((q+nu)/2)/(((pi*nu)^(q/2))*gamma(nu/2))) *
                          ((1+(grid/(nu-2)))^(-(q+nu)/2))

# Density of squared radius
R2 = function(t,q){(gamma((q+nu)/2)/(((nu-2)^(q/2))*gamma(nu/2)*gamma(q/2))) *
                   (t^((q/2)-1)) * ((1+(t/(nu-2)))^(-(q+nu)/2))}

# Sample from 4-dimensional Student-t distribution with 7 degrees of freedom
# and identity covariance matrix
sample = ElliptCopulas::EllDistrSim(n,q,diag(q),density_R2 = function(t){R2(t,q)})

# Tuning parameter selection for g_R
opt_parameters_joint = elliptselect(n,q,seq((3/4)-(1/q)+0.01,1-0.01,len = 200),
                                        seq(0.01,2,len = 200))

# Optimal tuning parameters for g_R
a = opt_parameters_joint$Opta ; p = opt_parameters_joint$Optp ;
                                h = opt_parameters_joint$Opth

# Tuning parameter selection for g_R_1 (same for g_R_2)
opt_parameters_marg = elliptselect(n,2,seq((3/4)-(1/2)+0.01,1-0.01,len = 200),
                                       seq(0.01,2,len = 200))

# Optimal tuning parameters for g_R_1 (same for g_R_2)
a1 = opt_parameters_marg$Opta ; p1 = opt_parameters_marg$Optp ;
                                h1 = opt_parameters_marg$Opth

a2 = a1 ; p2 = p1 ; h2 = h1
params = list("h" = c(h,h1,h2), "a" = c(a,a1,a2), "p" = c(p,p1,p2))

# Mutual information between two random vectors of size 2
est_phi = phiellip(sample, dim, function(t){t * log(t)}, grid, params)

phihac

Description

This function computes the $\Phi$ -dependence between all the child copulas of a hac object obtained by the function gethac, i.e., given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1},...,\mathbf{X}_{k})$ with $\mathbf{X}_{i}$ a $d_{i}$ -dimensional random vector, i.e., $q = d_{1} + ... + d_{k}$ , where $\mathbf{X}_{1},...,\mathbf{X}_{k}$ are connected via a hierarchical Archimedean copula with two nesting levels, phihac computes the $\Phi$ -dependence between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ .

Usage

phihac(cop, dim, M, phi)
phihac(cop, dim, M, phi)

Arguments

`cop`	A hac object as provided by the function `gethac`.
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ .
`M`	The size of the Monte Carlo sample used for approximating the integral of the $\Phi$ -dependence.
`phi`	The function $\Phi$ .

Details

for a certain continuous, convex function $\Phi : (0,\infty) \rightarrow \mathbb{R}$ . By drawing a sample of size $M$ from $c$ , say $\mathbf{U}^{(1)}, \dots, \mathbf{U}^{(M)}$ , with $\mathbf{U}^{(\ell)} = (\mathbf{U}_{1}^{(\ell)}, \dots, \mathbf{U}_{k}^{(\ell)})$ , we can approximate $\mathcal{D}_{\Phi}$ by

$\widehat{\mathcal{D}}_{\Phi} = \frac{1}{M} \sum_{\ell = 1}^{M} \frac{\prod_{i = 1}^{k} c_{i} \left (\mathbf{U}_{i}^{(\ell)} \right )}{c \left (\mathbf{U}^{(\ell)} \right )} \Phi \left (\frac{c \left (\mathbf{U}^{(\ell)} \right )}{\prod_{i = 1}^{k} c_{i} \left (\mathbf{U}_{i}^{(\ell)} \right )} \right ).$

The function phihac computes $\widehat{\mathcal{D}}_{\Phi}$ when $c$ is a hierarchical Archimedean copula with two nesting levels, as produced by the function gethac.

Value

The $\Phi$ -dependence between $\mathbf{X}_{1}, \dots, \mathbf{X}_{k}$ (i.e., between all the child copulas of the hac object).

References

Examples


dim = c(2,2)
thetas = c(2,3,4)

# 4 dimensional nested Gumbel copula with (theta_0,theta_1,theta_2) = (2,3,4)
HAC = gethac(dim,thetas,type = 1)

# Mutual information based on Monte Carlo sample of size 10000
Phi_dep = phihac(HAC,dim,10000,function(t){t * log(t)})


dim = c(2,2)
thetas = c(2,3,4)

# 4 dimensional nested Gumbel copula with (theta_0,theta_1,theta_2) = (2,3,4)
HAC = gethac(dim,thetas,type = 1)

# Mutual information based on Monte Carlo sample of size 10000
Phi_dep = phihac(HAC,dim,10000,function(t){t * log(t)})

phinp

Description

Given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1},...,\mathbf{X}_{k})$ with $\mathbf{X}_{i}$ a $d_{i}$ -dimensional random vector, i.e., $q = d_{1} + ... + d_{k}$ , this function estimates the $\Phi$ -dependence between $\mathbf{X}_{1},...,\mathbf{X}_{k}$ by estimating the joint and marginal copula densities via fully non-parametric copula kernel density estimation.

Usage

phinp(sample, cop = NULL, dim, phi, estimator, bw_method)
phinp(sample, cop = NULL, dim, phi, estimator, bw_method)

Arguments

`sample`	A sample from a $q$ -dimensional random vector $\mathbf{X}$ ( $n \times q$ matrix with observations in rows, variables in columns).
`cop`	A fitted reference hac object, in case bw_method = 0 (default = NULL).
`dim`	The vector of dimensions $(d_{1},...,d_{k})$ .
`phi`	The function $\Phi$ .
`estimator`	Either "beta" or "trans" for the beta kernel or the Gaussian transformation kernel copula density estimator.
`bw_method`	A number in $\{0,1,2\}$ specifying the method used for computing optimal local bandwidths.

Details

for a certain continuous, convex function $\Phi : (0,\infty) \rightarrow \mathbb{R}$ , and with $\mathbf{U} = (\mathbf{U}_{1}, \dots, \mathbf{U}_{k}) \sim c$ .

The expectation $\mathbb{E}$ is replaced by the empirical mean using the estimated copula sample $\widehat{\mathbf{U}}^{(1)}, \dots, \widehat{\mathbf{U}}^{(n)}$ with $\widehat{\mathbf{U}}^{(\ell)} = (\widehat{\mathbf{U}}_{1}^{(\ell)}, \dots, \widehat{\mathbf{U}}_{k}^{(\ell)})$ for $\ell = 1, \dots, n$ , where (recall that $\mathbf{X}_{i} = (X_{i1}, \dots, X_{id_{i}})$ for $i = 1, \dots, k$ )

$\widehat{\mathbf{U}}_{i}^{(\ell)} = \left (\widehat{U}_{i1}^{(\ell)}, \dots, \widehat{U}_{id_{i}}^{(\ell)} \right ) = \left (\widehat{F}_{i1} \left (X_{i1}^{(\ell)} \right ), \dots, \widehat{F}_{id_{i}} \left (X_{id_{i}}^{(\ell)} \right ) \right ).$

Hereby, $\widehat{F}_{ij}(x_{ij}) = \frac{1}{n+1} \sum_{\ell = 1}^{n} 1 \left (X_{ij}^{(\ell)} \leq x_{ij} \right )$ is the (rescaled) empirical cdf of $X_{ij}$ based on a sample $X_{ij}^{(1)}, \dots, X_{ij}^{(n)}$ for $i = 1, \dots, k$ and $j = 1, \dots, d_{i}$ .

The joint copula density $c$ and marginal copula densities $c_{i}$ for $i = 1, \dots, k$ are estimated via fully non-parametric copula kernel density estimation. When estimator = "beta", the beta kernel copula density estimator is used. When estimator = "trans", the Gaussian transformation kernel copula density estimator is used.

Bandwidth selection is done locally by using the function hamse. When bw_method = 0, then the given fitted (e.g., via MLE using mlehac) hac object (hierarchical Archimedean copula) cop is used as reference copula. When bw_method = 1, then a non-parametric (beta or Gaussian transformation) kernel copula density estimator based on the pseudos as pivot is used. This pivot is computed using the big O bandwidth (i.e., $n^{-2/(q+4)}$ in case of the beta estimator, and $n^{-1/(q+4)}$ for the transformation estimator, with $q$ the total dimension). When bw_method = 2, the big O bandwidths are taken.

Value

The estimated $\Phi$ -dependence between $\mathbf{X}_{1}, \dots, \mathbf{X}_{k}$ .

References

Examples


q = 4
dim = c(2,2)

# Sample size
n = 500

# Four dimensional hierarchical Gumbel copula
# with parameters (theta_0,theta_1,theta_2) = (2,3,4)
HAC = gethac(dim,c(2,3,4),type = 1)

# Sample
sample =  suppressWarnings(HAC::rHAC(n,HAC))

# Maximum pseudo-likelihood estimator to be used as reference copula for bw_method = 0
est_cop = mlehac(sample,dim,1,c(2,3,4))

# Estimate mutual information between two random vectors of size 2 in different ways

est_phi_1 = phinp(sample,cop = est_cop,dim = dim,phi = function(t){t * log(t)},
                  estimator = "beta",bw_method = 0)
est_phi_2 = phinp(sample,cop = est_cop,dim = dim,phi = function(t){t * log(t)},
                  estimator = "trans",bw_method = 0)
est_phi_3 = phinp(sample,dim = dim,phi = function(t){t * log(t)},
                  estimator = "beta",bw_method = 1)
est_phi_4 = phinp(sample,dim = dim,phi = function(t){t * log(t)},
                  estimator = "trans",bw_method = 1)
est_phi_5 = phinp(sample,dim = dim,phi = function(t){t * log(t)},
                  estimator = "beta",bw_method = 2)
est_phi_6 = phinp(sample,dim = dim,phi = function(t){t * log(t)},
                  estimator = "trans",bw_method = 2)


q = 4
dim = c(2,2)

# Sample size
n = 500

# Four dimensional hierarchical Gumbel copula
# with parameters (theta_0,theta_1,theta_2) = (2,3,4)
HAC = gethac(dim,c(2,3,4),type = 1)

# Sample
sample =  suppressWarnings(HAC::rHAC(n,HAC))

# Maximum pseudo-likelihood estimator to be used as reference copula for bw_method = 0
est_cop = mlehac(sample,dim,1,c(2,3,4))

# Estimate mutual information between two random vectors of size 2 in different ways

est_phi_1 = phinp(sample,cop = est_cop,dim = dim,phi = function(t){t * log(t)},
                  estimator = "beta",bw_method = 0)
est_phi_2 = phinp(sample,cop = est_cop,dim = dim,phi = function(t){t * log(t)},
                  estimator = "trans",bw_method = 0)
est_phi_3 = phinp(sample,dim = dim,phi = function(t){t * log(t)},
                  estimator = "beta",bw_method = 1)
est_phi_4 = phinp(sample,dim = dim,phi = function(t){t * log(t)},
                  estimator = "trans",bw_method = 1)
est_phi_5 = phinp(sample,dim = dim,phi = function(t){t * log(t)},
                  estimator = "beta",bw_method = 2)
est_phi_6 = phinp(sample,dim = dim,phi = function(t){t * log(t)},
                  estimator = "trans",bw_method = 2)

transformationestimator

Description

This function computes the non-parametric Gaussian transformation kernel copula density estimator.

Usage

transformationestimator(input, h, pseudos)
transformationestimator(input, h, pseudos)

Arguments

`input`	The copula argument at which the density estimate is to be computed.
`h`	The bandwidth to be used in the Gaussian kernel.
`pseudos`	The (estimated) copula observations from a $q$ -dimensional random vector $\mathbf{X}$ ( $n \times q$ matrix with observations in rows, variables in columns).

Details

Given a $q$ -dimensional random vector $\mathbf{X} = (\mathbf{X}_{1}, \dots, \mathbf{X}_{k})$ with $\mathbf{X}_{i} = (X_{i1}, \dots, X_{id_{i}})$ , and samples $X_{ij}^{(1)}, \dots, X_{ij}^{(n)}$ from $X_{ij}$ for $i = 1, \dots, k$ and $j = 1, \dots, d_{i}$ , the Gaussian transformation kernel estimator for the copula density of $\mathbf{X}$ equals, at $\mathbf{u} = (u_{11}, \dots, u_{kd_{k}}) \in \mathbb{R}^{q}$ ,

$\widehat{c}_{\text{T}}(\mathbf{u}) = \frac{1}{n h_{n}^{q} \prod_{i = 1}^{k} \prod_{j = 1}^{d_{i}} \phi \left (\Phi^{-1} \left (u_{ij} \right ) \right )} \sum_{\ell = 1}^{n} \prod_{i = 1}^{k} \prod_{j = 1}^{d_{i}} \phi \left (\frac{\Phi^{-1}(u_{ij}) - \Phi^{-1} \left (\widehat{U}_{ij}^{(\ell)} \right )}{h_{n}} \right ),$

where $h_{n} > 0$ is a bandwidth parameter, $\widehat{U}_{ij}^{(\ell)} = \widehat{F}_{ij} (X_{ij}^{(\ell)})$ with

$\widehat{F}_{ij}(x_{ij}) = \frac{1}{n+1} \sum_{\ell = 1}^{n} 1 \left (X_{ij}^{(\ell)} \leq x_{ij} \right )$

the (rescaled) empirical cdf of $X_{ij}$ , and $\Phi$ the standard normal distribution function with corresponding quantile function $\Phi^{-1}$ and density function $\phi$ .

Value

The Gaussian transformation kernel copula density estimator evaluated at the input.

References

Examples

q = 3
n = 100

# Sample from multivariate normal distribution with identity covariance matrix
sample = mvtnorm::rmvnorm(n,rep(0,q),diag(3),method = "chol")

# Copula pseudo-observations
pseudos = matrix(0,n,q)
for(j in 1:q){pseudos[,j] = (n/(n+1)) * ecdf(sample[,j])(sample[,j])}

# Argument at which to estimate the density
input = rep(0.5,q)

# Local bandwidth selection
h = hamse(input,pseudos = pseudos,n = n,estimator = "trans",bw_method = 1)

# Gaussian transformation kernel estimator
est_dens = transformationestimator(input,h,pseudos)

# True density
true = copula::dCopula(rep(0.5,q), copula::normalCopula(0, dim = q))

q = 3
n = 100

# Sample from multivariate normal distribution with identity covariance matrix
sample = mvtnorm::rmvnorm(n,rep(0,q),diag(3),method = "chol")

# Copula pseudo-observations
pseudos = matrix(0,n,q)
for(j in 1:q){pseudos[,j] = (n/(n+1)) * ecdf(sample[,j])(sample[,j])}

# Argument at which to estimate the density
input = rep(0.5,q)

# Local bandwidth selection
h = hamse(input,pseudos = pseudos,n = n,estimator = "trans",bw_method = 1)

# Gaussian transformation kernel estimator
est_dens = transformationestimator(input,h,pseudos)

# True density
true = copula::dCopula(rep(0.5,q), copula::normalCopula(0, dim = q))

Package 'VecDep'

Help Index

betakernelestimator

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bwd1

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bwd1asR0

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bwd1avar

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bwd2

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bwd2asR0

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bwd2avar

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covgpenal

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createR0

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