savvySh: Shrinkage Methods for Linear Regression Estimation

# `savvySh`: Shrinkage Methods for Linear Regression Estimation

# Introduction

`savvySh` is an R package that implements a suite of shrinkage estimators for multivariate linear regression. The motivation for shrinkage estimation originates from Stein’s paradox, which shows that it is possible to improve on the classical Ordinary Least Squares (OLS) estimator when estimating multiple parameters simultaneously. This improvement is achieved by introducing structured bias that reduces variance, yielding estimators with smaller overall Mean Squared Error (MSE).

The `savvySh` package provides a unified interface to four shrinkage strategies, each designed to improve prediction accuracy and estimation stability in finite samples. These methods do not require cross-validation or tuning parameter selection, with the exception of the Shrinkage Ridge Regression (SRR), for which the shrinkage intensity is chosen by minimizing an explicit MSE criterion.

The package is particularly suited for high-dimensional settings or cases where the design matrix exhibits near multicollinearity. Empirical results in both simulation and real data settings show that at least one of the shrinkage estimators consistently performs as well as or better than OLS, and in many cases leads to substantial improvements, especially when applied to generalized linear models.

For more details, please see:

Asimit, V., Cidota, M. A., Chen, Z., & Asimit, J. (2025). Slab and Shrinkage Linear Regression Estimation

Main features: `savvySh` provides four classes of shrinkage estimators for linear regression:

- Multiplicative Shrinkage: Modifies OLS estimates by applying data-driven multiplicative factors. This includes the Stein estimator (St), Diagonal Shrinkage (DSh), and the more general Shrinkage estimator (Sh) that solves a Sylvester equation.

- Slab Regression: Adds a quadratic penalty to shrink the coefficients in specific directions. The Simple Slab Regression (SR) penalizes along a fixed direction, and the Generalized Slab Regression (GSR) allows penalties along multiple directions, typically aligned with the data structure.

- Linear Shrinkage: Combines the OLS estimator (through the origin) with a target that assumes uncorrelated covariates. This method is designed for standardized data and avoids estimating the intercept.

- Shrinkage Ridge Regression: Improves on Ridge Regression (RR) by shrinking toward a diagonal matrix with equal entries, balancing the sample structure with a stable target.

Inputs: The primary inputs to `savvySh` are similar to those of a regression function:

- `x`: The design matrix (predictor matrix) of dimension \(n\times p\).

- `y`: The response vector of length \(n\).

- `model_class`: The shrinkage method to use (one of `"Multiplicative"`, `"Slab"`, `"Linear"`, or `"ShrinkageRR"`).

- Additional method-specific parameters (e.g., include `Sh`or not), with sensible defaults or automatic selection if not provided.

Output: The output of `savvySh` is a list containing several elements:

- `call`: the original function call.

- `model`: The data frame of `y` and `x` used in the analysis.

- `optimal_lambda`: the penalty parameter used (if applicable).

- `model_class`: the shrinkage method used (e.g.,`"Multiplicative"`, `"Slab"`, `"Linear"`, or `"ShrinkageRR"`).

- `coefficients`: A list of estimated coefficients for each applicable estimator for chosen `model_class`.

- Additional method-specific diagnostics (e.g., fitted values and predicted MSE).

This vignette provides an overview of the methods implemented in `savvySh` and demonstrates how to use them on simulated data and real data. We begin with a theoretical overview of each shrinkage class, then walk through simulation examples that illustrate how to apply `savvySh` for each method.

# Theoretical Overview

The `savvySh` function encompasses four shrinkage strategies for linear regression. All these methods aim to improve predictive accuracy and interpretability by trading a small amount of bias for a larger reduction in variance. Below we briefly summarize the theoretical background of each method.

Consider a response vector \(\mathbf{y} \in \Re^n\) and a predictor matrix \(\mathbf{X} \in \Re^{n \times (p+1)}\). Let \(\widehat{\boldsymbol{\beta}}^{\text{OLS}}\) be the OLS estimator of the coefficient vector, and \(\Sigma = \mathbf{X}^\top \mathbf{X}\) the Gram matrix of the design.

## Multiplicative Shrinkage

This class of estimators modifies the OLS solution by multiplying it with a matrix \(\mathbf{D}\), yielding the form \(\widehat{\boldsymbol{\beta}} = \mathbf{D} \widehat{\boldsymbol{\beta}}^{OLS}\). The goal is to choose \(\mathbf{D}\) to minimize the MSE of the resulting estimator. While earlier work such as Hocking et al. (1976) focused on the case where the design matrix is in canonical form (orthonormal), our framework generalizes these results to arbitrary design matrices without requiring that assumption. Common choices for \(\mathbf{D}\) include:

1. Stein Estimator (St): The St estimator shrinks all coefficients uniformly by a single factor \(\widehat{a^*}\):

\[ \widehat{\boldsymbol{\beta}}^{\text{St}} = \widehat{a^*} \widehat{\boldsymbol{\beta}}^{\text{OLS}}, \quad \text{where} \quad \widehat{a^*} = \frac{\left(\widehat{\boldsymbol\beta}^{OLS}\right)^T\widehat{\boldsymbol\beta}^{OLS}}{\left(\widehat{\boldsymbol\beta}^{OLS}\right)^T\widehat{\boldsymbol\beta}^{OLS} + \widehat{\text{MSE}\left(\widehat{\boldsymbol{\beta}}^{\text{OLS}}\right)}}. \]

This corresponds to \(\mathbf{D} = a \mathbf{I}_{p+1}\). It reduces variance by scaling all coefficients equally.

2. Diagonal Shrinkage Estimator (DSh): Extending the St estimator, DSh applies a separate shrinkage factor \(\widehat{b_k^*}\) to each coefficient:

\[ \widehat{\boldsymbol{\beta}}^{\text{DSh}} = \text{diag}\left(\widehat{\mathbf{b^*}}\right), \quad \text{where} \quad \widehat{b_k^*} = \frac{\left(\widehat{\beta}_k^{\text{OLS}}\right)^2}{\left(\widehat{\beta}_k^{\text{OLS}}\right)^2 + \widehat{\sigma^2} \sigma_k}. \]

This corresponds to \(\mathbf{D} = \text{diag}\left(\mathbf{b}\right)\) and \(\sigma_k\) is the \(k^{\text{th}}\) diagonal entry of \(\Sigma^{-1}\) and \(\widehat{\sigma^2}\) is the estimated residual variance.

3. Shrinkage Estimator (Sh): The Sh estimator is the most general form in the multiplicative shrinkage family. It applies a full (non-diagonal) matrix \(\widehat{\mathbf{C}^*}\) to the OLS estimate and requires solving a Sylvester equation:

\[ \widehat{\boldsymbol{\beta}}^{\text{Sh}} = \widehat{\mathbf{C}^*} \widehat{\boldsymbol{\beta}}^{\text{OLS}}, \quad \text{where } \widehat{\mathbf{C}^*} \text{ solves the Sylvester equation:} \ \Sigma^{-1} \mathbf{C} + \mathbf{C} \widehat{\boldsymbol{\beta}}^{\text{OLS}} \left(\widehat{\boldsymbol{\beta}}^{\text{OLS}}\right)^T = \widehat{\boldsymbol{\beta}}^{\text{OLS}} \left(\widehat{\boldsymbol{\beta}}^{\text{OLS}}\right)^T. \]

This corresponds to \(\mathbf{D} = \text{diag}\left(\mathbf{C}\right)\). Unlike St and DSh, the Sh estimator allows interactions across coefficients through off-diagonal entries in \(\widehat{\mathbf{C}^*}\), capturing richer shrinkage structures.

## Slab Regression

Slab regression introduces a structured quadratic penalty that shrinks the regression coefficients in specified directions. It is closely related to the Generalized LASSO estimator introduced by Tibshirani and Taylor (2011), but with key differences. Unlike the Generalized LASSO, slab regression does not aim for variable selection or sparsity, and it avoids cross-validation by selecting shrinkage levels through theoretical MSE criteria. These penalties are based on projection constraints that can be fixed (e.g., constant direction \(\mathbf{u} = \mathbf{1}\)) or structured (e.g., eigenvectors of \(\Sigma\)). This leads to two main estimators.

1. (Simple) Slab Regression (SR): The SR estimator applies a single penalty along a fixed direction vector \(\mathbf{u} \in \Re^{p+1}\). A common choice is \(\mathbf{u} = \mathbf{1}\). The estimator is given by:

\[ \widehat{\boldsymbol{\beta}}^{SR}\left(\mu;\textbf{u}\right) := \arg\min_{\boldsymbol{\beta}\in\Re^{p+1}} \left( \sum_{i=1}^n \big(y_i - \mathbf{x}_i^\top \boldsymbol{\beta}\big)^2 + \mu \big(\mathbf{u}^\top \boldsymbol{\beta}\big)^2 \right), \]

where \(\mu \geq 0\) is the penalty parameter controls the amount of shrinkage along \(\mathbf{u}\) and has a closed-form, chosen analytically to minimize MSE under the slab constraint \((\boldsymbol{\beta}^\top \mathbf{u})^2\).

2. Generalized Slab Regression (GSR): The GSR estimator extends SR by allowing shrinkage in multiple directions. These directions are typically chosen as eigenvectors of \(\Sigma\). The estimator is:

\[ \widehat{\boldsymbol{\beta}}^{GSR}(\boldsymbol{\mu}) := \arg\min_{\boldsymbol{\beta} \in \Re^{p+1}} \left(\sum_{i=1}^n \big(y_i - \mathbf{x}_i^\top \boldsymbol{\beta}\big)^2 + \sum_{l \in \mathcal{L}} \mu_l \big(\mathbf{u}_l^\top \boldsymbol{\beta}\big)^2 \right), \]

where each \(\mu_l \geq 0\) controls the strength of shrinkage along \(\mathbf{u}_l\), and the set \(\mathcal{L}\) indexes the selected directions. A special case arises when the \(\mathbf{u}_l\) form the standard basis vectors, recovering the classical Generalized RR of Hoerl and Kennard (1970).

## Linear Shrinkage

The LSh estimator combines the OLS estimator (computed through the origin) with a target estimator that assumes uncorrelated covariates (\(\widetilde{\Sigma} = \mathrm{diag}(\Sigma)\)). This target estimator is given by \(\widehat{\boldsymbol{\beta}}^{ind} = \widetilde{\Sigma}^{-1}\mathbf{X}^T\mathbf{y}\). The method assumes that the data are standardized (zero mean and unit variance) so that the intercept is not needed. The LSh estimator is defined as:

\[ \widehat{\boldsymbol{\beta}}^{ind}(\rho):=(1-\rho)\widehat{\widehat{\boldsymbol{\beta}\,}}^{OLS}+\rho \widehat{\boldsymbol{\beta}}^{ind}=\left(\rho\widetilde{\Sigma}^{-1}\Sigma + (1-\rho)\textbf{I}_p\right)\widehat{\widehat{\boldsymbol{\beta}\,}}^{OLS}:=\Sigma(\rho)\widehat{\widehat{\boldsymbol{\beta}\,}}^{OLS}, \]

where \(\widehat{\widehat{\boldsymbol{\beta}}}^{OLS}\) is the OLS estimator without intercept, and \(\rho\) is the shrinkage intensity chosen to improve stability and reduce MSE.

## Shrinkage Ridge Regression

The SRR estimator improves upon standard RR by shrinking the \(\Sigma\) toward a diagonal matrix with equal entries. Specifically, it shrinks toward \(v \mathbf{I}_{p+1}\), where \(v = \frac{1}{p+1} \mathrm{Tr}(\Sigma)\) is the average variance across all covariates and the intercept. The SRR estimator is given by:

\[ \widehat{\boldsymbol{\beta}}^{SRR}(\rho)=\big(\Sigma^*(\rho)\big)^{-1}\textbf{X}^T\textbf{y} \quad \text{with} \quad \Sigma^*(\rho)=(1-\rho)\Sigma+\rho v \textbf{I}_{p+1}. \]

Unlike the approach in Ledoit and Wolf (2004), which minimizes the MSE of the covariance matrix, SRR chooses the optimal \(\rho^*\) by directly minimizing the MSE of the coefficient estimator. Although \(\rho^*\) does not have a closed form, it can be selected numerically. This approach is especially useful when the design matrix has a low-rank or unstable covariance structure, as often encountered in high-dimensional or collinear settings.

## Summary of Shrinkage Estimators

Method | Shrinkage Direction | Shrinkage Form | Assumes Standardized Data? | Tuning or Optimizing Required? | Handles Multicollinearity?
--- | --- | --- | --- | --- | ---
OLS | None | No shrinkage | No | No | No
RR | Toward origin | \(\left(\mathbf{X}^\top\mathbf{X} + \lambda I\right)^{-1} \mathbf{X}^\top \mathbf{y}\) | No | Yes (cross-validation) | Yes
St | Global (scalar) | \(\widehat{a^*} \cdot \widehat{\beta}^{\text{OLS}}\) | No | No | No
DSh | Coordinate-wise (diagonal) | \(\text{diag}\left(\widehat{\mathbf{b^*}}\right) \cdot \widehat{\beta}^{\text{OLS}}\) | No | No | No
Sh | Matrix shrinkage (non-diagonal) | \(\widehat{\mathbf{C}^*} \cdot \widehat{\beta}^{\text{OLS}}\) | No | No | No
SR | Fixed direction (e.g., \(\mathbf{1}\)) | Penalized projection | No | No | No
GSR | Multiple directions (eigenvectors) | Penalized projection | No | No | No
LSh | Toward diagonal target | Convex combination | Yes | No | No
SRR | Toward scaled identity | Modified Ridge | No | Yes (numerical minimization) | Yes

# Simulation Examples

This section presents a set of simulation studies that demonstrate the performance of shrinkage estimators implemented in `savvySh`. We compare them against OLS using synthetic datasets. The performance metric is the \(L_2\) distance between the estimated coefficients and the true parameter vector. Lower \(L_2\) values indicate better recovery of the true coefficients.

We explore several generative scenarios based on the design matrix and error distribution. The structure of the design matrix includes different forms of correlation and dependence. Each simulation is followed by a table comparing \(L_2\) distances and estimated coefficients.

The following data-generating processes (DGPs) are considered:

- Multivariate Gaussian distributed covariates with Toeplitz covariance matrix - \(N(\pmb{\mu}, \pmb{\Psi}(\rho))\) where \(\pmb{\Psi}_{st}(\rho) = \rho^{|s-t|}\) for all \(1 \leq s, t \leq p\), Here, \(\pmb{\mu} = (\mu_1, \mu_2, \ldots, \mu_p)^T\) is the mean vector, \(\pmb{\Psi}(\rho)\) is the covariance matrix, and \(\rho\) represents the correlation coefficient that controls the dependence between covariates. The response is generated using normal noise.

- Student’s \(t\) distributed Multivariate Gaussian distributed covariates with Toeplitz covariance matrix - \(N(\pmb{\mu}, \pmb{\Psi}(\rho))\) where \(\pmb{\Psi}_{st}(\rho) = \rho^{|s-t|}\) for all \(1 \leq s, t \leq p\). Here, \(\pmb{\mu} = (\mu_1, \mu_2, \ldots, \mu_p)^T\) is the mean vector, \(\pmb{\Psi}(\rho)\) is the covariance matrix, and \(\rho\) represents the correlation coefficient that controls the dependence between covariates. The response includes heavier-tailed variation.

- Multivariate Gaussian Copula with Binomial marginal distributed covariates and Toeplitz covariance matrix - \(\textbf{Z}_i\sim N(\textbf{0}, \Psi(\rho))\) with \(X_{ik} = F^{-1}(\Phi(Z_{ik}))\), for \(1 \leq k \leq p\) where \(\Phi\) is the cumulative distribution function (CDF) of \(N(0,1)\), and \(F^{-1}\) is the inverse CDF of the binomial distribution.

- Latent Space Features - Covariates are generated by combining a low-rank structure with random variations, Specifically, we simulate \(\mathbf{X} = \mathbf{A} \mathbf{Z} + \mathbf{E}\), where \(\mathbf{A}\) is an \(n \times f\) matrix of factor loadings with entries drawn independently from a standard normal distribution \(N(0,1)\), and \(\mathbf{Z}\) is an \(f \times p\) matrix of latent factors, also with entries drawn independently from \(N(0,1)\). The term \(\mathbf{E}\) is an \(n \times p\) matrix of independent Gaussian noise with variance \(10^{-6}\), i.e., \(N(0,10^{-6})\).

In all four settings, the true regression coefficient vector alternates in sign with increasing magnitude, making it possible to assess the shrinkage effect across varying coefficient scales.

Note: Due to differences in underlying libraries and random number generation implementations (e.g., BLAS/LAPACK and RNG behavior), the data generated by functions like `mvrnorm` may differ slightly between Windows and macOS/Linux, even with the same seed.

## Multiplicative Shrinkage and Slab Regression

This section shows how `savvySh` implements multiplicative shrinkage including St, DSh, and Sh; Slab Shrinkage including SR and GSR. Each method is compared to OLS.

### Multivariate Gaussian Distribution

This example corresponds to the Multivariate Gaussian distributed covariates with Toeplitz covariance matrix setup described above. We simulate a design matrix from a multivariate normal distribution with a Toeplitz covariance matrix. The response is generated with Gaussian noise with variance \(\sigma^2 = 25\).

    # Load packages
    library(savvySh)
    library(MASS)
    library(knitr)

    # Parameters
    set.seed(123)
    n_val <- 1000
    p_val <- 10
    rho_val <- 0.75
    sigma_val <- 5
    mu_val <- 0

    # Correlation matrix
    sigma.rho <- function(rho_val, p_val) {
      rho_val ^ abs(outer(1:p_val, 1:p_val, "-"))
    }

    # True beta
    theta_func <- function(p_val) {
      sgn <- rep(c(1, -1), length.out = p_val)
      mag <- ceiling(seq_len(p_val) / 2)
      sgn * mag
    }

    # Simulate data
    Sigma <- sigma.rho(rho_val, p_val)
    X <- mvrnorm(n_val, mu = rep(mu_val, p_val), Sigma = Sigma)
    X_intercept <- cbind(1, X)
    beta_true <- theta_func(p_val + 1)
    y <- rnorm(n_val, mean = X_intercept %*% beta_true, sd = sigma_val)

    # Fit models
    ols_fit <- lm(y ~ X)
    beta_ols <- coef(ols_fit)

    multi_results <- savvySh(X, y, model_class = "Multiplicative", include_Sh = TRUE)
    beta_St  <- coef(multi_results, "St")
    beta_DSh <- coef(multi_results, "DSh")
    beta_Sh  <- coef(multi_results, "Sh")

    slab_results <- savvySh(X, y, model_class = "Slab")
    beta_SR  <- coef(slab_results, "SR")
    beta_GSR <- coef(slab_results, "GSR")

The tables below report the results of each estimator: the first table shows the \(L_2\) distance between the estimated coefficient vector and the ground truth, while the second table displays the actual estimated coefficients (rounded) for each method alongside the true values.

    # L2 comparison
    l2_table <- data.frame(
      Method = c("OLS", "St", "DSh", "Sh", "SR", "GSR"),
      L2_Distance = c(
        sqrt(sum((beta_ols - beta_true)^2)),
        sqrt(sum((beta_St  - beta_true)^2)),
        sqrt(sum((beta_DSh - beta_true)^2)),
        sqrt(sum((beta_Sh  - beta_true)^2)),
        sqrt(sum((beta_SR  - beta_true)^2)),
        sqrt(sum((beta_GSR - beta_true)^2))
      )
    )

    kable(l2_table, digits = 4, caption = "L2 Distance Between Estimated and True Coefficients")

L2 Distance Between Estimated and True Coefficients
Method | L2_Distance
--- | ---
OLS | 0.9791
St | 0.9292
DSh | 0.9261
Sh | 0.9787
SR | 1.0092
GSR | 0.9491

    # Coefficient comparison table
    coef_table <- data.frame(
      OLS = round(beta_ols, 3),
      St = round(beta_St, 3),
      DSh = round(beta_DSh, 3),
      Sh = round(beta_Sh, 3),
      SR = round(beta_SR, 3),
      GSR = round(beta_GSR, 3),
      True = round(beta_true, 3)
    )

    kable(coef_table, caption = "Estimated Coefficients by Method (rounded)")

Estimated Coefficients by Method (rounded)
| OLS | St | DSh | Sh | SR | GSR | True
--- | --- | --- | --- | --- | --- | --- | ---
(Intercept) | 1.135 | 1.129 | 1.113 | 1.135 | 0.751 | 1.150 | 1
X1 | -1.148 | -1.142 | -1.103 | -1.148 | -1.382 | -1.135 | -1
X2 | 2.348 | 2.336 | 2.311 | 2.348 | 2.262 | 2.310 | 2
X3 | -2.079 | -2.068 | -2.035 | -2.079 | -2.053 | -2.061 | -2
X4 | 3.120 | 3.103 | 3.090 | 3.120 | 3.014 | 3.144 | 3
X5 | -2.923 | -2.908 | -2.890 | -2.923 | -2.958 | -2.919 | -3
X6 | 4.286 | 4.263 | 4.264 | 4.285 | 4.195 | 4.288 | 4
X7 | -4.759 | -4.734 | -4.741 | -4.759 | -4.791 | -4.763 | -4
X8 | 5.196 | 5.168 | 5.178 | 5.195 | 5.171 | 5.201 | 5
X9 | -5.120 | -5.093 | -5.103 | -5.120 | -5.204 | -5.074 | -5
X10 | 6.245 | 6.212 | 6.235 | 6.245 | 6.045 | 6.146 | 6

### Student’s t Distribution

This example corresponds to the Student’s \(t\) distributed Multivariate Gaussian distributed covariates with Toeplitz covariance matrix setup. We repeat the same design as above, but instead of Gaussian noise, we add a scaled \(t\)-distributed noise with degrees of freedom \(\nu = \frac{50}{24}\).

    # Load packages
    library(savvySh)
    library(MASS)
    library(knitr)

    # Parameters
    set.seed(123)
    n_val <- 1000
    p_val <- 10
    rho_val <- 0.75
    df_val = 50/24
    mu_val <- 0

    # Correlation matrix
    sigma.rho <- function(rho_val, p_val) {
      rho_val ^ abs(outer(1:p_val, 1:p_val, "-"))
    }

    # True beta
    theta_func <- function(p_val) {
      sgn <- rep(c(1, -1), length.out = p_val)
      mag <- ceiling(seq_len(p_val) / 2)
      sgn * mag
    }

    # Simulate data
    Sigma <- sigma.rho(rho_val, p_val)
    X <- mvrnorm(n_val, mu = rep(mu_val, p_val), Sigma = Sigma)
    X_intercept <- cbind(1, X)
    beta_true <- theta_func(p_val + 1)
    y <- as.vector(X_intercept %*% beta_true) + rt(n = n_val, df = df_val)

    # Fit models
    ols_fit <- lm(y ~ X)
    beta_ols <- coef(ols_fit)

    multi_results <- savvySh(X, y, model_class = "Multiplicative", include_Sh = TRUE)
    beta_St  <- coef(multi_results, "St")
    beta_DSh <- coef(multi_results, "DSh")
    beta_Sh  <- coef(multi_results, "Sh")

    slab_results <- savvySh(X, y, model_class = "Slab")
    beta_SR  <- coef(slab_results, "SR")
    beta_GSR <- coef(slab_results, "GSR")

The tables below report the results of each estimator: the first table shows the \(L_2\) distance between the estimated coefficient vector and the ground truth, while the second table displays the actual estimated coefficients (rounded) for each method alongside the true values.

    # L2 comparison
    l2_table <- data.frame(
      Method = c("OLS", "St", "DSh", "Sh", "SR", "GSR"),
      L2_Distance = c(
        sqrt(sum((beta_ols - beta_true)^2)),
        sqrt(sum((beta_St  - beta_true)^2)),
        sqrt(sum((beta_DSh - beta_true)^2)),
        sqrt(sum((beta_Sh  - beta_true)^2)),
        sqrt(sum((beta_SR  - beta_true)^2)),
        sqrt(sum((beta_GSR - beta_true)^2))
      )
    )

    kable(l2_table, digits = 4, caption = "L2 Distance Between Estimated and True Coefficients")

L2 Distance Between Estimated and True Coefficients
Method | L2_Distance
--- | ---
OLS | 5.8495
St | 5.8271
DSh | 5.2781
Sh | 5.8494
SR | 5.9631
GSR | 5.1581

    # Coefficient comparison table
    coef_table <- data.frame(
      OLS = round(beta_ols, 3),
      St = round(beta_St, 3),
      DSh = round(beta_DSh, 3),
      Sh = round(beta_Sh, 3),
      SR = round(beta_SR, 3),
      GSR = round(beta_GSR, 3),
      True = round(beta_true, 3)
    )

    kable(coef_table, caption = "Estimated Coefficients by Method (rounded)")

Estimated Coefficients by Method (rounded)
| OLS | St | DSh | Sh | SR | GSR | True
--- | --- | --- | --- | --- | --- | --- | ---
(Intercept) | -0.345 | -0.252 | -0.023 | -0.345 | -0.623 | -0.368 | 1
X1 | -0.115 | -0.084 | 0.000 | -0.115 | -0.285 | 0.488 | -1
X2 | -0.811 | -0.592 | -0.082 | -0.811 | -0.873 | -0.426 | 2
X3 | 1.835 | 1.339 | 0.653 | 1.835 | 1.853 | 0.068 | -2
X4 | 3.308 | 2.413 | 2.118 | 3.308 | 3.232 | 3.587 | 3
X5 | -5.577 | -4.069 | -4.621 | -5.577 | -5.602 | -4.396 | -3
X6 | 3.148 | 2.297 | 1.955 | 3.148 | 3.082 | 2.635 | 4
X7 | -2.880 | -2.101 | -1.677 | -2.879 | -2.903 | -1.918 | -4
X8 | 5.121 | 3.736 | 4.178 | 5.121 | 5.103 | 3.825 | 5
X9 | -5.497 | -4.011 | -4.614 | -5.497 | -5.558 | -4.731 | -5
X10 | 5.805 | 4.235 | 5.207 | 5.805 | 5.660 | 4.447 | 6

### Gaussian Copula with Binomial Margins

This example corresponds to the Multivariate Gaussian Copula with Binomial marginal distributed covariates and Toeplitz covariance matrix setup. The covariates are transformed from a Gaussian copula to Binomial marginals using the inverse CDF transform. This simulates discrete predictor variables.

    # Load packages
    library(savvySh)
    library(MASS)
    library(knitr)

    # Parameters
    set.seed(123)
    n_val <- 1000
    p_val <- 10
    rho_val <- 0.75
    q_0 <- 0.01
    sigma_val <- 5

    # Correlation matrix
    sigma.rho <- function(rho_val, p_val) {
      rho_val ^ abs(outer(1:p_val, 1:p_val, "-"))
    }

    sigma.temp <- sigma.rho(rho_val, p_val)
    Z <- mvrnorm(n_val, mu = rep(0, p_val), Sigma = sigma.temp)
    X <- apply(Z, 2, function(z_col) qbinom(pnorm(z_col), size = 2, prob = q_0))
    X_intercept <- cbind(1, X)
    beta_true <- c(0, runif(p_val, 0.01, 0.3))
    y <- rnorm(n_val, mean = as.vector(X_intercept %*% beta_true), sd = sigma_val)

    # Fit models
    ols_fit <- lm(y ~ X)
    beta_ols <- coef(ols_fit)

    multi_results <- savvySh(X, y, model_class = "Multiplicative", include_Sh = TRUE)
    beta_St  <- coef(multi_results, "St")
    beta_DSh <- coef(multi_results, "DSh")
    beta_Sh  <- coef(multi_results, "Sh")

    slab_results <- savvySh(X, y, model_class = "Slab")
    beta_SR  <- coef(slab_results, "SR")
    beta_GSR <- coef(slab_results, "GSR")

The tables below report the results of each estimator: the first table shows the \(L_2\) distance between the estimated coefficient vector and the ground truth, while the second table displays the actual estimated coefficients (rounded) for each method alongside the true values.

    # L2 comparison
    l2_table <- data.frame(
      Method = c("OLS", "St", "DSh", "Sh", "SR", "GSR"),
      L2_Distance = c(
        sqrt(sum((beta_ols - beta_true)^2)),
        sqrt(sum((beta_St  - beta_true)^2)),
        sqrt(sum((beta_DSh - beta_true)^2)),
        sqrt(sum((beta_Sh  - beta_true)^2)),
        sqrt(sum((beta_SR  - beta_true)^2)),
        sqrt(sum((beta_GSR - beta_true)^2))
      )
    )

    kable(l2_table, digits = 4, caption = "L2 Distance Between Estimated and True Coefficients")

L2 Distance Between Estimated and True Coefficients
Method | L2_Distance
--- | ---
OLS | 3.0967
St | 1.0756
DSh | 1.8059
Sh | 3.0724
SR | 3.1182
GSR | 1.6176

    # Coefficient comparison table
    coef_table <- data.frame(
      OLS = round(beta_ols, 3),
      St = round(beta_St, 3),
      DSh = round(beta_DSh, 3),
      Sh = round(beta_Sh, 3),
      SR = round(beta_SR, 3),
      GSR = round(beta_GSR, 3),
      True = round(beta_true, 3)
    )

    kable(coef_table, caption = "Estimated Coefficients by Method (rounded)")

Estimated Coefficients by Method (rounded)
| OLS | St | DSh | Sh | SR | GSR | True
--- | --- | --- | --- | --- | --- | --- | ---
(Intercept) | 0.122 | 0.042 | 0.043 | 0.123 | 0.133 | 0.048 | 0.000
X1 | 0.442 | 0.153 | 0.045 | 0.439 | 0.420 | 0.060 | 0.297
X2 | -0.681 | -0.235 | -0.112 | -0.674 | -0.842 | -0.352 | 0.098
X3 | 0.549 | 0.190 | 0.070 | 0.545 | 0.459 | 0.081 | 0.136
X4 | 0.302 | 0.104 | 0.010 | 0.307 | 0.225 | 0.462 | 0.057
X5 | 1.634 | 0.564 | 0.979 | 1.622 | 1.542 | 1.167 | 0.249
X6 | -0.049 | -0.017 | 0.000 | -0.048 | -0.153 | 0.030 | 0.070
X7 | -0.278 | -0.096 | -0.014 | -0.277 | -0.308 | -0.194 | 0.093
X8 | -1.633 | -0.564 | -1.036 | -1.623 | -1.668 | -0.784 | 0.168
X9 | 1.858 | 0.642 | 1.223 | 1.841 | 1.797 | 0.759 | 0.181
X10 | -0.628 | -0.217 | -0.105 | -0.620 | -0.761 | -0.007 | 0.138

## Linear Shrinkage

This section describes the LSh estimator, which shrinks the OLS coefficients (through the origin) toward a target based on the diagonal of the \(\Sigma\). The method assumes standardized data.

### Multivariate Gaussian Distribution

This example corresponds to the Multivariate Gaussian distributed covariates with Toeplitz covariance matrix setup. We simulate from a Gaussian design with Toeplitz correlation, using additive Gaussian noise with variance \(\sigma^2 = 25\). Centering is applied before estimation.

    # Load packages
    library(savvySh)
    library(MASS)
    library(knitr)

    # Parameters
    set.seed(1)
    n_val <- 1000
    p_val <- 10
    rho_val <- 0.75
    sigma_val <- 5
    mu_val <- 0

    # Correlation matrix
    sigma.rho <- function(rho_val, p_val) {
      rho_val ^ abs(outer(1:p_val, 1:p_val, "-"))
    }

    # True beta
    theta_func <- function(p_val) {
      sgn <- rep(c(1, -1), length.out = p_val)
      mag <- ceiling(seq_len(p_val) / 2)
      sgn * mag
    }

    # Simulate data
    Sigma <- sigma.rho(rho_val, p_val)
    X <- mvrnorm(n_val, mu = rep(mu_val, p_val), Sigma = Sigma)
    X_centred <- scale(X, center = TRUE, scale = FALSE)
    beta_true <- theta_func(p_val)
    y <- rnorm(n_val, mean = X_centred %*% beta_true, sd = sigma_val)
    y_centred <- scale(y, center = TRUE, scale = FALSE)

    # Fit models
    ols_fit <- lm(y_centred ~ X_centred-1)
    beta_ols <- coef(ols_fit)

    linear_results <- savvySh(X_centred, y_centred, model_class = "Linear")
    beta_LSh <- coef(linear_results, "LSh")

The tables below report the results of each estimator: the first table shows the \(L_2\) distance between the estimated coefficient vector and the ground truth, while the second table displays the actual estimated coefficients (rounded) for each method alongside the true values.

    # L2 comparison
    l2_table <- data.frame(
      Method = c("OLS", "LSh"),
      L2_Distance = c(
        sqrt(sum((beta_ols - beta_true)^2)),
        sqrt(sum((beta_LSh  - beta_true)^2))
      )
    )

    kable(l2_table, digits = 4, caption = "L2 Distance Between Estimated and True Coefficients")

L2 Distance Between Estimated and True Coefficients
Method | L2_Distance
--- | ---
OLS | 0.7403
LSh | 0.7274

    # Coefficient comparison table
    coef_table <- data.frame(
      OLS = round(beta_ols, 3),
      LSh = round(beta_LSh, 3),
      True = round(beta_true, 3)
    )

    kable(coef_table, caption = "Estimated Coefficients by Method (rounded)")

Estimated Coefficients by Method (rounded)
| OLS | LSh | True
--- | --- | --- | ---
X_centred1 | 1.238 | 1.238 | 1
X_centred2 | -1.518 | -1.503 | -1
X_centred3 | 2.340 | 2.334 | 2
X_centred4 | -2.089 | -2.072 | -2
X_centred5 | 2.867 | 2.855 | 3
X_centred6 | -3.075 | -3.053 | -3
X_centred7 | 4.204 | 4.183 | 4
X_centred8 | -4.059 | -4.037 | -4
X_centred9 | 4.897 | 4.867 | 5
X_centred10 | -4.858 | -4.839 | -5

### Student’s t Distribution

This example corresponds to the Student’s \(t\) distributed Multivariate Gaussian distributed covariates with Toeplitz covariance matrix setup. We repeat the setup from above but replace Gaussian noise with \(t\)-distributed noise with degrees of freedom \(\nu = \frac{50}{24}\). Centering is applied before estimation.

    # Load packages
    library(savvySh)
    library(MASS)
    library(knitr)

    # Parameters
    set.seed(123)
    n_val <- 1000
    p_val <- 10
    df_val = 50/24
    sigma_val <- 5
    mu_val <- 0

    # Correlation matrix
    sigma.rho <- function(rho_val, p_val) {
      rho_val ^ abs(outer(1:p_val, 1:p_val, "-"))
    }

    # True beta
    theta_func <- function(p_val) {
      sgn <- rep(c(1, -1), length.out = p_val)
      mag <- ceiling(seq_len(p_val) / 2)
      sgn * mag
    }

    # Simulate data
    Sigma <- sigma.rho(rho_val, p_val)
    X <- mvrnorm(n_val, mu = rep(mu_val, p_val), Sigma = Sigma)
    X_centred <- scale(X, center = TRUE, scale = FALSE)
    beta_true <- theta_func(p_val)
    y <- as.vector(X_centred %*% beta_true) + rt(n = n_val, df = df_val)
    y_centred <- scale(y, center = TRUE, scale = FALSE)

    # Fit models
    ols_fit <- lm(y_centred ~ X_centred-1)
    beta_ols <- coef(ols_fit)

    linear_results <- savvySh(X_centred, y_centred, model_class = "Linear")
    beta_LSh <- coef(linear_results, "LSh")

The tables below report the results of each estimator: the first table shows the \(L_2\) distance between the estimated coefficient vector and the ground truth, while the second table displays the actual estimated coefficients (rounded) for each method alongside the true values.

    # L2 comparison
    l2_table <- data.frame(
      Method = c("OLS", "LSh"),
      L2_Distance = c(
        sqrt(sum((beta_ols - beta_true)^2)),
        sqrt(sum((beta_LSh  - beta_true)^2))
      )
    )

    kable(l2_table, digits = 4, caption = "L2 Distance Between Estimated and True Coefficients")

L2 Distance Between Estimated and True Coefficients
Method | L2_Distance
--- | ---
OLS | 5.6927
LSh | 4.8586

    # Coefficient comparison table
    coef_table <- data.frame(
      OLS = round(beta_ols, 3),
      LSh = round(beta_LSh, 3),
      True = round(beta_true, 3)
    )

    kable(coef_table, caption = "Estimated Coefficients by Method (rounded)")

Estimated Coefficients by Method (rounded)
| OLS | LSh | True
--- | --- | --- | ---
X_centred1 | 1.885 | 1.698 | 1
X_centred2 | -3.811 | -2.715 | -1
X_centred3 | 5.835 | 4.813 | 2
X_centred4 | -1.692 | -1.179 | -2
X_centred5 | 0.423 | 0.297 | 3
X_centred6 | -3.852 | -3.078 | -3
X_centred7 | 5.120 | 3.907 | 4
X_centred8 | -3.879 | -3.122 | -4
X_centred9 | 4.503 | 3.199 | 5
X_centred10 | -5.195 | -4.492 | -5

## Shrinkage Ridge Regression

The SRR estimator improves upon RR by replacing the \(\Sigma\) with a convex combination of \(\Sigma\) and a scaled identity matrix, chosen to minimize the MSE of the coefficients.

### Latent Space Features

This example corresponds to the Latent Space Features setup. Here, covariates are generated using a latent factor model with a small amount of additive Gaussian noise. This simulates a low-rank structure in the design matrix. We compare ridge regression estimates using `glmnet` against the SRR from `savvySh`.

    # Load packages
    library(savvySh)
    library(MASS)
    library(glmnet)
    #> Loading required package: Matrix
    #> Loaded glmnet 4.1-8
    library(knitr)

    # Parameters
    set.seed(123)
    n_val <- 1000
    p_val <- 10
    f_val <- 5
    sigma_val <- 5

    # True beta
    theta_func <- function(p_val) {
      sgn <- rep(c(1, -1), length.out = p_val)
      mag <- ceiling(seq_len(p_val) / 2)
      sgn * mag
    }

    A <- matrix(rnorm(n_val * f_val), nrow = n_val)
    Z <- matrix(rnorm(f_val * p_val), nrow = f_val)
    X <- A %*% Z  # n x p matrix
    noise <- matrix(rnorm(n_val * p_val, sd = sqrt(10^(-6))), nrow = n_val)
    X_noisy <- X + noise
    X_intercept <- cbind(rep(1, n_val), X_noisy)
    beta_true <- theta_func(p_val + 1)
    y <- rnorm(n_val,mean=as.vector(X_intercept%*%beta_true),sd=sigma_val)

    # Fit models
    OLS_results <- lm(y~X_noisy)
    beta_OLS <- coef(OLS_results)

    glmnet_fit <- cv.glmnet(X_noisy, y, alpha = 0)
    lambda_min_RR_glmnet <- glmnet_fit$lambda.min
    beta_RR <- as.vector(coef(glmnet_fit, s = "lambda.min"))

    SRR_results <- savvySh(X_noisy, y, model_class = "ShrinkageRR")
    beta_SRR <- coef(SRR_results, "SRR")

The tables below report the results of each estimator: the first table shows the \(L_2\) distance between the estimated coefficient vector and the ground truth, while the second table displays the actual estimated coefficients (rounded) for each method alongside the true values.

    # L2 comparison
    l2_table <- data.frame(
      Method = c("OLS", "RR", "SRR"),
      L2_Distance = c(
         sqrt(sum((beta_OLS - beta_true)^2)),
        sqrt(sum((beta_RR - beta_true)^2)),
        sqrt(sum((beta_SRR  - beta_true)^2))
      )
    )
    kable(l2_table, digits = 4, caption = "L2 Distance Between Estimated and True Coefficients")

L2 Distance Between Estimated and True Coefficients
Method | L2_Distance
--- | ---
OLS | 313.7002
RR | 13.8878
SRR | 9.0543

    # Coefficient comparison table
    coef_table <- data.frame(
      OLS = round(beta_OLS, 3),
      RR = round(beta_RR, 3),
      SRR = round(beta_SRR, 3),
      True = round(beta_true, 3)
    )
    kable(coef_table, caption = "Estimated Coefficients by Method (rounded)")

Estimated Coefficients by Method (rounded)
| OLS | RR | SRR | True
--- | --- | --- | --- | ---
(Intercept) | 1.010 | 1.011 | 1.007 | 1
X_noisy1 | 45.350 | 3.057 | 2.838 | -1
X_noisy2 | -4.960 | -8.059 | -2.278 | 2
X_noisy3 | 147.454 | -0.907 | -0.780 | -2
X_noisy4 | 42.069 | 2.850 | 4.477 | 3
X_noisy5 | -63.730 | 0.541 | 0.154 | -3
X_noisy6 | -186.510 | 1.760 | 1.627 | 4
X_noisy7 | 118.817 | 0.063 | -0.727 | -4
X_noisy8 | -17.079 | 2.482 | 3.598 | 5
X_noisy9 | -132.102 | -0.035 | -2.048 | -5
X_noisy10 | 31.292 | 3.009 | 3.117 | 6

# Real Data Analysis

This section provides example code and references for applying the shrinkage estimators implemented in `savvySh` to real-world datasets. These applications demonstrate how shrinkage methods can be used in areas such as generalized linear models, portfolio investment, and fine-mapping in genetics. We do not run the code or present specific results here; instead, we offer clean, reproducible examples that users can adapt. Full details and preprocessing steps can be found in the relevant repositories or the main paper.

- The cybersickness dataset is used for illustrating shrinkage GLMs using a Poisson model. The main Shrinkage GLMs function is part of the related package `savvyGLM`, you can find here.

- The returns_441 dataset contains portfolio returns and is used for demonstrating shrinkage estimation in financial asset allocation.

- The Statistical Fine-Mapping Application demonstrates the use of shrinkage-based estimators in a genetic context. We do not provide detailed descriptions here, as the full R code and analysis—including data preparation and model fitting—are available at:`flashfm-savvySh`.

## Cybersickness data

This example demonstrates how to apply Poisson GLMs and various shrinkage estimators to a dataset related to cybersickness severity scores. The response variable is ordinal and grouped into four categories. The goal is to predict this ordinal outcome using lagged predictors. Here we show how to preprocess, fit models, and evaluate prediction performance using metrics such as MSE, RMSE, and MAE.

    remotes::install_github("Ziwei-ChenChen/savvyGLM")
    library(savvyGLM)
    library(savvySh)
    library(savvyGLM)
    library(MASS)

    standardize_features<-function(dataset){
      dataset[2:(ncol(dataset)-1)] <- as.data.frame(scale(dataset[2:(ncol(dataset)-1)]))
      return(dataset)
    }

    set_classes<-function(data){
      data[,ncol(data)]<-replace(data[,ncol(data)], data[,ncol(data)]<1, 0)
      data[,ncol(data)]<-replace(data[,ncol(data)], data[,ncol(data)] %in% c(1,2,2.5,3,3.5), 1)
      data[,ncol(data)]<-replace(data[,ncol(data)], data[,ncol(data)] %in% c(4,5,6), 2)
      data[,ncol(data)]<-replace(data[,ncol(data)], data[,ncol(data)]>=7, 3)
      return(data)
    }

    fit_and_return_coefficients <- function(x, y) {

      control_list <- list(maxit = 200, epsilon = 1e-6, trace = TRUE)
      family_type <- poisson(link = "log")

      # Fitting models
      opt_glm2_OLS <- glm.fit2(x, y, family = family_type, control = control_list)
      opt_glm2_SR <- savvy_glm.fit2(x, y, model_class = "SR", family = family_type, control = control_list)
      opt_glm2_GSR <- savvy_glm.fit2(x, y, model_class = "GSR", family = family_type, control = control_list)
      opt_glm2_St <- savvy_glm.fit2(x, y, model_class = "St", family = family_type, control = control_list)
      opt_glm2_DSh <- savvy_glm.fit2(x, y, model_class = "DSh", family = family_type, control = control_list)
      opt_glm2_Sh <- savvy_glm.fit2(x, y, model_class = "Sh", family = family_type, control = control_list)

      return(list(
        glm2_OLS_result = opt_glm2_OLS$coefficients,
        glm2_SR_result = opt_glm2_SR$coefficients,
        glm2_GSR_result = opt_glm2_GSR$coefficients,
        glm2_St_result = opt_glm2_St$coefficients,
        glm2_DSh_result = opt_glm2_DSh$coefficients,
        glm2_Sh_result = opt_glm2_Sh$coefficients
      ))
    }

    test_model <- function(glm_coefficients, data_X, data_Y) {
      upper_limit <- 3  # =3 for 4 classes; =9 for 10 classes

      ### Model 1 ---> OLS ###
      predicted_glm2_OLS <- floor(exp(data_X %*% as.matrix(glm_coefficients$glm2_OLS_result)))
      predicted_glm2_OLS <- ifelse(predicted_glm2_OLS <= upper_limit, predicted_glm2_OLS, upper_limit)

      ### Model 2 ---> SR ###
      predicted_glm2_SR <- floor(exp(data_X %*% as.matrix(glm_coefficients$glm2_SR_result)))
      predicted_glm2_SR <- ifelse(predicted_glm2_SR <= upper_limit, predicted_glm2_SR, upper_limit)

      ### Model 3 ---> GSR ###
      predicted_glm2_GSR <- floor(exp(data_X %*% as.matrix(glm_coefficients$glm2_GSR_result)))
      predicted_glm2_GSR <- ifelse(predicted_glm2_GSR <= upper_limit, predicted_glm2_GSR, upper_limit)

      ### Model 4 ---> Stein ###
      predicted_glm2_St <- floor(exp(data_X %*% as.matrix(glm_coefficients$glm2_St_result)))
      predicted_glm2_St <- ifelse(predicted_glm2_St <= upper_limit, predicted_glm2_St, upper_limit)

      ### Model 5 ---> Diagonal Shrinkage ###
      predicted_glm2_DSh <- floor(exp(data_X %*% as.matrix(glm_coefficients$glm2_DSh_result)))
      predicted_glm2_DSh <- ifelse(predicted_glm2_DSh <= upper_limit, predicted_glm2_DSh, upper_limit)

      ### Model 6 ---> Sh ###
      predicted_glm2_Sh <- floor(exp(data_X %*% as.matrix(glm_coefficients$glm2_Sh_result)))
      predicted_glm2_Sh <- ifelse(predicted_glm2_Sh <= upper_limit, predicted_glm2_Sh, upper_limit)

      print(max(predicted_glm2_OLS))
      print(max(predicted_glm2_SR))

      r_OLS <- c(mse(data_Y, predicted_glm2_OLS), rmse(data_Y, predicted_glm2_OLS), mae(data_Y, predicted_glm2_OLS))
      r_SR <- c(mse(data_Y, predicted_glm2_SR), rmse(data_Y, predicted_glm2_SR), mae(data_Y, predicted_glm2_SR))
      r_GSR <- c(mse(data_Y, predicted_glm2_GSR), rmse(data_Y, predicted_glm2_GSR), mae(data_Y, predicted_glm2_GSR))
      r_St <- c(mse(data_Y, predicted_glm2_St), rmse(data_Y, predicted_glm2_St), mae(data_Y, predicted_glm2_St))
      r_DSh <- c(mse(data_Y, predicted_glm2_DSh), rmse(data_Y, predicted_glm2_DSh), mae(data_Y, predicted_glm2_DSh))
      r_Sh <- c(mse(data_Y, predicted_glm2_Sh), rmse(data_Y, predicted_glm2_Sh), mae(data_Y, predicted_glm2_Sh))

      return(list(
        results_OLS = r_OLS,
        results_SR = r_SR,
        results_GSR = r_GSR,
        results_St = r_St,
        results_DSh = r_DSh,
        results_Sh = r_Sh
      ))
    }

    out_of_sample_performance <- function(percentage = 0.3, no_trials = 50, filein = "data_for_regression10.csv", fileout = "results10.csv") {

      data <- read.csv(filein)
      agregated_results<-rep(0,4*3)

      data<-set_classes(data)   # for 4 classes
      #data[,ncol(data)]<-floor(data[,ncol(data)])  # for 10 classes -- the scores 2.5 and 3.5 are floored

      data<-standardize_features(data)

      for (r in 1:no_trials){
        #for train-test split with percentage e.g. 70-30
        bound <- floor(nrow(data)*(1-percentage)) #define % of training
        data <- data[sample(nrow(data)), ]           #sample rows
        train <- data[1:bound, ]
        test <- data[(bound+1):nrow(data), ]

        #training
        X.tilde <- train[,-ncol(train)]
        X <-  X.tilde[,-1]
        train_X <- as.matrix(train[,-ncol(train)])
        train_Y <-  train[,ncol(train)]
        glm_coefficients<-fit_and_return_coefficients(train_X, train_Y)

        #test
        test_X <- as.matrix(test[,-ncol(test)])
        test_Y <-  as.matrix(test[,ncol(test)])
        results<-test_model(glm_coefficients, test_X, test_Y)
        agregated_results<-agregated_results+unlist(results)
      }

      # Average results over trials
      aggregated_results <- aggregated_results / no_trials
      df <- data.frame(matrix(unlist(agregated_results), nrow=length(results), byrow=TRUE))
      colnames(df) <- c("MSE", "RMSE", "MAE")
      rownames(df) <- c("GLM2", "SR", "GSR", "St", "DSh", "Sh")
      write.csv(df, fileout)
    }

    input_file_path <- "data_for_regression10.csv"
    output_file_path <- "results10.csv"
    run_performance_test <- out_of_sample_performance(
      percentage = 0.3,
      no_trials = 50,
      filein = input_file_path,
      fileout = output_file_path
    )

## Portfolio Investment

This second example applies shrinkage methods to asset return data for constructing optimal portfolios. We use the `returns_441` dataset. The dataset consists of daily returns for 441 stocks including the index, with `Date` formatted as `YYYYMMDD`. For each rolling window, we:

- Fit multiple regression-based models (OLS, RR, POET_99%, St, DSh, Sh, SR, GSR, SRR).

- Extract the estimated coefficients and compute portfolio weights.

- Simulate out-of-sample portfolio performance.

- Compute rolling statistics: expected annual returns, volatility, and Sharpe ratios.

    library(savvySh)
    library(MASS)
    library(glmnet)
    library(PerformanceAnalytics)
    library(lubridate)
    library(quadprog)
    library(xts)
    library(POET)

    data <- returns_441
    data$Date <- as.Date(as.character(data$Date), format = "%Y%m%d")
    colnames(data)[2:442] <- paste0("Company", 1:441)

    training_size <- 5 * 252
    testing_size  <- 3 * 21
    step_size <- 3 * 21
    n_total <- nrow(data)
    max_windows <- floor((n_total - training_size - testing_size) / step_size) + 1
    cat("Total rows:", n_total, "\n")
    cat("Max windows:", max_windows, "\n")

    get_full_weights <- function(est_vector) {
      w <- est_vector[-1]
      w_last <- 1 - sum(w)
      return(c(w, w_last))
    }

    poet_est_99 <- function(x, y) {
      x <- as.matrix(x)
      y <- as.numeric(y)
      n <- nrow(x)
      p <- ncol(x)

      x_mean <- colMeans(x)
      y_mean <- mean(y)
      x_c <- x - matrix(rep(x_mean, each = n), n, p)
      y_c <- y - y_mean
      Y=t(x_c)

      # Choose K to explain 99% variance
      eigvals <- eigen(cov(x_c), symmetric = TRUE, only.values = TRUE)$values
      eigvals_sorted <- sort(eigvals, decreasing = TRUE)
      cumsum_vals <- cumsum(eigvals_sorted) / sum(eigvals_sorted)
      K <- which(cumsum_vals >= 0.99)[1]
      poet_result <- POET::POET(Y, K = K)
      Sigma_hat <- poet_result$SigmaY

      xcyc <- crossprod(x_c, y_c) / n
      beta_1p <- as.numeric(solve(Sigma_hat, xcyc))
      beta_0 <- y_mean - sum(x_mean * beta_1p)
      beta_full <- c(beta_0, beta_1p)

      return(as.vector(beta_full))
    }

    rolling_annual_expected_returns <- data.frame()
    rolling_annual_sharpe_ratios <- data.frame()
    rolling_annual_volatilities <- data.frame()

    for (window_index in seq_len(max_windows)) {
      start_index <- 1 + (window_index - 1) * step_size
      train_start <- start_index
      train_end <- start_index + training_size - 1
      test_start <- train_end + 1
      test_end <- train_end + testing_size

      train_data <- data[train_start:train_end, ]
      test_data <- data[test_start:test_end, ]
      train_returns <- as.matrix(train_data[, -1])
      test_returns <- as.matrix(test_data[, -1])

      # Create X_train and Y_train
      # Y_train is last column (Company441)
      # X_train is (Y_train - first 440 columns)
      Y_train <- train_returns[, 441]
      X_train <- matrix(Y_train, nrow = nrow(train_returns), ncol = 440) - train_returns[, 1:440]

      # Fit all estimators
      est_results <- list(
        OLS = OLS_est(X_train, Y_train)$est,
        RR = RR_est(X_train, Y_train)$est,
        POET_99 = poet_est_99(X_train, Y_train),
        St = St_ost(X_train, Y_train),
        DSh = DSh_ost(X_train, Y_train),
        Sh = Sh_ost(X_train, Y_train),
        SR = SR_ost(X_train, Y_train),
        GSR = GSR_ost(X_train, Y_train),
        SRR = SRR_shrinkage_ost(X_train, Y_train)
      )
      weights_list <- lapply(est_results, get_full_weights)
      names(weights_list) <- names(est_results)

      test_dates <- as.Date(test_data$Date)
      test_returns_xts <- xts(test_returns, order.by = test_dates)
      daily_returns_list <- lapply(weights_list, function(w) {
        rp <- Return.portfolio(R = test_returns_xts, weights = w)
        return(as.numeric(rp))
      })
      daily_values_list <- lapply(daily_returns_list, function(r) {
        cum_val <- cumprod(1 + r)
        return(cum_val)
      })

      model_names <- names(daily_returns_list)
      n_test <- length(test_start:test_end)
      daily_values_mat <- matrix(0, nrow = length(model_names), ncol = n_test)
      daily_returns_mat <- matrix(0, nrow = length(model_names), ncol = n_test)
      rownames(daily_values_mat) <- model_names
      rownames(daily_returns_mat) <- model_names
      for (i in seq_along(model_names)) {
        daily_values_mat[i, ]  <- daily_values_list[[i]]
        daily_returns_mat[i, ] <- daily_returns_list[[i]]
      }

      returns_xts_mat <- xts(t(daily_returns_mat), order.by = test_dates)
      annual_returns <- as.numeric(Return.annualized(R = returns_xts_mat, scale = 252))
      names(annual_returns) <- colnames(returns_xts_mat)
      annual_vols <- as.numeric(StdDev.annualized(x = returns_xts_mat, scale = 252))
      names(annual_vols) <- colnames(returns_xts_mat)
      annual_sharp <- as.numeric(SharpeRatio.annualized(R = returns_xts_mat, scale = 252))
      names(annual_sharp) <- colnames(returns_xts_mat)

      window_result_returns <- as.data.frame(t(annual_returns))
      window_result_returns$Window <- window_index
      rolling_annual_expected_returns <- rbind(rolling_annual_expected_returns, window_result_returns)

      window_result_sharpe <- as.data.frame(t(annual_sharp))
      window_result_sharpe$Window <- window_index
      rolling_annual_sharpe_ratios <- rbind(rolling_annual_sharpe_ratios, window_result_sharpe)

      window_result_vols <- as.data.frame(t(annual_vols))
      window_result_vols$Window <- window_index
      rolling_annual_volatilities <- rbind(rolling_annual_volatilities, window_result_vols)

      cat("Completed window", window_index,
          ": Training rows [", train_start, "to", train_end,
          "] (Dates:", format(train_data$Date[1], "%Y-%m-%d"),
          "to", format(train_data$Date[nrow(train_data)], "%Y-%m-%d"),
          "), Testing rows [", test_start, "to", test_end,
          "] (Dates:", format(test_data$Date[1], "%Y-%m-%d"),
          "to", format(test_data$Date[nrow(test_data)], "%Y-%m-%d"), ")\n")
    }