Package {MTLRF}

Type:	Package
Title:	Random Forest Regression with Modified Topp-Leone Error Model
Version:	1.0.0
Date:	2026-08-18
Description:	Implements Random Forest regression under the Modified Topp-Leone (MTL) distribution error model. Provides core distribution functions (density, cumulative distribution, exact closed-form quantile, random generation, hazard, and survival), parameter estimation via closed-form Expectation-Maximization/Maximum Likelihood (EM/MLE) and Bayesian Markov Chain Monte Carlo (MCMC), non-parametric bootstrap confidence intervals (at 90%, 95%, and 99% levels), Highest Posterior Density (HPD) intervals, Heidelberger and Welch MCMC convergence diagnostics, model evaluation metrics (estimated values, bias, mean squared error, risk value), homoscedastic prediction intervals, and goodness-of-fit diagnostic tests (Kolmogorov-Smirnov and Anderson-Darling tests, Akaike Information Criterion, and Bayesian Information Criterion). References: Breiman (2001) <doi:10.1023/A:1010933404324>; Singh, Tyagi, Singh, and Tyagi (2025) https://statassoc.or.th; Topp and Leone (1955) <doi:10.1080/01621459.1955.10501259>; Wright and Ziegler (2017) <doi:10.18637/jss.v077.i01>; Plummer, Best, Cowles, and Vines (2006) https://CRAN.R-project.org/package=coda; Heidelberger and Welch (1983) <doi:10.1287/opre.31.6.1109>.
License:	GPL (≥ 3)
Encoding:	UTF-8
RoxygenNote:	7.3.3
Depends:	R (≥ 4.0.0)
Imports:	ranger, coda, goftest, stats, graphics
Suggests:	testthat (≥ 3.0.0)
Config/testthat/edition:	3
Language:	en-US
NeedsCompilation:	no
Packaged:	2026-08-17 23:01:40 UTC; shikhar tyagi
Author:	Shikhar Tyagi [aut, cre], Aruna Rajballie [aut], Vrijesh Tripathi [aut]
Maintainer:	Shikhar Tyagi <shikhar1093tyagi@gmail.com>
Repository:	CRAN
Date/Publication:	2026-08-21 13:10:42 UTC

Bayesian MCMC Estimation, HPD Intervals, and Heidelberger-Welch Convergence Diagnostics

Description

Estimates the Modified Topp-Leone (MTL) parameter alpha using Markov Chain Monte Carlo (MCMC) sampling, evaluates Highest Posterior Density (HPD) intervals at 90

Usage

mcmc_mtl(
  r,
  n_iter = 5000,
  burn_in = 1000,
  thin = 2,
  init_alpha = NULL,
  seed = NULL
)

Arguments

Details

MCMC sampling is performed using an adaptive Metropolis-Hastings algorithm on the log-scale of \alpha (\phi = \log\alpha) to ensure positivity and numerical stability. A weakly informative Gamma(0.001, 0.001) prior is placed on \alpha. The posterior chain is analyzed using HPDinterval to extract HPD intervals at 90 Convergence is assessed via the Heidelberger and Welch diagnostic (heidel.diag), evaluating stationarity and halfwidth adequacy.

Value

A list containing:

posterior_mean

Posterior mean estimate of \alpha.

posterior_median

Posterior median estimate of \alpha.

posterior_sd

Posterior standard deviation of \alpha.

hpd_90

Highest Posterior Density interval at 90% level.

hpd_95

Highest Posterior Density interval at 95% level.

hpd_99

Highest Posterior Density interval at 99% level.

acceptance_rate

MCMC acceptance rate (convergence probability).

heidel_diag

Heidelberger and Welch's convergence diagnostic summary.

convergence_prob

Estimated convergence probability.

mcmc_chain

mcmc object of posterior samples.

Examples

set.seed(123)
r_sample <- rmtl(50, alpha = 2.0)
mcmc_fit <- mcmc_mtl(r_sample, n_iter = 2000, burn_in = 500)
print(mcmc_fit$posterior_mean)
print(mcmc_fit$hpd_95)

Maximum Likelihood Estimation and Bootstrap Confidence Intervals for MTL Model

Description

Computes the exact closed-form Maximum Likelihood Estimator (MLE) for the Modified Topp-Leone (MTL) parameter alpha, and evaluates non-parametric bootstrap confidence intervals at 90

Usage

mtl_mle(r)

mtl_loglik(alpha, r)

mtl_fisher(alpha, n)

bootstrap_ci(
  y,
  X,
  n_boot = 100,
  conf_levels = c(0.9, 0.95, 0.99),
  num.trees = 100,
  seed = NULL
)

Arguments

Details

For independent absolute residuals r_1, \ldots, r_n > 0, the log-likelihood function of the MTL distribution is:

\ell(\alpha) = n\log 2 + n\log\alpha + (\alpha - 1)\sum_{i=1}^n \log(2r_i + r_i^2) - (2\alpha + 1)\sum_{i=1}^n \log(1 + r_i)

Setting the score function \partial\ell / \partial\alpha = 0 yields the exact closed-form MLE:

\hat{\alpha} = \frac{n}{-\sum_{i=1}^n \log\left( 1 - \frac{1}{(1 + r_i)^2} \right)}

Under the EM/MLE estimation method, because asymptotic distribution may be impacted by Stage 1 non-parametric Random Forest estimation, non-parametric bootstrap resampling is utilized to compute empirical confidence intervals at 90

Value

mtl_mle returns the scalar MLE \hat{\alpha}. mtl_loglik returns the log-likelihood value. mtl_fisher returns the expected Fisher information. bootstrap_ci returns a list containing bootstrap distributions and confidence intervals at 90%, 95%, and 99% levels for alpha, bias, mse, and risk.

Examples

set.seed(123)
r <- rmtl(50, alpha = 2.5)
hat_alpha <- mtl_mle(r)
print(hat_alpha)

The Modified Topp-Leone (MTL) Distribution

Description

Density, distribution function, quantile function, random generation, hazard function, and survival function for the Modified Topp-Leone (MTL) distribution with shape parameter alpha.

Usage

dmtl(x, alpha, log = FALSE)

pmtl(q, alpha, lower.tail = TRUE, log.p = FALSE)

qmtl(p, alpha, lower.tail = TRUE, log.p = FALSE)

rmtl(n, alpha)

smtl(x, alpha, log = FALSE)

hmtl(x, alpha, log = FALSE)

Arguments

Details

The Modified Topp-Leone (MTL) distribution is a continuous probability distribution defined on (0, \infty) with shape parameter \alpha > 0. Its probability density function (PDF) is given by:

f(x; \alpha) = \frac{2\alpha (2x + x^2)^{\alpha - 1}}{(1 + x)^{2\alpha + 1}} = 2\alpha (1 + x)^{-2\alpha - 1} (2x + x^2)^{\alpha - 1}, \quad x > 0, \alpha > 0

Its cumulative distribution function (CDF) is given by:

F(x; \alpha) = \left( 1 - \frac{1}{(1 + x)^2} \right)^\alpha = \left( \frac{2x + x^2}{(1 + x)^2} \right)^\alpha, \quad x > 0

Its survival function (SF) is:

S(x; \alpha) = 1 - F(x; \alpha) = 1 - \left( 1 - \frac{1}{(1 + x)^2} \right)^\alpha, \quad x > 0

Its hazard rate function (HRF) is:

h(x; \alpha) = \frac{f(x; \alpha)}{S(x; \alpha)} = \frac{2\alpha (2x + x^2)^{\alpha - 1}}{(1 + x)^{2\alpha + 1} \left[ 1 - \left( 1 - \frac{1}{(1 + x)^2} \right)^\alpha \right]}, \quad x > 0

Its exact closed-form quantile function (QF) for probability p \in (0, 1) is:

Q(p; \alpha) = \left( 1 - p^{1/\alpha} \right)^{-1/2} - 1

In log-stable computation, Q(p; \alpha) = \left( -\mathrm{expm1}\left( \frac{\log p}{\alpha} \right) \right)^{-1/2} - 1. Random generation is performed by direct inversion sampling using runif.

Value

dmtl gives the density, pmtl gives the distribution function, qmtl gives the exact quantile function, rmtl generates random deviates, hmtl gives the hazard function, and smtl gives the survival function.

Examples

# Evaluate PDF and CDF at x = 1, alpha = 2
dmtl(1, alpha = 2)
pmtl(1, alpha = 2)

# Quantile function
qmtl(0.95, alpha = 2)

# Survival and hazard functions
smtl(1, alpha = 2)
hmtl(1, alpha = 2)

# Generate random samples
set.seed(123)
r_samples <- rmtl(10, alpha = 2)
print(r_samples)

Goodness-of-Fit and Model Selection Diagnostics for MTL Error Model

Description

Performs goodness-of-fit hypothesis testing (Kolmogorov-Smirnov and Anderson-Darling tests) and evaluates information-theoretic criteria (AIC and BIC) for a fitted RF-MTL model.

Usage

mtl_diagnostics(object, ...)

Arguments

Details

Goodness-of-fit evaluates whether absolute residuals r_i = |y_i - \hat{y}_i| follow the Modified Topp-Leone distribution with estimated parameter \hat{\alpha}.

Information criteria are defined as:

\mathrm{AIC} = 2k - 2\ell(\hat{\alpha}), \quad \mathrm{BIC} = k\log n - 2\ell(\hat{\alpha})

where k = 1 (single shape parameter) and \ell(\hat{\alpha}) is the maximized MTL log-likelihood.

Value

An S3 object of class "mtl_diagnostics", containing:

ks_stat

Kolmogorov-Smirnov test statistic D_n.

ks_pvalue

Asymptotic p-value for the KS test.

ad_stat

Anderson-Darling test statistic A_n^2.

ad_pvalue

p-value for the AD test via ad.test.

loglik

Maximized log-likelihood value.

aic

Akaike Information Criterion.

bic

Bayesian Information Criterion.

alpha

Estimated shape parameter \hat{\alpha}.

n

Number of training observations.

Examples

set.seed(123)
df <- data.frame(y = 5 + 2 * rnorm(50), x1 = rnorm(50), x2 = runif(50))
fit <- rf_mtl(y ~ x1 + x2, data = df, method = "em", num.trees = 50, n_boot = 20)
diag_res <- mtl_diagnostics(fit)
print(diag_res)

Predict Method for RF-MTL Model Fits

Description

Generates point predictions and exact closed-form prediction intervals for new observations using a fitted "rf_mtl" object.

Usage

## S3 method for class 'rf_mtl'
predict(
  object,
  newdata = NULL,
  level = 0.95,
  interval = c("none", "prediction"),
  ...
)

Arguments

Details

Point predictions are generated by ensembled Random Forest regression trees. Prediction intervals at confidence level level (e.g. 0.95) are calculated via the exact closed-form Modified Topp-Leone quantile function:

\mathrm{PI}_{1-\gamma}(\mathbf{x}^*) = \left[ \hat{f}(\mathbf{x}^*) - Q_{1-\gamma}(\hat{\alpha}), \quad \hat{f}(\mathbf{x}^*) + Q_{1-\gamma}(\hat{\alpha}) \right]

where \gamma = 1 - \mathrm{level} and Q_{1-\gamma}(\hat{\alpha}) = \left( 1 - (1-\gamma)^{1/\hat{\alpha}} \right)^{-1/2} - 1.

Value

If interval = "none", a numeric vector of point predictions is returned. If interval = "prediction", a data frame containing columns fit (point prediction), lwr (lower prediction bound), and upr (upper prediction bound) is returned.

Examples

set.seed(123)
df <- data.frame(y = 5 + 2 * rnorm(50), x1 = rnorm(50), x2 = runif(50))
fit <- rf_mtl(y ~ x1 + x2, data = df, method = "em", num.trees = 50, n_boot = 20)
preds <- predict(fit, newdata = df[1:5, ], interval = "prediction", level = 0.95)
print(preds)

Random Forest Regression with Modified Topp-Leone (MTL) Error Model

Description

Fits a Random Forest regression model combined with a Modified Topp-Leone (MTL) distribution error model. Supports parameter estimation via closed-form EM/MLE algorithm (with non-parametric bootstrap confidence intervals at 90

Usage

rf_mtl(
  formula,
  data,
  method = c("em", "mcmc"),
  num.trees = 500,
  n_boot = 100,
  n_iter = 5000,
  burn_in = 1000,
  conf_levels = c(0.9, 0.95, 0.99),
  na.action = stats::na.omit,
  seed = NULL,
  ...
)

Arguments

Details

The RF-MTL regression model assumes:

y_i = f(\mathbf{x}_i) + \varepsilon_i, \quad i = 1, \ldots, n

where f(\mathbf{x}) is non-parametrically estimated by a Random Forest predictor, and absolute errors |\varepsilon_i| follow the Modified Topp-Leone distribution with shape parameter \alpha > 0.

In Stage 1, Random Forest regression is fitted using ranger under the mean squared error criterion to predict point estimates \hat{y}_i = \hat{f}(\mathbf{x}_i). In Stage 2, absolute residuals r_i = |y_i - \hat{y}_i| are modeled using the MTL error distribution.

Parameter estimation can be performed via:

• EM / MLE Algorithm (method = "em"): Computes exact analytical closed-form MLE \hat{\alpha} and uses non-parametric bootstrap resampling to evaluate confidence intervals at 90

• Bayesian MCMC (method = "mcmc"): Draws MCMC posterior samples for \alpha via adaptive Metropolis-Hastings, computes Highest Posterior Density (HPD) intervals at 90

Missing values are processed according to the specified na.action. Logical parameters accept both standard R boolean flags (TRUE/FALSE) and character representations ("TRUE"/"FALSE").

Value

An S3 object of class "rf_mtl", containing:

rf_model

The fitted ranger Random Forest object.

alpha

Estimated Modified Topp-Leone shape parameter \alpha.

method

Estimation method used ("em" or "mcmc").

fitted_values

Fitted point predictions \hat{y}.

residuals

Raw residuals y - \hat{y}.

abs_residuals

Absolute residuals |y - \hat{y}|.

bias

Estimated model bias.

mse

Mean squared error.

rmse

Root mean squared error.

mae

Mean absolute error.

risk

Model risk value (empirical squared loss).

intervals

Bootstrap confidence intervals (for EM) or HPD intervals (for MCMC) at 90%, 95%, and 99% levels.

heidel_diag

Heidelberger and Welch convergence diagnostic summary (if method = "mcmc").

convergence_prob

MCMC convergence probability / acceptance rate (if method = "mcmc").

bootstrap_results

Detailed bootstrap outputs if method = "em".

mcmc_results

Detailed MCMC sampler outputs if method = "mcmc".

formula

Model formula.

data

Processed training data frame.

response_name

Name of response variable.

predictor_names

Vector of predictor variable names.

Examples

# Fit RF-MTL model on synthetic regression data
set.seed(123)
df <- data.frame(
  y = 5 + 2 * rnorm(50),
  x1 = rnorm(50),
  x2 = runif(50)
)
fit_em <- rf_mtl(y ~ x1 + x2, data = df, method = "em", num.trees = 50, n_boot = 30, seed = 123)
print(fit_em)

S3 Methods for RF-MTL Model Objects

Description

Print, summary, and plot methods for fitted "rf_mtl" objects.

Usage

## S3 method for class 'rf_mtl'
print(x, ...)

## S3 method for class 'rf_mtl'
summary(object, ...)

## S3 method for class 'summary_rf_mtl'
print(x, ...)

## S3 method for class 'rf_mtl'
plot(x, which = 1:3, ...)

Arguments

Value

print.rf_mtl and print.summary_rf_mtl return the input object invisibly. summary.rf_mtl returns a list of summary statistics. plot.rf_mtl returns NULL invisibly and displays diagnostic graphics.

Examples

set.seed(123)
df <- data.frame(y = 5 + 2 * rnorm(50), x1 = rnorm(50), x2 = runif(50))
fit <- rf_mtl(y ~ x1 + x2, data = df, method = "em", num.trees = 50, n_boot = 20)
print(fit)
summary(fit)