youyifong.r-universe.dev

[youyifong] kyotil 2025.12-12

youyifong@gmail.com (Youyi Fong) — Tue, 24 Mar 2026 20:39:47 GMT

Helper functions for creating formatted summary of regression models, writing publication-ready tables to latex files, and running Monte Carlo experiments.

[youyifong] marginalizedRisk 2026.2-4

youyifong@gmail.com (Youyi Fong) — Wed, 04 Feb 2026 20:17:23 GMT

Estimates risk as a function of a marker by integrating over other covariates in a conditional risk model.

[youyifong] mdw 2024.8-1

youyifong@gmail.com (Youyi Fong) — Sun, 27 Jul 2025 18:28:32 GMT

Dimension-reduction methods aim at defining a score that maximizes signal diversity. Three approaches, tree weight, maximum entropy weights, and maximum variance weights are provided. These methods are described in He and Fong (2019) .

[youyifong] FSDAM 2024.7-30

youyifong@gmail.com (Youyi Fong) — Wed, 23 Jul 2025 19:40:17 GMT

FS-DAM performs feature extraction through latent variables identification. Implementation is based on autoencoders with monotonicity and orthogonality constraints.

[youyifong] chngpt 2024.11-15

youyifong@gmail.com (Youyi Fong) — Wed, 15 Jan 2025 17:45:43 GMT

Threshold regression models are also called two-phase regression, broken-stick regression, split-point regression, structural change models, and regression kink models, with and without interaction terms. Methods for both continuous and discontinuous threshold models are included, but the support for the former is much greater. This package is described in Fong, Huang, Gilbert and Permar (2017) and the package vignette.

[youyifong] copcor 2024.7-31

youyifong@gmail.com (Youyi Fong) — Thu, 01 Aug 2024 02:49:50 GMT

Correlates of protection (CoP) and correlates of risk (CoR) study the immune biomarkers associated with an infectious disease outcome, e.g. COVID or HIV-1 infection. This package contains shared functions for analyzing CoP and CoR, including bootstrapping procedures, competing risk estimation, and bootstrapping marginalized risks.

[youyifong] robustrank 2024.1-28

youyifong@gmail.com (Youyi Fong) — Mon, 29 Jan 2024 02:30:12 GMT

Implements two-sample tests for paired data with missing values (Fong, Huang, Lemos and McElrath 2018, Biostatics, ) and modified Wilcoxon-Mann-Whitney two sample location test, also known as the Fligner-Policello test.

[youyifong] krm 2022.10-17

youyifong@gmail.com (Youyi Fong) — Tue, 18 Oct 2022 06:40:11 GMT

Implements several methods for testing the variance component parameter in regression models that contain kernel-based random effects, including a maximum of adjusted scores test. Several kernels are supported, including a profile hidden Markov model mutual information kernel for protein sequence. This package is described in Fong et al. (2015) .