Package: iPEB
Type: Package
Title: Improved Parametric Empirical Bayes for Longitudinal Biomarker
        Analysis
Version: 0.1.1
Authors@R: c(
    person("Bitan", "Sarkar", email = "bitansarkar010899@gmail.com",
           role = c("aut", "cre", "cph"), comment = c(ORCID = "0009-0000-5178-5934")),
    person(c("Ana", "Maria"), "Kenney", role = "aut"),
    person(c("James", "P."), "Long", role = "aut"),
    person(c("Johannes", "F."), "Fahrmann", role = "aut"),
    person("Samir", "Hanash", role = "aut"),
    person("Kim-Anh", "Do", role = "aut"),
    person("Ehsan", "Irajizad", role = "aut"))
Description: Extends parametric empirical Bayes (PEB) for longitudinal
        biomarker screening with a time-gap-aware standardization
        layer, covariate adjustment, and objective-driven multi-marker
        weighting. The layer models each subject's biomarker history
        with a random intercept (and an optional random slope) and
        autocorrelated, gap-scaled residuals, so that prediction
        uncertainty grows with the time between visits and per-visit
        specificity is preserved under irregular sampling. Marker
        weights are learned to optimize a user-selected clinical
        objective -- maximizing sensitivity at a fixed specificity,
        extending detection lead time, or a combined objective -- with
        optional feature selection and a choice of scalar or
        multivariate combiner. Functions for fitting, prediction, and
        evaluation (sensitivity, lead time, and specificity at chosen
        operating points) are provided. A manuscript describing the
        method is in preparation.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0.0)
Imports: nlme, stats, graphics, utils
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, shiny
VignetteBuilder: knitr
URL: https://github.com/bitansa/iPEB
BugReports: https://github.com/bitansa/iPEB/issues
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Repository: https://bitansa.r-universe.dev
Date/Publication: 2026-09-24 01:59:32 UTC
RemoteUrl: https://github.com/bitansa/ipeb
RemoteRef: HEAD
RemoteSha: e5364ec3418582e0c103f546b7b77eb6b7c7a2b0
NeedsCompilation: no
Packaged: 2026-09-24 05:25:33 UTC; root
Author: Bitan Sarkar [aut, cre, cph] (ORCID:
    <https://orcid.org/0009-0000-5178-5934>),
  Ana Maria Kenney [aut],
  James P. Long [aut],
  Johannes F. Fahrmann [aut],
  Samir Hanash [aut],
  Kim-Anh Do [aut],
  Ehsan Irajizad [aut]
Maintainer: Bitan Sarkar <bitansarkar010899@gmail.com>