Package: serodynamics
Title: Modeling Longitudinal Antibody Responses to Infection
Version: 0.1.0.9024
Authors@R: c(
    person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"),
           comment = c("Author of the method and original code.",
           ORCID = "0000-0003-1904-6044")),
    person("Samuel", "Schildhauer", , "sschildhauer@ucdavis.edu", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-7139-1086")),
    person("Kwan Ho", "Lee", , "ksjlee@ucdavis.edu", role = "aut",
           comment = c(ORCID = "0009-0004-9723-2007")),
    person("Yuxuan", "Wang", , "yxewang@ucdavis.edu", role = "aut",
           comment = c(ORCID = "0009-0004-2041-8831")),
    person("Kristen", "Aiemjoy", , "kaiemjoy@ucdavis.edu", role = "aut",
           comment = c(ORCID = "0000-0003-1886-2699")),
    person("Douglas Ezra", "Morrison", , "demorrison@ucdavis.edu", role = "aut",
           comment = c(ORCID = "0000-0002-7195-830X"))
  )
Description: Implements Bayesian hierarchical models for estimating
        antibody kinetic parameters from longitudinal serological data.
        Fits two-phase within-host models capturing antibody rise,
        peak, and decay following pathogen infection, using 'JAGS' for
        posterior inference. Designed as the upstream companion to the
        'serocalculator' package for end-to-end seroepidemiological
        analysis. Methods are described in Teunis and colleagues (2016)
        <doi:10.1016/j.epidem.2016.04.001> and Teunis and van Eijkeren
        (2020) <doi:10.1002/sim.8578>.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
URL: https://github.com/UCD-SERG/serodynamics,
        https://ucd-serg.github.io/serodynamics/
BugReports: https://github.com/UCD-SERG/serodynamics/issues
SystemRequirements: JAGS (>= 4.3.1)
Imports: cli, coda, dplyr (>= 1.2.0), ggmcmc (>= 1.5.1.2), ggplot2,
        lifecycle, purrr, rlang, runjags, scales, serocalculator (>=
        1.4.1), stats, tibble, tidyr, tidyselect, utils
Suggests: Hmisc, knitr, readr, rlist, sessioninfo, spelling, stringr,
        testthat (>= 3.0.0), tidyverse, withr, vdiffr, fs, here, rjags,
        rmarkdown, magrittr, rex, quarto
Language: en-US
Config/testthat/edition: 3
Config/needs/test: withr, vdiffr, here, readr, magrittr, rlist
Config/needs/check: commonmark, xml2
Depends: R (>= 4.1.0)
LazyData: true
VignetteBuilder: knitr, quarto
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: cmake make jags libicu-dev libuv1-dev libssl-dev
        libudunits2-dev libx11-dev zlib1g-dev
Repository: https://ucd-serg.r-universe.dev
Date/Publication: 2026-09-24 18:01:39 UTC
RemoteUrl: https://github.com/ucd-serg/serodynamics
RemoteRef: HEAD
RemoteSha: c051209356caba77c29fe26d130d7d4504c6649a
NeedsCompilation: no
Packaged: 2026-10-09 03:02:19 UTC; root
Author: Peter Teunis [aut, cph] (Author of the method and original code.,
    ORCID: <https://orcid.org/0000-0003-1904-6044>),
  Samuel Schildhauer [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-7139-1086>),
  Kwan Ho Lee [aut] (ORCID: <https://orcid.org/0009-0004-9723-2007>),
  Yuxuan Wang [aut] (ORCID: <https://orcid.org/0009-0004-2041-8831>),
  Kristen Aiemjoy [aut] (ORCID: <https://orcid.org/0000-0003-1886-2699>),
  Douglas Ezra Morrison [aut] (ORCID:
    <https://orcid.org/0000-0002-7195-830X>)
Maintainer: Samuel Schildhauer <sschildhauer@ucdavis.edu>