Package: baker
Type: Package
Title: "Nested Partially Latent Class Models"
Version: 1.0.4.9000
Date: 2025-12-11
Authors@R: c(
     person("Zhenke", "Wu", email="zhenkewu@gmail.com",role=c("cre","aut","cph"),
     comment = c(ORCID = "0000-0001-7582-669X")),
     person("Scott", "Zeger", email="sz@jhu.edu",role="aut",
     comment = c(ORCID = "0000-0001-8907-1603")),
     person("John", "Muschelli", email="muschellij2@gmail.com", role="ctb", 
     comment = c(ORCID = "0000-0001-6469-1750")),
     person("Irena", "Chen", email="irena@umich.edu", role="ctb",
     comment = c(ORCID = "0000-0002-9366-8506"))
     )
Description: Provides functions to specify, fit and visualize nested
        partially-latent class models ( Wu, Deloria-Knoll, Hammitt, and
        Zeger (2016) <doi:10.1111/rssc.12101>; Wu, Deloria-Knoll, and
        Zeger (2017) <doi:10.1093/biostatistics/kxw037>; Wu and Chen
        (2021) <doi:10.1002/sim.8804>) for inference of population
        disease etiology and individual diagnosis. In the motivating
        Pneumonia Etiology Research for Child Health (PERCH) study,
        because both quantities of interest sum to one hundred percent,
        the PERCH scientists frequently refer to them as population
        etiology pie and individual etiology pie, hence the name of the
        package.
Depends: R(>= 4.3.0)
Imports: rjags(>= 4-6), R2jags(>= 0.5), lubridate(>= 1.3), binom(>=
        1.1), coda(>= 0.16), robCompositions(>= 2.0.3), ggplot2(>=
        1.0), ggpubr(>= 0.4.0), gridExtra(>= 2.0), reshape2(>= 1.4),
        mgcv(>= 1.8-6), mvbutils(>= 2.7.4.1), shinyFiles(>= 0.6),
        shinydashboard(>= 0.5.1), stats, utils, abind
License: MIT + file LICENSE
Language: en-US
SystemRequirements: JAGS (>= 4.3.2) (http://mcmc-jags.sourceforge.net)
Suggests: spelling, knitr, testthat, rmarkdown, covr, knitcitations, sf
VignetteBuilder: knitr
RoxygenNote: 7.3.3
Encoding: UTF-8
URL: https://github.com/zhenkewu/baker, https://zhenkewu.com/baker/
BugReports: https://github.com/zhenkewu/baker/issues
Roxygen: list(markdown = TRUE)
Config/pak/sysreqs: cmake make jags libicu-dev libuv1-dev zlib1g-dev
Repository: https://zhenkewu.r-universe.dev
Date/Publication: 2025-12-12 19:29:25 UTC
RemoteUrl: https://github.com/zhenkewu/baker
RemoteRef: HEAD
RemoteSha: 43c1dde892347e0b1908b67f06da66544eda881d
NeedsCompilation: no
Packaged: 2026-07-10 08:00:17 UTC; root
Author: Zhenke Wu [cre, aut, cph] (ORCID:
    <https://orcid.org/0000-0001-7582-669X>),
  Scott Zeger [aut] (ORCID: <https://orcid.org/0000-0001-8907-1603>),
  John Muschelli [ctb] (ORCID: <https://orcid.org/0000-0001-6469-1750>),
  Irena Chen [ctb] (ORCID: <https://orcid.org/0000-0002-9366-8506>)
Maintainer: Zhenke Wu <zhenkewu@gmail.com>