Package baker details

Bayesian Analysis Kit for Etiology Research

Provides functions to specify, fit and visualize nested partially-latent class models (Wu, 2016, 'JRSS-C' ; Wu, 2017, Biostatistics ) 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.

Maintainer: Zhenke Wu < zhenkewu at >

From within R, enter citation('baker')

To cite baker in publications, please use:

Wu, Z., Deloria-Knoll, M., Hammitt, L.L., Zeger, S.L. and the
Pneumonia Etiology Research for Child Health Core Team (2016),
Partially latent class models for case-control studies of childhood
pneumonia aetiology. Journal of the Royal Statistical Society: Series
C (Applied Statistics). doi: 10.1111/rssc.12101.

A BibTeX entry for LaTeX users is

author = {Zhenke Wu and Maria Deloria-Knoll and Laura L Hammitt and Scott L Zeger},
title = {Partially Latent Class Models for Case-Control Studies
of Childhood Pneumonia Aetiology},
journal = {Journal of the Royal Statistical Society: Series C (Applied Statistics)},
year = {2015},
doi = {10.1111/rssc.12101},
url = {},


If you have any problems with this package you can open a new issue or check the already existing ones here.

  Versions(Pending - no previous version)
To install this package, start R and enter:


# Default Install

# from GitHub
osler_install('baker', release = "stable", release_repo = "github")
osler_install('baker', release = "current", release_repo = "github")

More detailed installation instructions can be found here.


Initially submitted on April 28 2021 10:00AM
Last updated on April 28 2021 10:00AM
Package type standard
Source GitHub GitHub
OslerinHealth GitHub GitHub
System requirementsJAGS (>= 4.1.0) (
DependsR (3.5.0)
Importsrjags(>=4-6), R2jags (0.5), lubridate (1.3), binom (1.1), coda (0.16), ks (1.9), robCompositions (2.0.3), ggplot2 (1.0), gridExtra (2.0), reshape2 (1.4), mgcv(>=1.8-6), mvbutils (, shiny (0.12), shinyFiles (0.6), shinydashboard (0.5.1), stats, utils, abind
Suggestsspelling, knitr, testthat, bibtex, rmarkdown, covr