baker: baker: *B*ayesian *A*nalytic *K*it for *E*tiology *R*esearch

bakerR Documentation

baker: Bayesian Analytic Kit for Etiology Research


baker is designed for disease etiology studies from case-control data with multiple sources of measurements with potential errors. If you are interested in estimating the population etiology pie (a vector of fractions that sum to one), and the probability of each cause for a particular individual case, try baker.


baker implements hierarchical Bayesian models to infer disease etiology for multivariate binary data. We created baker to catalyze effective communications between analysts and practicing clinicians that are vital to the success of etiology studies. The baker package offers modules to

  • Import and tidy the PERCH data (the study that motivates the creation of this package),

  • Transform, explore the data,

  • Specify, automatically generate the model files, and fit the models (npLCM),

  • Store and visualize posterior summaries for communicating scientific findings, and

  • Check and compare the fitted models.

baker has implemented models for dependent measurements given disease status, regression analyses of etiology, multiple imperfect measurements, different priors for true positive rates among cases with differential measurement characteristics, and multiple-pathogen etiology. Scientists in Pneumonia Etiology Research for Child Health (PERCH) study usually refer to the etiology distribution as "population etiology pie" and "individual etiology pie" for their compositional nature, hence the name of the package (baking the pie).


No returned value; documentation purpose only.

baker functions


See Also

zhenkewu/baker documentation built on March 17, 2022, 9:54 p.m.